Title: | ADaM in R Asset Library |
---|---|
Description: | A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>). |
Authors: | Ben Straub [aut, cre], Stefan Bundfuss [aut] , Jeffrey Dickinson [aut], Ross Farrugia [aut], Fanny Gautier [aut], G Gayatri [aut], Asha Chakma [aut], Dinakar Kulkarni [aut], Edoardo Mancini [aut] , Sadchla Mascary [aut], Gordon Miller [aut], Lina Patil [aut], Sophie Shapcott [aut], Eric Simms [aut], Daniel Sjoberg [aut] , Stefan Thoma [aut] , Phillip Webster [aut], Kangjie Zhang [aut], Zelos Zhu [aut], F. Hoffmann-La Roche AG [cph, fnd], GlaxoSmithKline LLC [cph, fnd] |
Maintainer: | Ben Straub <[email protected]> |
License: | Apache License (>= 2) |
Version: | 1.1.1.9016 |
Built: | 2024-11-03 16:19:18 UTC |
Source: | https://github.com/pharmaverse/admiral |
See magrittr::%>%
for more details.
lhs %>% rhs
lhs %>% rhs
lhs |
A value or the magrittr placeholder. |
rhs |
A function call using the magrittr semantics. |
An example of lab analysis dataset
admiral_adlb
admiral_adlb
An object of class tbl_df
(inherits from tbl
, data.frame
) with 3779 rows and 111 columns.
Derived from the adlb
template, then further filtered
due to dataset size by the following USUBJIDs:
01-701-1015, 01-701-1023, 01-701-1028, 01-701-1033,
01-701-1034, 01-701-1047, 01-701-1097, 01-705-1186,
01-705-1292, 01-705-1310, 01-708-1286
Other datasets:
admiral_adsl
,
ex_single
,
example_qs
,
queries
,
queries_mh
An example subject level analysis dataset
admiral_adsl
admiral_adsl
An object of class tbl_df
(inherits from tbl
, data.frame
) with 306 rows and 54 columns.
Derived from the dm
and ds
datasets using {admiral}
(https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adsl.R)
Other datasets:
admiral_adlb
,
ex_single
,
example_qs
,
queries
,
queries_mh
Metadata Holding Grading Criteria for NCI-CTCAEv4
atoxgr_criteria_ctcv4
atoxgr_criteria_ctcv4
An object of class tbl_df
(inherits from tbl
, data.frame
) with 40 rows and 13 columns.
This metadata has its origin in the ADLB Grading Spec Excel file which ships with {admiral}
and can be accessed using system.file("adlb_grading/adlb_grading_spec.xlsx", package = "admiral")
in sheet = "NCICTCAEv4".
The dataset contained in there has the following columns:
SOC
: variable to hold the SOC of the lab test criteria.
TERM
: variable to hold the term describing the criteria applied to a particular lab test,
eg. 'Anemia' or 'INR Increased'. Note: the variable is case insensitive.
Grade 1
: Criteria defining lab value as Grade 1.
Grade 2
: Criteria defining lab value as Grade 2.
Grade 3
: Criteria defining lab value as Grade 3.
Grade 4
: Criteria defining lab value as Grade 4.
Grade 5
: Criteria defining lab value as Grade 5.
Definition
: Holds the definition of the lab test abnormality.
GRADE_CRITERIA_CODE
: variable to hold code that creates grade based on defined criteria.
SI_UNIT_CHECK
: variable to hold unit of particular lab test. Used to check against input data
if criteria is based on absolute values.
VAR_CHECK
: List of variables required to implement lab grade criteria. Use to check against
input data.
DIRECTION
: variable to hold the direction of the abnormality of a particular lab test
value. 'L' is for LOW values, 'H' is for HIGH values. Note: the variable is case insensitive.
COMMENT
: Holds any information regarding rationale behind implementation of grading criteria.
Note: Variables SOC
, TERM
, Grade 1
, Grade 2
,Grade 3
,Grade 4
,Grade 5
, Definition
are from the source document on NCI-CTC website defining the grading criteria.
Common Terminology Criteria for Adverse Events (CTCAE)v4.0
From these variables only 'TERM' is used in the {admiral}
code, the rest are for information and
traceability only.
Other metadata:
atoxgr_criteria_ctcv5
,
atoxgr_criteria_daids
,
country_code_lookup
,
dose_freq_lookup
Metadata Holding Grading Criteria for NCI-CTCAEv5
atoxgr_criteria_ctcv5
atoxgr_criteria_ctcv5
An object of class tbl_df
(inherits from tbl
, data.frame
) with 37 rows and 13 columns.
This metadata has its origin in the ADLB Grading Spec Excel file which ships with {admiral}
and can be accessed using system.file("adlb_grading/adlb_grading_spec.xlsx", package = "admiral")
in sheet = "NCICTCAEv5".
The dataset contained in there has the following columns:
SOC
: variable to hold the SOC of the lab test criteria.
TERM
: variable to hold the term describing the criteria applied to a particular lab test,
eg. 'Anemia' or 'INR Increased'. Note: the variable is case insensitive.
Grade 1
: Criteria defining lab value as Grade 1.
Grade 2
: Criteria defining lab value as Grade 2.
Grade 3
: Criteria defining lab value as Grade 3.
Grade 4
: Criteria defining lab value as Grade 4.
Grade 5
: Criteria defining lab value as Grade 5.
Definition
: Holds the definition of the lab test abnormality.
GRADE_CRITERIA_CODE
: variable to hold code that creates grade based on defined criteria.
SI_UNIT_CHECK
: variable to hold unit of particular lab test. Used to check against input data
if criteria is based on absolute values.
VAR_CHECK
: List of variables required to implement lab grade criteria. Use to check against
input data.
DIRECTION
: variable to hold the direction of the abnormality of a particular lab test
value. 'L' is for LOW values, 'H' is for HIGH values. Note: the variable is case insensitive.
COMMENT
: Holds any information regarding rationale behind implementation of grading criteria.
Note: Variables SOC
, TERM
, Grade 1
, Grade 2
,Grade 3
,Grade 4
,Grade 5
, Definition
are from the source document on NCI-CTC website defining the grading criteria.
Common Terminology Criteria for Adverse Events (CTCAE)v5.0
From these variables only 'TERM' is used in the {admiral}
code, the rest are for information and
traceability only.
Other metadata:
atoxgr_criteria_ctcv4
,
atoxgr_criteria_daids
,
country_code_lookup
,
dose_freq_lookup
Metadata Holding Grading Criteria for DAIDs
atoxgr_criteria_daids
atoxgr_criteria_daids
An object of class tbl_df
(inherits from tbl
, data.frame
) with 63 rows and 15 columns.
This metadata has its origin in the ADLB Grading Spec Excel file which ships with {admiral}
and can be accessed using system.file("adlb_grading/adlb_grading_spec.xlsx", package = "admiral")
in sheet = "DAIDS".
The dataset contained in there has the following columns:
SOC
: variable to hold the SOC of the lab test criteria.
TERM
: variable to hold the term describing the criteria applied to a particular lab test,
eg. 'Anemia' or 'INR Increased'. Note: the variable is case insensitive.
SUBGROUP
: Description of sub-group of subjects were grading will be applied (i.e. >= 18 years)
Grade 1
: Criteria defining lab value as Grade 1.
Grade 2
: Criteria defining lab value as Grade 2.
Grade 3
: Criteria defining lab value as Grade 3.
Grade 4
: Criteria defining lab value as Grade 4.
Grade 5
: Criteria defining lab value as Grade 5.
Definition
: Holds the definition of the lab test abnormality.
FILTER
: admiral
code to apply the filter based on SUBGROUP column.
GRADE_CRITERIA_CODE
: variable to hold code that creates grade based on defined criteria.
SI_UNIT_CHECK
: variable to hold unit of particular lab test. Used to check against input data
if criteria is based on absolute values.
VAR_CHECK
: List of variables required to implement lab grade criteria. Use to check against
input data.
DIRECTION
: variable to hold the direction of the abnormality of a particular lab test
value. 'L' is for LOW values, 'H' is for HIGH values. Note: the variable is case insensitive.
COMMENT
: Holds any information regarding rationale behind implementation of grading criteria.
Note: Variables SOC
, TERM
, SUBGROUP
, Grade 1
, Grade 2
,Grade 3
,Grade 4
,Grade 5
, Definition
are from the source document on DAIDS website defining the grading criteria.
[Division of AIDS (DAIDS) Table for Grading the Severity of Adult and Pediatric Adverse Events
From these variables only 'TERM' is used in the {admiral}
code, the rest are for information and
traceability only.
Other metadata:
atoxgr_criteria_ctcv4
,
atoxgr_criteria_ctcv5
,
country_code_lookup
,
dose_freq_lookup
basket_select
objectCreate a basket_select
object
basket_select(name = NULL, id = NULL, scope = NULL, type, ...)
basket_select(name = NULL, id = NULL, scope = NULL, type, ...)
name |
Name of the query used to select the definition of the query from the company database. |
id |
Identifier of the query used to select the definition of the query from the company database. |
scope |
Scope of the query used to select the definition of the query from the company database. Permitted Values: |
type |
The type argument expects a character scalar. It is passed to the company specific get_terms() function such that the function can determine which sort of basket is requested |
... |
Any number of named function arguments. Can be used to pass in company
specific conditions or flags that will then be used in user-defined function that is
passed into argument |
Exactly one of name
or id
must be specified.
An object of class basket_select
.
Source Objects:
censor_source()
,
death_event
,
event()
,
event_joined()
,
event_source()
,
flag_event()
,
query()
,
records_source()
,
tte_source()
Call a single derivation multiple times with some parameters/arguments being fixed across iterations and others varying.
call_derivation(dataset = NULL, derivation, variable_params, ...)
call_derivation(dataset = NULL, derivation, variable_params, ...)
dataset |
Input dataset |
derivation |
The derivation function to call A function that performs a specific derivation is expected. A derivation
adds variables or observations to a dataset. The first argument of a
derivation must expect a dataset and the derivation must return a dataset.
The function must provide the Please note that it is not possible to specify |
variable_params |
A |
... |
Any number of named function arguments that stay the same across iterations.
If a function argument is specified both inside |
The input dataset with additional records/variables added depending on
which derivation
has been used.
Higher Order Functions:
derivation_slice()
,
restrict_derivation()
,
slice_derivation()
library(dplyr, warn.conflicts = FALSE) adsl <- tribble( ~STUDYID, ~USUBJID, ~TRTSDT, ~TRTEDT, "PILOT01", "01-1307", NA, NA, "PILOT01", "05-1377", "2014-01-04", "2014-01-25", "PILOT01", "06-1384", "2012-09-15", "2012-09-24", "PILOT01", "15-1085", "2013-02-16", "2013-08-18", "PILOT01", "16-1298", "2013-04-08", "2013-06-28" ) %>% mutate( across(TRTSDT:TRTEDT, as.Date) ) ae <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AESTDTC, ~AEENDTC, "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "16-1298", "2013-06-08", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-06-08", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06" ) adae <- ae %>% derive_vars_merged( dataset_add = adsl, new_vars = exprs(TRTSDT, TRTEDT), by_vars = exprs(USUBJID) ) ## While `derive_vars_dt()` can only add one variable at a time, using `call_derivation()` ## one can add multiple variables in one go call_derivation( dataset = adae, derivation = derive_vars_dt, variable_params = list( params(dtc = AESTDTC, date_imputation = "first", new_vars_prefix = "AST"), params(dtc = AEENDTC, date_imputation = "last", new_vars_prefix = "AEN") ), min_dates = exprs(TRTSDT), max_dates = exprs(TRTEDT) ) ## The above call using `call_derivation()` is equivalent to the following adae %>% derive_vars_dt( new_vars_prefix = "AST", dtc = AESTDTC, date_imputation = "first", min_dates = exprs(TRTSDT), max_dates = exprs(TRTEDT) ) %>% derive_vars_dt( new_vars_prefix = "AEN", dtc = AEENDTC, date_imputation = "last", min_dates = exprs(TRTSDT), max_dates = exprs(TRTEDT) )
library(dplyr, warn.conflicts = FALSE) adsl <- tribble( ~STUDYID, ~USUBJID, ~TRTSDT, ~TRTEDT, "PILOT01", "01-1307", NA, NA, "PILOT01", "05-1377", "2014-01-04", "2014-01-25", "PILOT01", "06-1384", "2012-09-15", "2012-09-24", "PILOT01", "15-1085", "2013-02-16", "2013-08-18", "PILOT01", "16-1298", "2013-04-08", "2013-06-28" ) %>% mutate( across(TRTSDT:TRTEDT, as.Date) ) ae <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AESTDTC, ~AEENDTC, "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "16-1298", "2013-06-08", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-06-08", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06" ) adae <- ae %>% derive_vars_merged( dataset_add = adsl, new_vars = exprs(TRTSDT, TRTEDT), by_vars = exprs(USUBJID) ) ## While `derive_vars_dt()` can only add one variable at a time, using `call_derivation()` ## one can add multiple variables in one go call_derivation( dataset = adae, derivation = derive_vars_dt, variable_params = list( params(dtc = AESTDTC, date_imputation = "first", new_vars_prefix = "AST"), params(dtc = AEENDTC, date_imputation = "last", new_vars_prefix = "AEN") ), min_dates = exprs(TRTSDT), max_dates = exprs(TRTEDT) ) ## The above call using `call_derivation()` is equivalent to the following adae %>% derive_vars_dt( new_vars_prefix = "AST", dtc = AESTDTC, date_imputation = "first", min_dates = exprs(TRTSDT), max_dates = exprs(TRTEDT) ) %>% derive_vars_dt( new_vars_prefix = "AEN", dtc = AEENDTC, date_imputation = "last", min_dates = exprs(TRTSDT), max_dates = exprs(TRTEDT) )
Calls a function provided by the user and adds the function call to the error message if the call fails.
call_user_fun(call)
call_user_fun(call)
call |
Call to be executed |
The return value of the function call
Utilities used within Derivation functions:
extract_unit()
,
get_flagged_records()
,
get_not_mapped()
,
get_vars_query()
call_user_fun(compute_bmi( height = 172, weight = 60 )) try(call_user_fun(compute_bmi( height = 172, weight = "hallo" )))
call_user_fun(compute_bmi( height = 172, weight = 60 )) try(call_user_fun(compute_bmi( height = 172, weight = "hallo" )))
censor_source
Objectcensor_source
objects are used to define censorings as input for the
derive_param_tte()
function.
Note: This is a wrapper function for the more generic tte_source()
.
censor_source( dataset_name, filter = NULL, date, censor = 1, set_values_to = NULL )
censor_source( dataset_name, filter = NULL, date, censor = 1, set_values_to = NULL )
dataset_name |
The name of the source dataset The name refers to the dataset provided by the |
filter |
An unquoted condition for selecting the observations from
|
date |
A variable or expression providing the date of the event or censoring. A date, or a datetime can be specified. An unquoted symbol or expression is expected. Refer to |
censor |
Censoring value CDISC strongly recommends using |
set_values_to |
A named list returned by |
An object of class censor_source
, inheriting from class tte_source
derive_param_tte()
, event_source()
Source Objects:
basket_select()
,
death_event
,
event()
,
event_joined()
,
event_source()
,
flag_event()
,
query()
,
records_source()
,
tte_source()
# Last study date known alive censor censor_source( dataset_name = "adsl", date = LSTALVDT, set_values_to = exprs( EVNTDESC = "ALIVE", SRCDOM = "ADSL", SRCVAR = "LSTALVDT" ) )
# Last study date known alive censor censor_source( dataset_name = "adsl", date = LSTALVDT, set_values_to = exprs( EVNTDESC = "ALIVE", SRCDOM = "ADSL", SRCVAR = "LSTALVDT" ) )
Turn a character vector into a list of expressions
chr2vars(chr)
chr2vars(chr)
chr |
A character vector |
A list
of expressions as returned by exprs()
Utilities for working with quosures/list of expressions:
negate_vars()
chr2vars(c("USUBJID", "AVAL"))
chr2vars(c("USUBJID", "AVAL"))
Converts a set of age values from the specified time unit to years.
compute_age_years(age, age_unit)
compute_age_years(age, age_unit)
age |
The ages to convert. A numeric vector is expected. |
age_unit |
Age unit. Either a string containing the time unit of all ages in Permitted Values: |
Returns a numeric vector of ages in years as doubles. Note
that passing NA_character_
as a unit will result in an NA
value for the outputted
age. Also note, underlying computations assume an equal number of days in each
year (365.25).
The ages contained in age
converted to years.
Date/Time Computation Functions that returns a vector:
compute_dtf()
,
compute_duration()
,
compute_tmf()
,
convert_date_to_dtm()
,
convert_dtc_to_dt()
,
convert_dtc_to_dtm()
,
impute_dtc_dt()
,
impute_dtc_dtm()
compute_age_years( age = c(240, 360, 480), age_unit = "MONTHS" ) compute_age_years( age = c(10, 520, 3650, 1000), age_unit = c("YEARS", "WEEKS", "DAYS", NA_character_) )
compute_age_years( age = c(240, 360, 480), age_unit = "MONTHS" ) compute_age_years( age = c(10, 520, 3650, 1000), age_unit = c("YEARS", "WEEKS", "DAYS", NA_character_) )
Computes BMI from height and weight
compute_bmi(height, weight)
compute_bmi(height, weight)
height |
HEIGHT value It is expected that HEIGHT is in cm. Permitted Values: numeric vector |
weight |
WEIGHT value It is expected that WEIGHT is in kg. Permitted Values: numeric vector |
Usually this computation function can not be used with %>%
.
The BMI (Body Mass Index Area) in kg/m^2.
BDS-Findings Functions that returns a vector:
compute_bsa()
,
compute_egfr()
,
compute_framingham()
,
compute_map()
,
compute_qtc()
,
compute_qual_imputation()
,
compute_qual_imputation_dec()
,
compute_rr()
,
compute_scale()
compute_bmi(height = 170, weight = 75)
compute_bmi(height = 170, weight = 75)
Computes BSA from height and weight making use of the specified derivation method
compute_bsa(height = height, weight = weight, method)
compute_bsa(height = height, weight = weight, method)
height |
HEIGHT value It is expected that HEIGHT is in cm. Permitted Values: numeric vector |
weight |
WEIGHT value It is expected that WEIGHT is in kg. Permitted Values: numeric vector |
method |
Derivation method to use: Mosteller: sqrt(height * weight / 3600) DuBois-DuBois: 0.20247 * (height/100) ^ 0.725 * weight ^ 0.425 Haycock: 0.024265 * height ^ 0.3964 * weight ^ 0.5378 Gehan-George: 0.0235 * height ^ 0.42246 * weight ^ 0.51456 Boyd: 0.0003207 * (height ^ 0.3) * (1000 * weight) ^ (0.7285 - (0.0188 * log10(1000 * weight))) Fujimoto: 0.008883 * height ^ 0.663 * weight ^ 0.444 Takahira: 0.007241 * height ^ 0.725 * weight ^ 0.425 Permitted Values: character value |
Usually this computation function can not be used with %>%
.
The BSA (Body Surface Area) in m^2.
BDS-Findings Functions that returns a vector:
compute_bmi()
,
compute_egfr()
,
compute_framingham()
,
compute_map()
,
compute_qtc()
,
compute_qual_imputation()
,
compute_qual_imputation_dec()
,
compute_rr()
,
compute_scale()
# Derive BSA by the Mosteller method compute_bsa( height = 170, weight = 75, method = "Mosteller" ) # Derive BSA by the DuBois & DuBois method compute_bsa( height = c(170, 185), weight = c(75, 90), method = "DuBois-DuBois" )
# Derive BSA by the Mosteller method compute_bsa( height = 170, weight = 75, method = "Mosteller" ) # Derive BSA by the DuBois & DuBois method compute_bsa( height = c(170, 185), weight = c(75, 90), method = "DuBois-DuBois" )
Derive the date imputation flag ('--DTF'
) comparing a date character vector
('--DTC'
) with a Date vector ('--DT'
).
compute_dtf(dtc, dt)
compute_dtf(dtc, dt)
dtc |
The date character vector ( A character date is expected in a format like |
dt |
The Date vector to compare. A date object is expected. |
Usually this computation function can not be used with %>%
.
The date imputation flag ('--DTF'
) (character value of 'D'
, 'M'
, 'Y'
or NA
)
Date/Time Computation Functions that returns a vector:
compute_age_years()
,
compute_duration()
,
compute_tmf()
,
convert_date_to_dtm()
,
convert_dtc_to_dt()
,
convert_dtc_to_dtm()
,
impute_dtc_dt()
,
impute_dtc_dtm()
compute_dtf(dtc = "2019-07", dt = as.Date("2019-07-18")) compute_dtf(dtc = "2019", dt = as.Date("2019-07-18")) compute_dtf(dtc = "--06-01T00:00", dt = as.Date("2022-06-01")) compute_dtf(dtc = "2022-06--T00:00", dt = as.Date("2022-06-01")) compute_dtf(dtc = "2022---01T00:00", dt = as.Date("2022-06-01")) compute_dtf(dtc = "2022----T00:00", dt = as.Date("2022-06-01"))
compute_dtf(dtc = "2019-07", dt = as.Date("2019-07-18")) compute_dtf(dtc = "2019", dt = as.Date("2019-07-18")) compute_dtf(dtc = "--06-01T00:00", dt = as.Date("2022-06-01")) compute_dtf(dtc = "2022-06--T00:00", dt = as.Date("2022-06-01")) compute_dtf(dtc = "2022---01T00:00", dt = as.Date("2022-06-01")) compute_dtf(dtc = "2022----T00:00", dt = as.Date("2022-06-01"))
Compute duration between two dates, e.g., duration of an adverse event, relative day, age, ...
compute_duration( start_date, end_date, in_unit = "days", out_unit = "days", floor_in = TRUE, add_one = TRUE, trunc_out = FALSE, type = "duration" )
compute_duration( start_date, end_date, in_unit = "days", out_unit = "days", floor_in = TRUE, add_one = TRUE, trunc_out = FALSE, type = "duration" )
start_date |
The start date A date or date-time object is expected. Refer to Refer to |
end_date |
The end date A date or date-time object is expected. Refer to Refer to |
in_unit |
Input unit See floor_in and add_one parameter for details. Permitted Values (case-insensitive): For years: For months: For days: For hours: For minutes: For seconds: |
out_unit |
Output unit The duration is derived in the specified unit Permitted Values (case-insensitive): For years: For months: For weeks: For days: For hours: For minutes: For seconds: |
floor_in |
Round down input dates? The input dates are round down with respect to the input unit, e.g., if the input unit is 'days', the time of the input dates is ignored. Default: Permitted Values: |
add_one |
Add one input unit? If the duration is non-negative, one input unit is added. i.e., the duration can not be zero. Default: Permitted Values: |
trunc_out |
Return integer part The fractional part of the duration (in output unit) is removed, i.e., the integer part is returned. Default: Permitted Values: |
type |
lubridate duration type. See below for details. Default: Permitted Values: |
The output is a numeric vector providing the duration as time from start to end date in the specified unit. If the end date is before the start date, the duration is negative.
The duration between the two date in the specified unit
The lubridate package calculates two types of spans between two dates: duration and interval. While these calculations are largely the same, when the unit of the time period is month or year the result can be slightly different.
The difference arises from the ambiguity in the length of "1 month"
or
"1 year"
.
Months may have 31, 30, 28, or 29 days, and years are 365 days and 366 during leap years.
Durations and intervals help solve the ambiguity in these measures.
The interval between 2000-02-01
and 2000-03-01
is 1
(i.e. one month).
The duration between these two dates is 0.95
, which accounts for the fact
that the year 2000 is a leap year, February has 29 days, and the average month
length is 30.4375
, i.e. 29 / 30.4375 = 0.95
.
For additional details, review the lubridate time span reference page.
Date/Time Computation Functions that returns a vector:
compute_age_years()
,
compute_dtf()
,
compute_tmf()
,
convert_date_to_dtm()
,
convert_dtc_to_dt()
,
convert_dtc_to_dtm()
,
impute_dtc_dt()
,
impute_dtc_dtm()
library(lubridate) # Derive duration in days (integer), i.e., relative day compute_duration( start_date = ymd_hms("2020-12-06T15:00:00"), end_date = ymd_hms("2020-12-24T08:15:00") ) # Derive duration in days (float) compute_duration( start_date = ymd_hms("2020-12-06T15:00:00"), end_date = ymd_hms("2020-12-24T08:15:00"), floor_in = FALSE, add_one = FALSE ) # Derive age in years compute_duration( start_date = ymd("1984-09-06"), end_date = ymd("2020-02-24"), trunc_out = TRUE, out_unit = "years", add_one = FALSE ) # Derive duration in hours compute_duration( start_date = ymd_hms("2020-12-06T9:00:00"), end_date = ymd_hms("2020-12-06T13:30:00"), out_unit = "hours", floor_in = FALSE, add_one = FALSE, )
library(lubridate) # Derive duration in days (integer), i.e., relative day compute_duration( start_date = ymd_hms("2020-12-06T15:00:00"), end_date = ymd_hms("2020-12-24T08:15:00") ) # Derive duration in days (float) compute_duration( start_date = ymd_hms("2020-12-06T15:00:00"), end_date = ymd_hms("2020-12-24T08:15:00"), floor_in = FALSE, add_one = FALSE ) # Derive age in years compute_duration( start_date = ymd("1984-09-06"), end_date = ymd("2020-02-24"), trunc_out = TRUE, out_unit = "years", add_one = FALSE ) # Derive duration in hours compute_duration( start_date = ymd_hms("2020-12-06T9:00:00"), end_date = ymd_hms("2020-12-06T13:30:00"), out_unit = "hours", floor_in = FALSE, add_one = FALSE, )
Compute Kidney Function Tests:
Estimated Creatinine Clearance (CRCL) by Cockcroft-Gault equation
Estimated Glomerular Filtration Rate (eGFR) by CKD-EPI or MDRD equations
compute_egfr(creat, creatu = "SI", age, weight, sex, race = NULL, method)
compute_egfr(creat, creatu = "SI", age, weight, sex, race = NULL, method)
creat |
Creatinine A numeric vector is expected. |
creatu |
Creatinine Units A character vector is expected. Default: Expected Values: |
age |
Age (years) A numeric vector is expected. |
weight |
Weight (kg) A numeric vector is expected if |
sex |
Gender A character vector is expected. Expected Values: |
race |
Race A character vector is expected if Expected Values: |
method |
Method A character vector is expected. Expected Values: |
Calculates an estimate of Glomerular Filtration Rate (eGFR)
CRCL Creatinine Clearance (Cockcroft-Gault)
For Creatinine in umol/L:
For Creatinine in mg/dL:
units = mL/min
CKD-EPI Chronic Kidney Disease Epidemiology Collaboration formula
SCr = standardized serum creatinine in mg/dL (Note SCr(mg/dL) = Creat(umol/L) / 88.42)
= 0.7 (females) or 0.9 (males)
= -0.241 (female) or -0.302 (male) units = mL/min/1.73 m2
MDRD Modification of Diet in Renal Disease formula
SCr = standardized serum creatinine in mg/dL (Note SCr(mg/dL) = Creat(umol/L) / 88.42)
units = mL/min/1.73 m2
A numeric vector of egfr values
BDS-Findings Functions that returns a vector:
compute_bmi()
,
compute_bsa()
,
compute_framingham()
,
compute_map()
,
compute_qtc()
,
compute_qual_imputation()
,
compute_qual_imputation_dec()
,
compute_rr()
,
compute_scale()
compute_egfr( creat = 90, creatu = "umol/L", age = 53, weight = 85, sex = "M", method = "CRCL" ) compute_egfr( creat = 90, creatu = "umol/L", age = 53, sex = "M", race = "ASIAN", method = "MDRD" ) compute_egfr( creat = 70, creatu = "umol/L", age = 52, sex = "F", race = "BLACK OR AFRICAN AMERICAN", method = "MDRD" ) compute_egfr( creat = 90, creatu = "umol/L", age = 53, sex = "M", method = "CKD-EPI" ) base <- tibble::tribble( ~STUDYID, ~USUBJID, ~AGE, ~SEX, ~RACE, ~WTBL, ~CREATBL, ~CREATBLU, "P01", "P01-1001", 55, "M", "WHITE", 90.7, 96.3, "umol/L", "P01", "P01-1002", 52, "F", "BLACK OR AFRICAN AMERICAN", 68.5, 70, "umol/L", "P01", "P01-1003", 67, "M", "BLACK OR AFRICAN AMERICAN", 85.0, 77, "umol/L", "P01", "P01-1004", 76, "F", "ASIAN", 60.7, 65, "umol/L", ) base %>% dplyr::mutate( CRCL_CG = compute_egfr( creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX, method = "CRCL" ), EGFR_EPI = compute_egfr( creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX, method = "CKD-EPI" ), EGFR_MDRD = compute_egfr( creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX, race = RACE, method = "MDRD" ), )
compute_egfr( creat = 90, creatu = "umol/L", age = 53, weight = 85, sex = "M", method = "CRCL" ) compute_egfr( creat = 90, creatu = "umol/L", age = 53, sex = "M", race = "ASIAN", method = "MDRD" ) compute_egfr( creat = 70, creatu = "umol/L", age = 52, sex = "F", race = "BLACK OR AFRICAN AMERICAN", method = "MDRD" ) compute_egfr( creat = 90, creatu = "umol/L", age = 53, sex = "M", method = "CKD-EPI" ) base <- tibble::tribble( ~STUDYID, ~USUBJID, ~AGE, ~SEX, ~RACE, ~WTBL, ~CREATBL, ~CREATBLU, "P01", "P01-1001", 55, "M", "WHITE", 90.7, 96.3, "umol/L", "P01", "P01-1002", 52, "F", "BLACK OR AFRICAN AMERICAN", 68.5, 70, "umol/L", "P01", "P01-1003", 67, "M", "BLACK OR AFRICAN AMERICAN", 85.0, 77, "umol/L", "P01", "P01-1004", 76, "F", "ASIAN", 60.7, 65, "umol/L", ) base %>% dplyr::mutate( CRCL_CG = compute_egfr( creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX, method = "CRCL" ), EGFR_EPI = compute_egfr( creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX, method = "CKD-EPI" ), EGFR_MDRD = compute_egfr( creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX, race = RACE, method = "MDRD" ), )
Computes Framingham Heart Study Cardiovascular Disease 10-Year Risk Score (FCVD101) based on systolic blood pressure, total serum cholesterol (mg/dL), HDL serum cholesterol (mg/dL), sex, smoking status, diabetic status, and treated for hypertension flag.
compute_framingham(sysbp, chol, cholhdl, age, sex, smokefl, diabetfl, trthypfl)
compute_framingham(sysbp, chol, cholhdl, age, sex, smokefl, diabetfl, trthypfl)
sysbp |
Systolic blood pressure A numeric vector is expected. |
chol |
Total serum cholesterol (mg/dL) A numeric vector is expected. |
cholhdl |
HDL serum cholesterol (mg/dL) A numeric vector is expected. |
age |
Age (years) A numeric vector is expected. |
sex |
Gender A character vector is expected. Expected Values: 'M' 'F' |
smokefl |
Smoking Status A character vector is expected. Expected Values: 'Y' 'N' |
diabetfl |
Diabetic Status A character vector is expected. Expected Values: 'Y' 'N' |
trthypfl |
Treated for hypertension status A character vector is expected. Expected Values: 'Y' 'N' |
The predicted probability of having cardiovascular disease (CVD) within 10-years according to Framingham formula. See AHA Journal article General Cardiovascular Risk Profile for Use in Primary Care for reference.
For Women:
Factor | Amount |
Age | 2.32888 |
Total Chol | 1.20904 |
HDL Chol | -0.70833 |
Sys BP | 2.76157 |
Sys BP + Hypertension Meds | 2.82263 |
Smoker | 0.52873 |
Non-Smoker | 0 |
Diabetic | 0.69154 |
Not Diabetic | 0 |
Average Risk | 26.1931 |
Risk Period | 0.95012 |
For Men:
Factor | Amount |
Age | 3.06117 |
Total Chol | 1.12370 |
HDL Chol | -0.93263 |
Sys BP | 1.93303 |
Sys BP + Hypertension Meds | 2.99881 |
Smoker | .65451 |
Non-Smoker | 0 |
Diabetic | 0.57367 |
Not Diabetic | 0 |
Average Risk | 23.9802 |
Risk Period | 0.88936 |
The equation for calculating risk:
A numeric vector of Framingham values
BDS-Findings Functions that returns a vector:
compute_bmi()
,
compute_bsa()
,
compute_egfr()
,
compute_map()
,
compute_qtc()
,
compute_qual_imputation()
,
compute_qual_imputation_dec()
,
compute_rr()
,
compute_scale()
compute_framingham( sysbp = 133, chol = 216.16, cholhdl = 54.91, age = 53, sex = "M", smokefl = "N", diabetfl = "N", trthypfl = "N" ) compute_framingham( sysbp = 161, chol = 186.39, cholhdl = 64.19, age = 52, sex = "F", smokefl = "Y", diabetfl = "N", trthypfl = "Y" )
compute_framingham( sysbp = 133, chol = 216.16, cholhdl = 54.91, age = 53, sex = "M", smokefl = "N", diabetfl = "N", trthypfl = "N" ) compute_framingham( sysbp = 161, chol = 186.39, cholhdl = 64.19, age = 52, sex = "F", smokefl = "Y", diabetfl = "N", trthypfl = "Y" )
Computes mean arterial pressure (MAP) based on diastolic and systolic blood pressure. Optionally heart rate can be used as well.
compute_map(diabp, sysbp, hr = NULL)
compute_map(diabp, sysbp, hr = NULL)
diabp |
Diastolic blood pressure A numeric vector is expected. |
sysbp |
Systolic blood pressure A numeric vector is expected. |
hr |
Heart rate A numeric vector or |
if it is based on diastolic and systolic blood pressure and
if it is based on diastolic, systolic blood pressure, and heart rate.
Usually this computation function can not be used with %>%
.
A numeric vector of MAP values
BDS-Findings Functions that returns a vector:
compute_bmi()
,
compute_bsa()
,
compute_egfr()
,
compute_framingham()
,
compute_qtc()
,
compute_qual_imputation()
,
compute_qual_imputation_dec()
,
compute_rr()
,
compute_scale()
# Compute MAP based on diastolic and systolic blood pressure compute_map(diabp = 51, sysbp = 121) # Compute MAP based on diastolic and systolic blood pressure and heart rate compute_map(diabp = 51, sysbp = 121, hr = 59)
# Compute MAP based on diastolic and systolic blood pressure compute_map(diabp = 51, sysbp = 121) # Compute MAP based on diastolic and systolic blood pressure and heart rate compute_map(diabp = 51, sysbp = 121, hr = 59)
Computes corrected QT using Bazett's, Fridericia's or Sagie's formula.
compute_qtc(qt, rr, method)
compute_qtc(qt, rr, method)
qt |
QT interval A numeric vector is expected. It is expected that QT is measured in msec. |
rr |
RR interval A numeric vector is expected. It is expected that RR is measured in msec. |
method |
Method used to QT correction Permitted Values: |
Depending on the chosen method
one of the following formulae is used.
Bazett:
Fridericia:
Sagie:
Usually this computation function can not be used with %>%
.
QT interval in msec
BDS-Findings Functions that returns a vector:
compute_bmi()
,
compute_bsa()
,
compute_egfr()
,
compute_framingham()
,
compute_map()
,
compute_qual_imputation()
,
compute_qual_imputation_dec()
,
compute_rr()
,
compute_scale()
compute_qtc(qt = 350, rr = 56.54, method = "Bazett") compute_qtc(qt = 350, rr = 56.54, method = "Fridericia") compute_qtc(qt = 350, rr = 56.54, method = "Sagie")
compute_qtc(qt = 350, rr = 56.54, method = "Bazett") compute_qtc(qt = 350, rr = 56.54, method = "Fridericia") compute_qtc(qt = 350, rr = 56.54, method = "Sagie")
Derive an imputed value
compute_qual_imputation(character_value, imputation_type = 1, factor = 0)
compute_qual_imputation(character_value, imputation_type = 1, factor = 0)
character_value |
Character version of value to be imputed |
imputation_type |
(default value=1) Valid Values: 1: Strip <, >, = and convert to numeric. 2: imputation_type=1 and if the character value contains a < or >, the number of of decimals associated with the character value is found and then a factor of 1/10^(number of decimals + 1) will be added/subtracted from the numeric value. If no decimals exists, a factor of 1/10 will be added/subtracted from the value. |
factor |
Numeric value (default=0), when using |
The imputed value
BDS-Findings Functions that returns a vector:
compute_bmi()
,
compute_bsa()
,
compute_egfr()
,
compute_framingham()
,
compute_map()
,
compute_qtc()
,
compute_qual_imputation_dec()
,
compute_rr()
,
compute_scale()
compute_qual_imputation("<40")
compute_qual_imputation("<40")
Function to compute factor for value imputation when character value contains < or >. The factor is calculated using the number of decimals. If there are no decimals, the factor is 1, otherwise the factor = 1/10^decimal place. For example, the factor for 100 = 1, the factor for 5.4 = 1/10^1, the factor for 5.44 = 1/10^2. This results in no additional false precision added to the value. This is an intermediate function.
compute_qual_imputation_dec(character_value_decimal)
compute_qual_imputation_dec(character_value_decimal)
character_value_decimal |
Character value to determine decimal precision |
Derive an imputed value
Decimal precision value to add or subtract
BDS-Findings Functions that returns a vector:
compute_bmi()
,
compute_bsa()
,
compute_egfr()
,
compute_framingham()
,
compute_map()
,
compute_qtc()
,
compute_qual_imputation()
,
compute_rr()
,
compute_scale()
compute_qual_imputation_dec("<40.1")
compute_qual_imputation_dec("<40.1")
Computes RR interval from heart rate.
compute_rr(hr)
compute_rr(hr)
hr |
Heart rate A numeric vector is expected. It is expected that heart rate is measured in beats/min. |
Usually this computation function can not be used with %>%
.
RR interval in msec:
BDS-Findings Functions that returns a vector:
compute_bmi()
,
compute_bsa()
,
compute_egfr()
,
compute_framingham()
,
compute_map()
,
compute_qtc()
,
compute_qual_imputation()
,
compute_qual_imputation_dec()
,
compute_scale()
compute_rr(hr = 70.14)
compute_rr(hr = 70.14)
Computes the average of a set of source values and transforms the result from the source range to the target range. For example, for calculating the average of a set of questionnaire response scores and re-coding the average response to obtain a subscale score.
compute_scale( source, source_range = NULL, target_range = NULL, flip_direction = FALSE, min_n = 1 )
compute_scale( source, source_range = NULL, target_range = NULL, flip_direction = FALSE, min_n = 1 )
source |
A vector of values to be scaled A numeric vector is expected. |
source_range |
The permitted source range A numeric vector containing two elements is expected, representing the
lower and upper bounds of the permitted source range. Alternatively, if no
argument is specified for |
target_range |
The target range A numeric vector containing two elements is expected, representing the
lower and upper bounds of the target range. Alternatively, if no
argument is specified for |
flip_direction |
Flip direction of the scale? The transformed values will be reversed within the target range, e.g. within the range 0 to 100, 25 would be reversed to 75. This argument will be ignored if Default: Permitted Values: |
min_n |
Minimum number of values for computation The minimum number of non-missing values in source for the computation to
be carried out. If the number of non-missing values is below A positive integer is expected. Default: 1 |
Returns a numeric value. If source contains less than min_n
values,
the result is set to NA
. If source_range
and target_range
aren't
specified, the mean will be computed without any transformation being
performed.
The average of source transformed to the target range or NA
if
source doesn't contain min_n
values.
BDS-Findings Functions that returns a vector:
compute_bmi()
,
compute_bsa()
,
compute_egfr()
,
compute_framingham()
,
compute_map()
,
compute_qtc()
,
compute_qual_imputation()
,
compute_qual_imputation_dec()
,
compute_rr()
compute_scale( source = c(1, 4, 3, 5), source_range = c(1, 5), target_range = c(0, 100), flip_direction = TRUE, min_n = 3 )
compute_scale( source = c(1, 4, 3, 5), source_range = c(1, 5), target_range = c(0, 100), flip_direction = TRUE, min_n = 3 )
Derive the time imputation flag ('--TMF'
) comparing a date character vector
('--DTC'
) with a Datetime vector ('--DTM'
).
compute_tmf(dtc, dtm, ignore_seconds_flag = FALSE)
compute_tmf(dtc, dtm, ignore_seconds_flag = FALSE)
dtc |
The date character vector ( A character date is expected in a format like |
dtm |
The Date vector to compare ( A datetime object is expected. |
ignore_seconds_flag |
ADaM IG states that given SDTM ( Permitted Values: A logical value |
Usually this computation function can not be used with %>%
.
The time imputation flag ('--TMF'
) (character value of 'H'
, 'M'
, 'S'
or NA
)
Date/Time Computation Functions that returns a vector:
compute_age_years()
,
compute_dtf()
,
compute_duration()
,
convert_date_to_dtm()
,
convert_dtc_to_dt()
,
convert_dtc_to_dtm()
,
impute_dtc_dt()
,
impute_dtc_dtm()
library(lubridate) compute_tmf(dtc = "2019-07-18T15:25", dtm = ymd_hms("2019-07-18T15:25:00")) compute_tmf(dtc = "2019-07-18T15", dtm = ymd_hms("2019-07-18T15:25:00")) compute_tmf(dtc = "2019-07-18", dtm = ymd("2019-07-18")) compute_tmf(dtc = "2022-05--T00:00", dtm = ymd_hms("2022-05-15T23:59:59")) compute_tmf(dtc = "2022-05--T23:00", dtm = ymd_hms("2022-05-15T23:59:59")) compute_tmf(dtc = "2022-05--T23:59:00", dtm = ymd_hms("2022-05-15T23:59:59"))
library(lubridate) compute_tmf(dtc = "2019-07-18T15:25", dtm = ymd_hms("2019-07-18T15:25:00")) compute_tmf(dtc = "2019-07-18T15", dtm = ymd_hms("2019-07-18T15:25:00")) compute_tmf(dtc = "2019-07-18", dtm = ymd("2019-07-18")) compute_tmf(dtc = "2022-05--T00:00", dtm = ymd_hms("2022-05-15T23:59:59")) compute_tmf(dtc = "2022-05--T23:00", dtm = ymd_hms("2022-05-15T23:59:59")) compute_tmf(dtc = "2022-05--T23:59:00", dtm = ymd_hms("2022-05-15T23:59:59"))
The purpose of the function is to consolidate multiple meta datasets into a single one. For example, from global and project specific parameter mappings a single lookup table can be created.
consolidate_metadata( datasets, key_vars, source_var = SOURCE, check_vars = "warning", check_type = "error" )
consolidate_metadata( datasets, key_vars, source_var = SOURCE, check_vars = "warning", check_type = "error" )
datasets |
List of datasets to consolidate Permitted Values: A named list of datasets |
key_vars |
Key variables The specified variables must be a unique of all input datasets. Permitted Values: A list of variables created by |
source_var |
Source variable The specified variable is added to the output dataset. It is set the name of the dataset the observation is originating from. Permitted Values: A symbol |
check_vars |
Check variables? If Permitted Values: |
check_type |
Check uniqueness? If Permitted Values: |
All observations of the input datasets are put together into a
single dataset. If a by group (defined by key_vars
) exists in more than
one of the input datasets, the observation from the last dataset is
selected.
A dataset which contains one row for each by group occurring in any of the input datasets.
Creating auxiliary datasets:
create_period_dataset()
,
create_query_data()
,
create_single_dose_dataset()
library(tibble) glob_ranges <- tribble( ~PARAMCD, ~ANRLO, ~ANRHI, "PULSE", 60, 100, "SYSBP", 90, 130, "DIABP", 60, 80 ) proj_ranges <- tribble( ~PARAMCD, ~ANRLO, ~ANRHI, "SYSBP", 100, 140, "DIABP", 70, 90 ) stud_ranges <- tribble( ~PARAMCD, ~ANRLO, ~ANRHI, "BMI", 18, 25 ) consolidate_metadata( datasets = list( global = glob_ranges, project = proj_ranges, study = stud_ranges ), key_vars = exprs(PARAMCD) )
library(tibble) glob_ranges <- tribble( ~PARAMCD, ~ANRLO, ~ANRHI, "PULSE", 60, 100, "SYSBP", 90, 130, "DIABP", 60, 80 ) proj_ranges <- tribble( ~PARAMCD, ~ANRLO, ~ANRHI, "SYSBP", 100, 140, "DIABP", 70, 90 ) stud_ranges <- tribble( ~PARAMCD, ~ANRLO, ~ANRHI, "BMI", 18, 25 ) consolidate_metadata( datasets = list( global = glob_ranges, project = proj_ranges, study = stud_ranges ), key_vars = exprs(PARAMCD) )
Turn SAS blank strings into proper R NA
s.
convert_blanks_to_na(x) ## Default S3 method: convert_blanks_to_na(x) ## S3 method for class 'character' convert_blanks_to_na(x) ## S3 method for class 'list' convert_blanks_to_na(x) ## S3 method for class 'data.frame' convert_blanks_to_na(x)
convert_blanks_to_na(x) ## Default S3 method: convert_blanks_to_na(x) ## S3 method for class 'character' convert_blanks_to_na(x) ## S3 method for class 'list' convert_blanks_to_na(x) ## S3 method for class 'data.frame' convert_blanks_to_na(x)
x |
Any R object |
The default methods simply returns its input unchanged. The character
method
turns every instance of ""
into NA_character_
while preserving all attributes.
When given a data frame as input the function keeps all non-character columns
as is and applies the just described logic to character
columns. Once again
all attributes such as labels are preserved.
An object of the same class as the input
Utilities for Formatting Observations:
convert_na_to_blanks()
,
yn_to_numeric()
library(tibble) convert_blanks_to_na(c("a", "b", "", "d", "")) df <- tribble( ~USUBJID, ~RFICDTC, "1001", "2000-01-01", "1002", "2001-01-01", "1003", "" ) print(df) convert_blanks_to_na(df)
library(tibble) convert_blanks_to_na(c("a", "b", "", "d", "")) df <- tribble( ~USUBJID, ~RFICDTC, "1001", "2000-01-01", "1002", "2001-01-01", "1003", "" ) print(df) convert_blanks_to_na(df)
Convert a date (datetime, date, or date character) into a Date
vector (usually '--DTM'
).
Note: This is a wrapper function for the function convert_dtc_to_dtm()
.
convert_date_to_dtm( dt, highest_imputation = "h", date_imputation = "first", time_imputation = "first", min_dates = NULL, max_dates = NULL, preserve = FALSE )
convert_date_to_dtm( dt, highest_imputation = "h", date_imputation = "first", time_imputation = "first", min_dates = NULL, max_dates = NULL, preserve = FALSE )
dt |
The date to convert. A date or character date is expected in a format like |
highest_imputation |
Highest imputation level The If a component at a higher level than the highest imputation level is
missing, If If Permitted Values: |
date_imputation |
The value to impute the day/month when a datepart is missing. A character value is expected, either as a
The argument is ignored if |
time_imputation |
The value to impute the time when a timepart is missing. A character value is expected, either as a
The argument is ignored if |
min_dates |
Minimum dates A list of dates is expected. It is ensured that the imputed date is not
before any of the specified dates, e.g., that the imputed adverse event start
date is not before the first treatment date. Only dates which are in the
range of possible dates of the impute_dtc_dtm( "2020-11", min_dates = list( ymd_hms("2020-12-06T12:12:12"), ymd_hms("2020-11-11T11:11:11") ), highest_imputation = "M" ) returns For date variables (not datetime) in the list the time is imputed to
|
max_dates |
Maximum dates A list of dates is expected. It is ensured that the imputed date is not after any of the specified dates, e.g., that the imputed date is not after the data cut off date. Only dates which are in the range of possible dates are considered. A date or date-time object is expected. For date variables (not datetime) in the list the time is imputed to
|
preserve |
Preserve lower level date/time part when higher order part is missing, e.g. preserve day if month is missing or preserve minute when hour is missing. For example Permitted Values: |
Usually this computation function can not be used with %>%
.
A datetime object
Date/Time Computation Functions that returns a vector:
compute_age_years()
,
compute_dtf()
,
compute_duration()
,
compute_tmf()
,
convert_dtc_to_dt()
,
convert_dtc_to_dtm()
,
impute_dtc_dt()
,
impute_dtc_dtm()
convert_date_to_dtm("2019-07-18T15:25:00") convert_date_to_dtm(Sys.time()) convert_date_to_dtm(as.Date("2019-07-18"), time_imputation = "23:59:59") convert_date_to_dtm("2019-07-18", time_imputation = "23:59:59") convert_date_to_dtm("2019-07-18")
convert_date_to_dtm("2019-07-18T15:25:00") convert_date_to_dtm(Sys.time()) convert_date_to_dtm(as.Date("2019-07-18"), time_imputation = "23:59:59") convert_date_to_dtm("2019-07-18", time_imputation = "23:59:59") convert_date_to_dtm("2019-07-18")
Convert a date character vector (usually '–DTC') into a Date vector (usually '–DT').
convert_dtc_to_dt( dtc, highest_imputation = "n", date_imputation = "first", min_dates = NULL, max_dates = NULL, preserve = FALSE )
convert_dtc_to_dt( dtc, highest_imputation = "n", date_imputation = "first", min_dates = NULL, max_dates = NULL, preserve = FALSE )
dtc |
The –DTC date to convert. |
highest_imputation |
Highest imputation level The If a component at a higher level than the highest imputation level is
missing, If If Permitted Values: |
date_imputation |
The value to impute the day/month when a datepart is missing. A character value is expected, either as a
The argument is ignored if |
min_dates |
Minimum dates A list of dates is expected. It is ensured that the imputed date is not
before any of the specified dates, e.g., that the imputed adverse event start
date is not before the first treatment date. Only dates which are in the
range of possible dates of the impute_dtc_dtm( "2020-11", min_dates = list( ymd_hms("2020-12-06T12:12:12"), ymd_hms("2020-11-11T11:11:11") ), highest_imputation = "M" ) returns |
max_dates |
Maximum dates A list of dates is expected. It is ensured that the imputed date is not after any of the specified dates, e.g., that the imputed date is not after the data cut off date. Only dates which are in the range of possible dates are considered. A date or date-time object is expected. |
preserve |
Preserve day if month is missing and day is present For example Permitted Values: |
Usually this computation function can not be used with %>%
.
a date object
Date/Time Computation Functions that returns a vector:
compute_age_years()
,
compute_dtf()
,
compute_duration()
,
compute_tmf()
,
convert_date_to_dtm()
,
convert_dtc_to_dtm()
,
impute_dtc_dt()
,
impute_dtc_dtm()
convert_dtc_to_dt("2019-07-18") convert_dtc_to_dt("2019-07")
convert_dtc_to_dt("2019-07-18") convert_dtc_to_dt("2019-07")
Convert a date character vector (usually '--DTC'
) into a Date vector (usually '--DTM'
).
convert_dtc_to_dtm( dtc, highest_imputation = "h", date_imputation = "first", time_imputation = "first", min_dates = NULL, max_dates = NULL, preserve = FALSE )
convert_dtc_to_dtm( dtc, highest_imputation = "h", date_imputation = "first", time_imputation = "first", min_dates = NULL, max_dates = NULL, preserve = FALSE )
dtc |
The |
highest_imputation |
Highest imputation level The If a component at a higher level than the highest imputation level is
missing, If If Permitted Values: |
date_imputation |
The value to impute the day/month when a datepart is missing. A character value is expected, either as a
The argument is ignored if |
time_imputation |
The value to impute the time when a timepart is missing. A character value is expected, either as a
The argument is ignored if |
min_dates |
Minimum dates A list of dates is expected. It is ensured that the imputed date is not
before any of the specified dates, e.g., that the imputed adverse event start
date is not before the first treatment date. Only dates which are in the
range of possible dates of the impute_dtc_dtm( "2020-11", min_dates = list( ymd_hms("2020-12-06T12:12:12"), ymd_hms("2020-11-11T11:11:11") ), highest_imputation = "M" ) returns For date variables (not datetime) in the list the time is imputed to
|
max_dates |
Maximum dates A list of dates is expected. It is ensured that the imputed date is not after any of the specified dates, e.g., that the imputed date is not after the data cut off date. Only dates which are in the range of possible dates are considered. A date or date-time object is expected. For date variables (not datetime) in the list the time is imputed to
|
preserve |
Preserve lower level date/time part when higher order part is missing, e.g. preserve day if month is missing or preserve minute when hour is missing. For example Permitted Values: |
Usually this computation function can not be used with %>%
.
A datetime object
Date/Time Computation Functions that returns a vector:
compute_age_years()
,
compute_dtf()
,
compute_duration()
,
compute_tmf()
,
convert_date_to_dtm()
,
convert_dtc_to_dt()
,
impute_dtc_dt()
,
impute_dtc_dtm()
convert_dtc_to_dtm("2019-07-18T15:25:00") convert_dtc_to_dtm("2019-07-18T00:00:00") # note Time = 00:00:00 is not printed convert_dtc_to_dtm("2019-07-18")
convert_dtc_to_dtm("2019-07-18T15:25:00") convert_dtc_to_dtm("2019-07-18T00:00:00") # note Time = 00:00:00 is not printed convert_dtc_to_dtm("2019-07-18")
Turn NA
s to blank strings .
convert_na_to_blanks(x) ## Default S3 method: convert_na_to_blanks(x) ## S3 method for class 'character' convert_na_to_blanks(x) ## S3 method for class 'list' convert_na_to_blanks(x) ## S3 method for class 'data.frame' convert_na_to_blanks(x)
convert_na_to_blanks(x) ## Default S3 method: convert_na_to_blanks(x) ## S3 method for class 'character' convert_na_to_blanks(x) ## S3 method for class 'list' convert_na_to_blanks(x) ## S3 method for class 'data.frame' convert_na_to_blanks(x)
x |
Any R object |
The default methods simply returns its input unchanged. The character
method
turns every instance of NA_character_
or NA
into ""
while preserving all attributes.
When given a data frame as input the function keeps all non-character columns
as is and applies the just described logic to character
all attributes such as labels are preserved.
An object of the same class as the input
Utilities for Formatting Observations:
convert_blanks_to_na()
,
yn_to_numeric()
library(tibble) convert_na_to_blanks(c("a", "b", NA, "d", NA)) df <- tribble( ~USUBJID, ~RFICDTC, "1001", "2000-01-01", "1002", "2001-01-01", "1003", NA ) print(df) convert_na_to_blanks(df)
library(tibble) convert_na_to_blanks(c("a", "b", NA, "d", NA)) df <- tribble( ~USUBJID, ~RFICDTC, "1001", "2000-01-01", "1002", "2001-01-01", "1003", NA ) print(df) convert_na_to_blanks(df)
Count number of observations where a variable equals a value.
count_vals(var, val)
count_vals(var, val)
var |
A vector |
val |
A value |
Utilities for Filtering Observations:
filter_exist()
,
filter_extreme()
,
filter_joined()
,
filter_not_exist()
,
filter_relative()
,
max_cond()
,
min_cond()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(admiral) data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "PR", "1", 2, "CR", "1", 3, "NE", "1", 4, "CR", "1", 5, "NE", "2", 1, "CR", "2", 2, "PR", "2", 3, "CR", "3", 1, "CR", "4", 1, "CR", "4", 2, "NE", "4", 3, "NE", "4", 4, "CR", "4", 5, "PR" ) # add variable providing the number of NEs for each subject group_by(data, USUBJID) %>% mutate(nr_nes = count_vals(var = AVALC, val = "NE"))
library(tibble) library(dplyr, warn.conflicts = FALSE) library(admiral) data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "PR", "1", 2, "CR", "1", 3, "NE", "1", 4, "CR", "1", 5, "NE", "2", 1, "CR", "2", 2, "PR", "2", 3, "CR", "3", 1, "CR", "4", 1, "CR", "4", 2, "NE", "4", 3, "NE", "4", 4, "CR", "4", 5, "PR" ) # add variable providing the number of NEs for each subject group_by(data, USUBJID) %>% mutate(nr_nes = count_vals(var = AVALC, val = "NE"))
These pre-defined country codes are sourced from ISO 3166 Standards. See also Wikipedia.
country_code_lookup
country_code_lookup
An object of class tbl_df
(inherits from tbl
, data.frame
) with 249 rows and 3 columns.
country_code
is the 3-letter ISO 3166-1 county code commonly found in the
ADSL COUNTRY
variable.
country_name
is the country long name corresponding to to the 3-letter code.
country_number
is the numeric code corresponding to an alphabetic sorting of
the 3-letter codes.
To see the entire table in the console, run print(country_code_lookup)
.
Other metadata:
atoxgr_criteria_ctcv4
,
atoxgr_criteria_ctcv5
,
atoxgr_criteria_daids
,
dose_freq_lookup
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) # Create reference dataset for periods adsl <- tribble( ~USUBJID, ~SEX, ~COUNTRY, "ST01-01", "F", "AUT", "ST01-02", "M", "MWI", "ST01-03", "F", "GBR", "ST01-04", "M", "CHE", "ST01-05", "M", "NOR", "ST01-06", "F", "JPN", "ST01-07", "F", "USA" ) covar <- adsl %>% derive_vars_merged( dataset_add = country_code_lookup, new_vars = exprs(COUNTRYN = country_number, COUNTRYL = country_name), by_vars = exprs(COUNTRY = country_code) ) covar
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) # Create reference dataset for periods adsl <- tribble( ~USUBJID, ~SEX, ~COUNTRY, "ST01-01", "F", "AUT", "ST01-02", "M", "MWI", "ST01-03", "F", "GBR", "ST01-04", "M", "CHE", "ST01-05", "M", "NOR", "ST01-06", "F", "JPN", "ST01-07", "F", "USA" ) covar <- adsl %>% derive_vars_merged( dataset_add = country_code_lookup, new_vars = exprs(COUNTRYN = country_number, COUNTRYL = country_name), by_vars = exprs(COUNTRY = country_code) ) covar
The function creates a reference dataset for subperiods, periods, or phases
from the ADSL
dataset. The reference dataset can be used to derive
subperiod, period, or phase variables like ASPER
, ASPRSDT
, ASPREDT
,
APERIOD
, APERSDT
, APEREDT
, TRTA
, APHASEN
, PHSDTM
, PHEDTM
, ...
in OCCDS and BDS datasets.
create_period_dataset( dataset, new_vars, subject_keys = get_admiral_option("subject_keys") )
create_period_dataset( dataset, new_vars, subject_keys = get_admiral_option("subject_keys") )
dataset |
Input dataset The variables specified by the |
new_vars |
New variables A named list of variables like If the lower case letter "w" is used it refers to a phase variable, if the lower case letters "xx" are used it refers to a period variable, and if both "xx" and "w" are used it refers to a subperiod variable. Only one type must be used, e.g., all right hand side values must refer to period variables. It is not allowed to mix for example period and subperiod variables. If period and subperiod variables are required, separate reference datasets must be created. |
subject_keys |
Variables to uniquely identify a subject A list of expressions where the expressions are symbols as returned by
|
For each subject and each subperiod/period/phase where at least one
of the source variable is not NA
an observation is added to the output
dataset.
Depending on the type of the source variable (subperiod, period, or phase)
the variable ASPER
, APERIOD
, or APHASEN
is added and set to the
number of the subperiod, period, or phase.
The variables specified for new_vars
(left hand side) are added to the
output dataset and set to the value of the source variable (right hand
side).
A period reference dataset (see "Details" section)
Creating auxiliary datasets:
consolidate_metadata()
,
create_query_data()
,
create_single_dose_dataset()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) # Create reference dataset for periods adsl <- tribble( ~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT, ~TRT01A, ~TRT02A, "1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "A", "B", "2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01", "B", "A", ) %>% mutate( across(matches("AP\\d\\d[ES]DT"), ymd) ) %>% mutate( STUDYID = "xyz" ) create_period_dataset( adsl, new_vars = exprs(APERSDT = APxxSDT, APEREDT = APxxEDT, TRTA = TRTxxA) ) # Create reference dataset for phases adsl <- tribble( ~USUBJID, ~PH1SDT, ~PH1EDT, ~PH2SDT, ~PH2EDT, ~APHASE1, ~APHASE2, "1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "TREATMENT", "FUP", "2", "2021-02-02", "2021-03-02", NA, NA, "TREATMENT", NA ) %>% mutate( across(matches("PH\\d[ES]DT"), ymd) ) %>% mutate( STUDYID = "xyz" ) create_period_dataset( adsl, new_vars = exprs(PHSDT = PHwSDT, PHEDT = PHwEDT, APHASE = APHASEw) ) # Create reference datasets for subperiods adsl <- tribble( ~USUBJID, ~P01S1SDT, ~P01S1EDT, ~P01S2SDT, ~P01S2EDT, ~P02S1SDT, ~P02S1EDT, "1", "2021-01-04", "2021-01-19", "2021-01-20", "2021-02-06", "2021-02-07", "2021-03-07", "2", "2021-02-02", "2021-03-02", NA, NA, "2021-03-03", "2021-04-01" ) %>% mutate( across(matches("P\\d\\dS\\d[ES]DT"), ymd) ) %>% mutate( STUDYID = "xyz" ) create_period_dataset( adsl, new_vars = exprs(ASPRSDT = PxxSwSDT, ASPREDT = PxxSwEDT) )
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) # Create reference dataset for periods adsl <- tribble( ~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT, ~TRT01A, ~TRT02A, "1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "A", "B", "2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01", "B", "A", ) %>% mutate( across(matches("AP\\d\\d[ES]DT"), ymd) ) %>% mutate( STUDYID = "xyz" ) create_period_dataset( adsl, new_vars = exprs(APERSDT = APxxSDT, APEREDT = APxxEDT, TRTA = TRTxxA) ) # Create reference dataset for phases adsl <- tribble( ~USUBJID, ~PH1SDT, ~PH1EDT, ~PH2SDT, ~PH2EDT, ~APHASE1, ~APHASE2, "1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "TREATMENT", "FUP", "2", "2021-02-02", "2021-03-02", NA, NA, "TREATMENT", NA ) %>% mutate( across(matches("PH\\d[ES]DT"), ymd) ) %>% mutate( STUDYID = "xyz" ) create_period_dataset( adsl, new_vars = exprs(PHSDT = PHwSDT, PHEDT = PHwEDT, APHASE = APHASEw) ) # Create reference datasets for subperiods adsl <- tribble( ~USUBJID, ~P01S1SDT, ~P01S1EDT, ~P01S2SDT, ~P01S2EDT, ~P02S1SDT, ~P02S1EDT, "1", "2021-01-04", "2021-01-19", "2021-01-20", "2021-02-06", "2021-02-07", "2021-03-07", "2", "2021-02-02", "2021-03-02", NA, NA, "2021-03-03", "2021-04-01" ) %>% mutate( across(matches("P\\d\\dS\\d[ES]DT"), ymd) ) %>% mutate( STUDYID = "xyz" ) create_period_dataset( adsl, new_vars = exprs(ASPRSDT = PxxSwSDT, ASPREDT = PxxSwEDT) )
dataset_queries
argument in
derive_vars_query()
Creates a queries dataset as input dataset to the dataset_queries
argument
in the derive_vars_query()
function as defined in the Queries Dataset Documentation.
create_query_data(queries, version = NULL, get_terms_fun = NULL)
create_query_data(queries, version = NULL, get_terms_fun = NULL)
queries |
List of queries A list of |
version |
Dictionary version The dictionary version used for coding the terms should be specified. If any of the queries is a basket (SMQ, SDG, ....) or a customized query including a basket, the parameter needs to be specified. Permitted Values: A character string (the expected format is company-specific) |
get_terms_fun |
Function which returns the terms For each query specified for the The function must return a dataset with all the terms defining the basket. The output dataset must contain the following variables.
The function must provide the following parameters
|
For each query()
object listed in the queries
argument, the terms belonging
to the query (SRCVAR
, TERMCHAR
, TERMNUM
) are determined with respect
to the definition
field of the query: if the definition field of the
query()
object is
a basket_select()
object, the terms are read from the basket
database by calling the function specified for the get_terms_fun
parameter.
a data frame, the terms stored in the data frame are used.
a list of data frames and basket_select()
objects, all terms from
the data frames and all terms read from the basket database referenced by the
basket_select()
objects are collated.
The following variables (as described in Queries Dataset Documentation) are created:
PREFIX
: Prefix of the variables to be created by
derive_vars_query()
as specified by the prefix
element.
GRPNAME
: Name of the query as specified by the name
element.
GRPID
: Id of the query as specified by the id
element. If the id
element is not specified for a query, the variable is set to NA
. If the
id
element is not specified for any query, the variable is not created.
SCOPE
: scope of the query as specified by the scope
element of
the basket_select()
object. For queries not defined by a basket_select()
object, the variable is set to NA
. If none of the queries is defined by a
basket_select()
object, the variable is not created.
SCOPEN
: numeric scope of the query. It is set to 1
if the
scope is broad. Otherwise it is set to 2
. If the add_scope_num
element
equals FALSE
, the variable is set to NA
. If the add_scope_num
element
equals FALSE
for all baskets or none of the queries is an basket , the variable
is not created.
SRCVAR
: Name of the variable used to identify the terms.
TERMCHAR
: Value of the term variable if it is a character variable.
TERMNUM
: Value of the term variable if it is a numeric variable.
VERSION
: Set to the value of the version
argument. If it is not
specified, the variable is not created.
A dataset to be used as input dataset to the dataset_queries
argument in derive_vars_query()
derive_vars_query()
, query()
, basket_select()
, Queries Dataset Documentation
Creating auxiliary datasets:
consolidate_metadata()
,
create_period_dataset()
,
create_single_dose_dataset()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(pharmaversesdtm) library(admiral) # creating a query dataset for a customized query cqterms <- tribble( ~TERMCHAR, ~TERMNUM, "APPLICATION SITE ERYTHEMA", 10003041L, "APPLICATION SITE PRURITUS", 10003053L ) %>% mutate(SRCVAR = "AEDECOD") cq <- query( prefix = "CQ01", name = "Application Site Issues", definition = cqterms ) create_query_data(queries = list(cq)) # create a query dataset for SMQs pregsmq <- query( prefix = "SMQ02", id = auto, definition = basket_select( name = "Pregnancy and neonatal topics (SMQ)", scope = "NARROW", type = "smq" ) ) bilismq <- query( prefix = "SMQ04", definition = basket_select( id = 20000121L, scope = "BROAD", type = "smq" ) ) # The get_terms function from pharmaversesdtm is used for this example. # In a real application a company-specific function must be used. create_query_data( queries = list(pregsmq, bilismq), get_terms_fun = pharmaversesdtm:::get_terms, version = "20.1" ) # create a query dataset for SDGs sdg <- query( prefix = "SDG01", id = auto, definition = basket_select( name = "5-aminosalicylates for ulcerative colitis", scope = NA_character_, type = "sdg" ) ) # The get_terms function from pharmaversesdtm is used for this example. # In a real application a company-specific function must be used. create_query_data( queries = list(sdg), get_terms_fun = pharmaversesdtm:::get_terms, version = "2019-09" ) # creating a query dataset for a customized query including SMQs # The get_terms function from pharmaversesdtm is used for this example. # In a real application a company-specific function must be used. create_query_data( queries = list( query( prefix = "CQ03", name = "Special issues of interest", definition = list( basket_select( name = "Pregnancy and neonatal topics (SMQ)", scope = "NARROW", type = "smq" ), cqterms ) ) ), get_terms_fun = pharmaversesdtm:::get_terms, version = "20.1" )
library(tibble) library(dplyr, warn.conflicts = FALSE) library(pharmaversesdtm) library(admiral) # creating a query dataset for a customized query cqterms <- tribble( ~TERMCHAR, ~TERMNUM, "APPLICATION SITE ERYTHEMA", 10003041L, "APPLICATION SITE PRURITUS", 10003053L ) %>% mutate(SRCVAR = "AEDECOD") cq <- query( prefix = "CQ01", name = "Application Site Issues", definition = cqterms ) create_query_data(queries = list(cq)) # create a query dataset for SMQs pregsmq <- query( prefix = "SMQ02", id = auto, definition = basket_select( name = "Pregnancy and neonatal topics (SMQ)", scope = "NARROW", type = "smq" ) ) bilismq <- query( prefix = "SMQ04", definition = basket_select( id = 20000121L, scope = "BROAD", type = "smq" ) ) # The get_terms function from pharmaversesdtm is used for this example. # In a real application a company-specific function must be used. create_query_data( queries = list(pregsmq, bilismq), get_terms_fun = pharmaversesdtm:::get_terms, version = "20.1" ) # create a query dataset for SDGs sdg <- query( prefix = "SDG01", id = auto, definition = basket_select( name = "5-aminosalicylates for ulcerative colitis", scope = NA_character_, type = "sdg" ) ) # The get_terms function from pharmaversesdtm is used for this example. # In a real application a company-specific function must be used. create_query_data( queries = list(sdg), get_terms_fun = pharmaversesdtm:::get_terms, version = "2019-09" ) # creating a query dataset for a customized query including SMQs # The get_terms function from pharmaversesdtm is used for this example. # In a real application a company-specific function must be used. create_query_data( queries = list( query( prefix = "CQ03", name = "Special issues of interest", definition = list( basket_select( name = "Pregnancy and neonatal topics (SMQ)", scope = "NARROW", type = "smq" ), cqterms ) ) ), get_terms_fun = pharmaversesdtm:::get_terms, version = "20.1" )
Derives dataset of single dose from aggregate dose information. This may be
necessary when e.g. calculating last dose before an adverse event in ADAE
or deriving a total dose parameter in ADEX
when EXDOSFRQ != ONCE
.
create_single_dose_dataset( dataset, dose_freq = EXDOSFRQ, start_date = ASTDT, start_datetime = NULL, end_date = AENDT, end_datetime = NULL, lookup_table = dose_freq_lookup, lookup_column = CDISC_VALUE, nominal_time = NULL, keep_source_vars = expr_c(exprs(USUBJID), dose_freq, start_date, start_datetime, end_date, end_datetime) )
create_single_dose_dataset( dataset, dose_freq = EXDOSFRQ, start_date = ASTDT, start_datetime = NULL, end_date = AENDT, end_datetime = NULL, lookup_table = dose_freq_lookup, lookup_column = CDISC_VALUE, nominal_time = NULL, keep_source_vars = expr_c(exprs(USUBJID), dose_freq, start_date, start_datetime, end_date, end_datetime) )
dataset |
Input dataset The variables specified by the |
dose_freq |
The dose frequency The aggregate dosing frequency used for multiple doses in a row. Permitted Values: defined by lookup table. |
start_date |
The start date A date object is expected. This object cannot contain Refer to |
start_datetime |
The start date-time A date-time object is expected. This object cannot contain Refer to If the input dataset contains frequencies which refer to |
end_date |
The end date A date or date-time object is expected. This object cannot contain Refer to |
end_datetime |
The end date-time A date-time object is expected. This object cannot contain Refer to If the input dataset contains frequencies which refer to |
lookup_table |
The dose frequency value lookup table The table used to look up Permitted Values for |
lookup_column |
The dose frequency value column in the lookup table The column of |
nominal_time |
The nominal relative time from first dose ( Used for PK analysis, this will be in hours and should be 0 for
the first dose. It can be derived as The value can be NULL if not needed. |
keep_source_vars |
List of variables to be retained from source dataset This parameter can be specified if additional information is required in
the output dataset. For example |
Each aggregate dose row is split into multiple rows which each
represent a single dose.The number of completed dose periods between
start_date
or start_datetime
and end_date
or end_datetime
is
calculated with compute_duration
and multiplied by DOSE_COUNT
.
For DOSE_WINDOW
values of "WEEK"
, "MONTH"
, and "YEAR"
,
CONVERSION_FACTOR
is used to convert into days the time object
to be added to start_date
.
Observations with dose frequency "ONCE"
are copied to the output dataset
unchanged.
The input dataset with a single dose per row.
Creating auxiliary datasets:
consolidate_metadata()
,
create_period_dataset()
,
create_query_data()
# Example with default lookup library(lubridate) library(stringr) library(tibble) library(dplyr) data <- tribble( ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM, "P01", "Q2D", ymd("2021-01-01"), ymd_hms("2021-01-01 10:30:00"), ymd("2021-01-07"), ymd_hms("2021-01-07 11:30:00"), "P01", "Q3D", ymd("2021-01-08"), ymd_hms("2021-01-08 12:00:00"), ymd("2021-01-14"), ymd_hms("2021-01-14 14:00:00"), "P01", "EVERY 2 WEEKS", ymd("2021-01-15"), ymd_hms("2021-01-15 09:57:00"), ymd("2021-01-29"), ymd_hms("2021-01-29 10:57:00") ) create_single_dose_dataset(data) # Example with custom lookup custom_lookup <- tribble( ~Value, ~DOSE_COUNT, ~DOSE_WINDOW, ~CONVERSION_FACTOR, "Q30MIN", (1 / 30), "MINUTE", 1, "Q90MIN", (1 / 90), "MINUTE", 1 ) data <- tribble( ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM, "P01", "Q30MIN", ymd("2021-01-01"), ymd_hms("2021-01-01T06:00:00"), ymd("2021-01-01"), ymd_hms("2021-01-01T07:00:00"), "P02", "Q90MIN", ymd("2021-01-01"), ymd_hms("2021-01-01T06:00:00"), ymd("2021-01-01"), ymd_hms("2021-01-01T09:00:00") ) create_single_dose_dataset(data, lookup_table = custom_lookup, lookup_column = Value, start_datetime = ASTDTM, end_datetime = AENDTM ) # Example with nominal time data <- tribble( ~USUBJID, ~EXDOSFRQ, ~NFRLT, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM, "P01", "BID", 0, ymd("2021-01-01"), ymd_hms("2021-01-01 08:00:00"), ymd("2021-01-07"), ymd_hms("2021-01-07 20:00:00"), "P01", "BID", 168, ymd("2021-01-08"), ymd_hms("2021-01-08 08:00:00"), ymd("2021-01-14"), ymd_hms("2021-01-14 20:00:00"), "P01", "BID", 336, ymd("2021-01-15"), ymd_hms("2021-01-15 08:00:00"), ymd("2021-01-29"), ymd_hms("2021-01-29 20:00:00") ) create_single_dose_dataset(data, dose_freq = EXDOSFRQ, start_date = ASTDT, start_datetime = ASTDTM, end_date = AENDT, end_datetime = AENDTM, lookup_table = dose_freq_lookup, lookup_column = CDISC_VALUE, nominal_time = NFRLT, keep_source_vars = exprs( USUBJID, EXDOSFRQ, ASTDT, ASTDTM, AENDT, AENDTM, NFRLT ) ) # Example - derive a single dose dataset with imputations # For either single drug administration records, or multiple drug administration # records covering a range of dates, fill-in of missing treatment end datetime # `EXENDTC` by substitution with an acceptable alternate, for example date of # death, date of datacut may be required. This example shows the # maximum possible number of single dose records to be derived. The example # requires the date of datacut `DCUTDT` to be specified correctly, or # if not appropriate to use `DCUTDT` as missing treatment end data and missing # treatment end datetime could set equal to treatment start date and treatment # start datetime. ADSL variables `DTHDT` and `DCUTDT` are preferred for # imputation use. # # All available trial treatments are included, allowing multiple different # last dose variables to be created in for example `use_ad_template("ADAE")` # if required. adsl <- tribble( ~STUDYID, ~USUBJID, ~DTHDT, "01", "1211", ymd("2013-01-14"), "01", "1083", ymd("2013-08-02"), "01", "1445", ymd("2014-11-01"), "01", "1015", NA, "01", "1023", NA ) ex <- tribble( ~STUDYID, ~USUBJID, ~EXSEQ, ~EXTRT, ~EXDOSE, ~EXDOSU, ~EXDOSFRQ, ~EXSTDTC, ~EXENDTC, "01", "1015", 1, "PLAC", 0, "mg", "QD", "2014-01-02", "2014-01-16", "01", "1015", 2, "PLAC", 0, "mg", "QD", "2014-06-17", "2014-06-18", "01", "1015", 3, "PLAC", 0, "mg", "QD", "2014-06-19", NA_character_, "01", "1023", 1, "PLAC", 0, "mg", "QD", "2012-08-05", "2012-08-27", "01", "1023", 2, "PLAC", 0, "mg", "QD", "2012-08-28", "2012-09-01", "01", "1211", 1, "XANO", 54, "mg", "QD", "2012-11-15", "2012-11-28", "01", "1211", 2, "XANO", 54, "mg", "QD", "2012-11-29", NA_character_, "01", "1445", 1, "PLAC", 0, "mg", "QD", "2014-05-11", "2014-05-25", "01", "1445", 2, "PLAC", 0, "mg", "QD", "2014-05-26", "2014-11-01", "01", "1083", 1, "PLAC", 0, "mg", "QD", "2013-07-22", "2013-08-01" ) adsl_death <- adsl %>% mutate( DTHDTM = convert_date_to_dtm(DTHDT), # Remove `DCUT` setup line below if ADSL `DCUTDT` is populated. DCUTDT = convert_dtc_to_dt("2015-03-06"), # Example only, enter date. DCUTDTM = convert_date_to_dtm(DCUTDT) ) # Select valid dose records, non-missing `EXSTDTC` and `EXDOSE`. ex_mod <- ex %>% filter(!is.na(EXSTDTC) & !is.na(EXDOSE)) %>% derive_vars_merged(adsl_death, by_vars = exprs(STUDYID, USUBJID)) %>% # Example, set up missing `EXDOSFRQ` as QD daily dosing regime. # Replace with study dosing regime per trial treatment. mutate(EXDOSFRQ = if_else(is.na(EXDOSFRQ), "QD", EXDOSFRQ)) %>% # Create EXxxDTM variables and replace missing `EXENDTM`. derive_vars_dtm( dtc = EXSTDTC, new_vars_prefix = "EXST", date_imputation = "first", time_imputation = "first", flag_imputation = "none", ) %>% derive_vars_dtm_to_dt(exprs(EXSTDTM)) %>% derive_vars_dtm( dtc = EXENDTC, new_vars_prefix = "EXEN", # Maximum imputed treatment end date must not be not greater than # date of death or after the datacut date. max_dates = exprs(DTHDTM, DCUTDTM), date_imputation = "last", time_imputation = "last", flag_imputation = "none", highest_imputation = "Y", ) %>% derive_vars_dtm_to_dt(exprs(EXENDTM)) %>% # Select only unique values. # Removes duplicated records before final step. distinct( STUDYID, USUBJID, EXTRT, EXDOSE, EXDOSFRQ, DCUTDT, DTHDT, EXSTDT, EXSTDTM, EXENDT, EXENDTM, EXSTDTC, EXENDTC ) create_single_dose_dataset( ex_mod, start_date = EXSTDT, start_datetime = EXSTDTM, end_date = EXENDT, end_datetime = EXENDTM, keep_source_vars = exprs( STUDYID, USUBJID, EXTRT, EXDOSE, EXDOSFRQ, DCUTDT, EXSTDT, EXSTDTM, EXENDT, EXENDTM, EXSTDTC, EXENDTC ) )
# Example with default lookup library(lubridate) library(stringr) library(tibble) library(dplyr) data <- tribble( ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM, "P01", "Q2D", ymd("2021-01-01"), ymd_hms("2021-01-01 10:30:00"), ymd("2021-01-07"), ymd_hms("2021-01-07 11:30:00"), "P01", "Q3D", ymd("2021-01-08"), ymd_hms("2021-01-08 12:00:00"), ymd("2021-01-14"), ymd_hms("2021-01-14 14:00:00"), "P01", "EVERY 2 WEEKS", ymd("2021-01-15"), ymd_hms("2021-01-15 09:57:00"), ymd("2021-01-29"), ymd_hms("2021-01-29 10:57:00") ) create_single_dose_dataset(data) # Example with custom lookup custom_lookup <- tribble( ~Value, ~DOSE_COUNT, ~DOSE_WINDOW, ~CONVERSION_FACTOR, "Q30MIN", (1 / 30), "MINUTE", 1, "Q90MIN", (1 / 90), "MINUTE", 1 ) data <- tribble( ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM, "P01", "Q30MIN", ymd("2021-01-01"), ymd_hms("2021-01-01T06:00:00"), ymd("2021-01-01"), ymd_hms("2021-01-01T07:00:00"), "P02", "Q90MIN", ymd("2021-01-01"), ymd_hms("2021-01-01T06:00:00"), ymd("2021-01-01"), ymd_hms("2021-01-01T09:00:00") ) create_single_dose_dataset(data, lookup_table = custom_lookup, lookup_column = Value, start_datetime = ASTDTM, end_datetime = AENDTM ) # Example with nominal time data <- tribble( ~USUBJID, ~EXDOSFRQ, ~NFRLT, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM, "P01", "BID", 0, ymd("2021-01-01"), ymd_hms("2021-01-01 08:00:00"), ymd("2021-01-07"), ymd_hms("2021-01-07 20:00:00"), "P01", "BID", 168, ymd("2021-01-08"), ymd_hms("2021-01-08 08:00:00"), ymd("2021-01-14"), ymd_hms("2021-01-14 20:00:00"), "P01", "BID", 336, ymd("2021-01-15"), ymd_hms("2021-01-15 08:00:00"), ymd("2021-01-29"), ymd_hms("2021-01-29 20:00:00") ) create_single_dose_dataset(data, dose_freq = EXDOSFRQ, start_date = ASTDT, start_datetime = ASTDTM, end_date = AENDT, end_datetime = AENDTM, lookup_table = dose_freq_lookup, lookup_column = CDISC_VALUE, nominal_time = NFRLT, keep_source_vars = exprs( USUBJID, EXDOSFRQ, ASTDT, ASTDTM, AENDT, AENDTM, NFRLT ) ) # Example - derive a single dose dataset with imputations # For either single drug administration records, or multiple drug administration # records covering a range of dates, fill-in of missing treatment end datetime # `EXENDTC` by substitution with an acceptable alternate, for example date of # death, date of datacut may be required. This example shows the # maximum possible number of single dose records to be derived. The example # requires the date of datacut `DCUTDT` to be specified correctly, or # if not appropriate to use `DCUTDT` as missing treatment end data and missing # treatment end datetime could set equal to treatment start date and treatment # start datetime. ADSL variables `DTHDT` and `DCUTDT` are preferred for # imputation use. # # All available trial treatments are included, allowing multiple different # last dose variables to be created in for example `use_ad_template("ADAE")` # if required. adsl <- tribble( ~STUDYID, ~USUBJID, ~DTHDT, "01", "1211", ymd("2013-01-14"), "01", "1083", ymd("2013-08-02"), "01", "1445", ymd("2014-11-01"), "01", "1015", NA, "01", "1023", NA ) ex <- tribble( ~STUDYID, ~USUBJID, ~EXSEQ, ~EXTRT, ~EXDOSE, ~EXDOSU, ~EXDOSFRQ, ~EXSTDTC, ~EXENDTC, "01", "1015", 1, "PLAC", 0, "mg", "QD", "2014-01-02", "2014-01-16", "01", "1015", 2, "PLAC", 0, "mg", "QD", "2014-06-17", "2014-06-18", "01", "1015", 3, "PLAC", 0, "mg", "QD", "2014-06-19", NA_character_, "01", "1023", 1, "PLAC", 0, "mg", "QD", "2012-08-05", "2012-08-27", "01", "1023", 2, "PLAC", 0, "mg", "QD", "2012-08-28", "2012-09-01", "01", "1211", 1, "XANO", 54, "mg", "QD", "2012-11-15", "2012-11-28", "01", "1211", 2, "XANO", 54, "mg", "QD", "2012-11-29", NA_character_, "01", "1445", 1, "PLAC", 0, "mg", "QD", "2014-05-11", "2014-05-25", "01", "1445", 2, "PLAC", 0, "mg", "QD", "2014-05-26", "2014-11-01", "01", "1083", 1, "PLAC", 0, "mg", "QD", "2013-07-22", "2013-08-01" ) adsl_death <- adsl %>% mutate( DTHDTM = convert_date_to_dtm(DTHDT), # Remove `DCUT` setup line below if ADSL `DCUTDT` is populated. DCUTDT = convert_dtc_to_dt("2015-03-06"), # Example only, enter date. DCUTDTM = convert_date_to_dtm(DCUTDT) ) # Select valid dose records, non-missing `EXSTDTC` and `EXDOSE`. ex_mod <- ex %>% filter(!is.na(EXSTDTC) & !is.na(EXDOSE)) %>% derive_vars_merged(adsl_death, by_vars = exprs(STUDYID, USUBJID)) %>% # Example, set up missing `EXDOSFRQ` as QD daily dosing regime. # Replace with study dosing regime per trial treatment. mutate(EXDOSFRQ = if_else(is.na(EXDOSFRQ), "QD", EXDOSFRQ)) %>% # Create EXxxDTM variables and replace missing `EXENDTM`. derive_vars_dtm( dtc = EXSTDTC, new_vars_prefix = "EXST", date_imputation = "first", time_imputation = "first", flag_imputation = "none", ) %>% derive_vars_dtm_to_dt(exprs(EXSTDTM)) %>% derive_vars_dtm( dtc = EXENDTC, new_vars_prefix = "EXEN", # Maximum imputed treatment end date must not be not greater than # date of death or after the datacut date. max_dates = exprs(DTHDTM, DCUTDTM), date_imputation = "last", time_imputation = "last", flag_imputation = "none", highest_imputation = "Y", ) %>% derive_vars_dtm_to_dt(exprs(EXENDTM)) %>% # Select only unique values. # Removes duplicated records before final step. distinct( STUDYID, USUBJID, EXTRT, EXDOSE, EXDOSFRQ, DCUTDT, DTHDT, EXSTDT, EXSTDTM, EXENDT, EXENDTM, EXSTDTC, EXENDTC ) create_single_dose_dataset( ex_mod, start_date = EXSTDT, start_datetime = EXSTDTM, end_date = EXENDT, end_datetime = EXENDTM, keep_source_vars = exprs( STUDYID, USUBJID, EXTRT, EXDOSE, EXDOSFRQ, DCUTDT, EXSTDT, EXSTDTM, EXENDT, EXENDTM, EXSTDTC, EXENDTC ) )
date_source
object The date_source()
function has been superseded in favor of derive_vars_extreme_event()
.
Create a date_source
object as input for derive_var_extreme_dt()
and
derive_var_extreme_dtm()
.
date_source(dataset_name, filter = NULL, date, set_values_to = NULL)
date_source(dataset_name, filter = NULL, date, set_values_to = NULL)
dataset_name |
The name of the dataset, i.e. a string, used to search for the date. |
filter |
An unquoted condition for filtering |
date |
A variable or an expression providing a date. A date or a datetime can be specified. An unquoted symbol or expression is expected. |
set_values_to |
Variables to be set |
An object of class date_source
.
derive_var_extreme_dtm()
, derive_var_extreme_dt()
Other superseded:
derive_param_extreme_record()
,
derive_var_dthcaus()
,
derive_var_extreme_dt()
,
derive_var_extreme_dtm()
,
dthcaus_source()
,
get_summary_records()
# treatment end date from ADSL trt_end_date <- date_source( dataset_name = "adsl", date = TRTEDT ) # lab date from LB where assessment was taken, i.e. not "NOT DONE" lb_date <- date_source( dataset_name = "lb", filter = LBSTAT != "NOT DONE" | is.na(LBSTAT), date = convert_dtc_to_dt(LBDTC) ) # death date from ADSL including traceability variables death_date <- date_source( dataset_name = "adsl", date = DTHDT, set_values_to = exprs( LALVDOM = "ADSL", LALVVAR = "DTHDT" ) )
# treatment end date from ADSL trt_end_date <- date_source( dataset_name = "adsl", date = TRTEDT ) # lab date from LB where assessment was taken, i.e. not "NOT DONE" lb_date <- date_source( dataset_name = "lb", filter = LBSTAT != "NOT DONE" | is.na(LBSTAT), date = convert_dtc_to_dt(LBDTC) ) # death date from ADSL including traceability variables death_date <- date_source( dataset_name = "adsl", date = DTHDT, set_values_to = exprs( LALVDOM = "ADSL", LALVVAR = "DTHDT" ) )
These pre-defined tte_source
objects can be used as input to derive_param_tte()
.
death_event lastalive_censor ae_event ae_ser_event ae_gr1_event ae_gr2_event ae_gr3_event ae_gr4_event ae_gr5_event ae_gr35_event ae_sev_event ae_wd_event
death_event lastalive_censor ae_event ae_ser_event ae_gr1_event ae_gr2_event ae_gr3_event ae_gr4_event ae_gr5_event ae_gr35_event ae_sev_event ae_wd_event
To see the definition of the various objects simply print the object in the
R console, e.g. print(death_event)
. For details of how to use these objects
please refer to derive_param_tte()
.
derive_param_tte()
, tte_source()
, event_source()
, censor_source()
Source Objects:
basket_select()
,
censor_source()
,
event()
,
event_joined()
,
event_source()
,
flag_event()
,
query()
,
records_source()
,
tte_source()
# This shows the definition of all pre-defined `tte_source` objects that ship # with {admiral} for (obj in list_tte_source_objects()$object) { cat(obj, "\n") print(get(obj)) cat("\n") }
# This shows the definition of all pre-defined `tte_source` objects that ship # with {admiral} for (obj in list_tte_source_objects()$object) { cat(obj, "\n") print(get(obj)) cat("\n") }
Get Default Parameter Code for Corrected QT
default_qtc_paramcd(method)
default_qtc_paramcd(method)
method |
Method used to QT correction Permitted Values: |
"QTCBR"
if method
is "Bazett"
, "QTCFR"
if it's "Fridericia"
or
"QTLCR"
if it's "Sagie"
. An error otherwise.
BDS-Findings Functions for adding Parameters/Records:
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
default_qtc_paramcd("Sagie")
default_qtc_paramcd("Sagie")
derivation_slice
ObjectCreate a derivation_slice
object as input for slice_derivation()
.
derivation_slice(filter, args = NULL)
derivation_slice(filter, args = NULL)
filter |
An unquoted condition for defining the observations of the slice |
args |
Arguments of the derivation to be used for the slice A |
An object of class derivation_slice
Higher Order Functions:
call_derivation()
,
restrict_derivation()
,
slice_derivation()
Baseline Type BASETYPE
is needed when there is more than one definition of
baseline for a given Analysis Parameter PARAM
in the same dataset. For a
given parameter, if Baseline Value BASE
is populated, and there is more than
one definition of baseline, then BASETYPE
must be non-null on all records of
any type for that parameter. Each value of BASETYPE
refers to a definition of
baseline that characterizes the value of BASE
on that row. Please see
section 4.2.1.6 of the ADaM Implementation Guide, version 1.3 for further
background.
derive_basetype_records(dataset, basetypes)
derive_basetype_records(dataset, basetypes)
dataset |
Input dataset The variables specified by the |
basetypes |
A named list of expressions created using the
The names corresponds to the values of the newly created |
Adds the BASETYPE
variable to a dataset and duplicates records based upon
the provided conditions.
For each element of basetypes
the input dataset is subset based upon
the provided expression and the BASETYPE
variable is set to the name of the
expression. Then, all subsets are stacked. Records which do not match any
condition are kept and BASETYPE
is set to NA
.
The input dataset with variable BASETYPE
added
BDS-Findings Functions that returns variable appended to dataset:
derive_var_analysis_ratio()
,
derive_var_anrind()
,
derive_var_atoxgr()
,
derive_var_atoxgr_dir()
,
derive_var_base()
,
derive_var_chg()
,
derive_var_ontrtfl()
,
derive_var_pchg()
,
derive_var_shift()
,
derive_vars_crit_flag()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(rlang) bds <- tribble( ~USUBJID, ~EPOCH, ~PARAMCD, ~ASEQ, ~AVAL, "P01", "RUN-IN", "PARAM01", 1, 10.0, "P01", "RUN-IN", "PARAM01", 2, 9.8, "P01", "DOUBLE-BLIND", "PARAM01", 3, 9.2, "P01", "DOUBLE-BLIND", "PARAM01", 4, 10.1, "P01", "OPEN-LABEL", "PARAM01", 5, 10.4, "P01", "OPEN-LABEL", "PARAM01", 6, 9.9, "P02", "RUN-IN", "PARAM01", 1, 12.1, "P02", "DOUBLE-BLIND", "PARAM01", 2, 10.2, "P02", "DOUBLE-BLIND", "PARAM01", 3, 10.8, "P02", "OPEN-LABEL", "PARAM01", 4, 11.4, "P02", "OPEN-LABEL", "PARAM01", 5, 10.8 ) bds_with_basetype <- derive_basetype_records( dataset = bds, basetypes = exprs( "RUN-IN" = EPOCH %in% c("RUN-IN", "STABILIZATION", "DOUBLE-BLIND", "OPEN-LABEL"), "DOUBLE-BLIND" = EPOCH %in% c("DOUBLE-BLIND", "OPEN-LABEL"), "OPEN-LABEL" = EPOCH == "OPEN-LABEL" ) ) # Below print statement will print all 23 records in the data frame # bds_with_basetype print(bds_with_basetype, n = Inf) count(bds_with_basetype, BASETYPE, name = "Number of Records") # An example where all parameter records need to be included for 2 different # baseline type derivations (such as LAST and WORST) bds <- tribble( ~USUBJID, ~EPOCH, ~PARAMCD, ~ASEQ, ~AVAL, "P01", "RUN-IN", "PARAM01", 1, 10.0, "P01", "RUN-IN", "PARAM01", 2, 9.8, "P01", "DOUBLE-BLIND", "PARAM01", 3, 9.2, "P01", "DOUBLE-BLIND", "PARAM01", 4, 10.1 ) bds_with_basetype <- derive_basetype_records( dataset = bds, basetypes = exprs( "LAST" = TRUE, "WORST" = TRUE ) ) print(bds_with_basetype, n = Inf) count(bds_with_basetype, BASETYPE, name = "Number of Records")
library(tibble) library(dplyr, warn.conflicts = FALSE) library(rlang) bds <- tribble( ~USUBJID, ~EPOCH, ~PARAMCD, ~ASEQ, ~AVAL, "P01", "RUN-IN", "PARAM01", 1, 10.0, "P01", "RUN-IN", "PARAM01", 2, 9.8, "P01", "DOUBLE-BLIND", "PARAM01", 3, 9.2, "P01", "DOUBLE-BLIND", "PARAM01", 4, 10.1, "P01", "OPEN-LABEL", "PARAM01", 5, 10.4, "P01", "OPEN-LABEL", "PARAM01", 6, 9.9, "P02", "RUN-IN", "PARAM01", 1, 12.1, "P02", "DOUBLE-BLIND", "PARAM01", 2, 10.2, "P02", "DOUBLE-BLIND", "PARAM01", 3, 10.8, "P02", "OPEN-LABEL", "PARAM01", 4, 11.4, "P02", "OPEN-LABEL", "PARAM01", 5, 10.8 ) bds_with_basetype <- derive_basetype_records( dataset = bds, basetypes = exprs( "RUN-IN" = EPOCH %in% c("RUN-IN", "STABILIZATION", "DOUBLE-BLIND", "OPEN-LABEL"), "DOUBLE-BLIND" = EPOCH %in% c("DOUBLE-BLIND", "OPEN-LABEL"), "OPEN-LABEL" = EPOCH == "OPEN-LABEL" ) ) # Below print statement will print all 23 records in the data frame # bds_with_basetype print(bds_with_basetype, n = Inf) count(bds_with_basetype, BASETYPE, name = "Number of Records") # An example where all parameter records need to be included for 2 different # baseline type derivations (such as LAST and WORST) bds <- tribble( ~USUBJID, ~EPOCH, ~PARAMCD, ~ASEQ, ~AVAL, "P01", "RUN-IN", "PARAM01", 1, 10.0, "P01", "RUN-IN", "PARAM01", 2, 9.8, "P01", "DOUBLE-BLIND", "PARAM01", 3, 9.2, "P01", "DOUBLE-BLIND", "PARAM01", 4, 10.1 ) bds_with_basetype <- derive_basetype_records( dataset = bds, basetypes = exprs( "LAST" = TRUE, "WORST" = TRUE ) ) print(bds_with_basetype, n = Inf) count(bds_with_basetype, BASETYPE, name = "Number of Records")
Add expected records as new observations for each 'by group' when the dataset contains missing observations.
derive_expected_records( dataset, dataset_ref, by_vars = NULL, set_values_to = NULL )
derive_expected_records( dataset, dataset_ref, by_vars = NULL, set_values_to = NULL )
dataset |
Input dataset The variables specified by the |
dataset_ref |
Expected observations dataset Data frame with the expected observations, e.g., all the expected
combinations of |
by_vars |
Grouping variables For each group defined by Permitted Values: list of variables created by |
set_values_to |
Variables to be set The specified variables are set to the specified values for the new observations. A list of variable name-value pairs is expected.
|
For each group (the variables specified in the by_vars
parameter),
those records from dataset_ref
that are missing in the input
dataset are added to the output dataset.
The input dataset with the missed expected observations added for each
by_vars
. Note, a variable will only be populated in the new parameter rows
if it is specified in by_vars
or set_values_to
.
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(tibble) adqs <- tribble( ~USUBJID, ~PARAMCD, ~AVISITN, ~AVISIT, ~AVAL, "1", "a", 1, "WEEK 1", 10, "1", "b", 1, "WEEK 1", 11, "2", "a", 2, "WEEK 2", 12, "2", "b", 2, "WEEK 2", 14 ) # Example 1. visit variables are parameter independent parm_visit_ref <- tribble( ~AVISITN, ~AVISIT, 1, "WEEK 1", 2, "WEEK 2" ) derive_expected_records( dataset = adqs, dataset_ref = parm_visit_ref, by_vars = exprs(USUBJID, PARAMCD), set_values_to = exprs(DTYPE = "DERIVED") ) # Example 2. visit variables are parameter dependent parm_visit_ref <- tribble( ~PARAMCD, ~AVISITN, ~AVISIT, "a", 1, "WEEK 1", "a", 2, "WEEK 2", "b", 1, "WEEK 1" ) derive_expected_records( dataset = adqs, dataset_ref = parm_visit_ref, by_vars = exprs(USUBJID, PARAMCD), set_values_to = exprs(DTYPE = "DERIVED") )
library(tibble) adqs <- tribble( ~USUBJID, ~PARAMCD, ~AVISITN, ~AVISIT, ~AVAL, "1", "a", 1, "WEEK 1", 10, "1", "b", 1, "WEEK 1", 11, "2", "a", 2, "WEEK 2", 12, "2", "b", 2, "WEEK 2", 14 ) # Example 1. visit variables are parameter independent parm_visit_ref <- tribble( ~AVISITN, ~AVISIT, 1, "WEEK 1", 2, "WEEK 2" ) derive_expected_records( dataset = adqs, dataset_ref = parm_visit_ref, by_vars = exprs(USUBJID, PARAMCD), set_values_to = exprs(DTYPE = "DERIVED") ) # Example 2. visit variables are parameter dependent parm_visit_ref <- tribble( ~PARAMCD, ~AVISITN, ~AVISIT, "a", 1, "WEEK 1", "a", 2, "WEEK 2", "b", 1, "WEEK 1" ) derive_expected_records( dataset = adqs, dataset_ref = parm_visit_ref, by_vars = exprs(USUBJID, PARAMCD), set_values_to = exprs(DTYPE = "DERIVED") )
Add the first available record from events
for each by group as new
records, all variables of the selected observation are kept. It can be used
for selecting the extreme observation from a series of user-defined events.
This distinguishes derive_extreme_event()
from derive_extreme_records()
,
where extreme records are derived based on certain order of existing
variables.
derive_extreme_event( dataset = NULL, by_vars, events, tmp_event_nr_var = NULL, order, mode, source_datasets = NULL, check_type = "warning", set_values_to = NULL, keep_source_vars = exprs(everything()) )
derive_extreme_event( dataset = NULL, by_vars, events, tmp_event_nr_var = NULL, order, mode, source_datasets = NULL, check_type = "warning", set_values_to = NULL, keep_source_vars = exprs(everything()) )
dataset |
Input dataset The variables specified by the |
by_vars |
Grouping variables Default: Permitted Values: list of variables created by |
events |
Conditions and new values defining events A list of For |
tmp_event_nr_var |
Temporary event number variable The specified variable is added to all source datasets and is set to the number of the event before selecting the records of the event. It can be used in The variable is not included in the output dataset. |
order |
Sort order If a particular event from For handling of Permitted Values: list of expressions created by |
mode |
Selection mode (first or last) If a particular event from Permitted Values: |
source_datasets |
Source datasets A named list of datasets is expected. The |
check_type |
Check uniqueness? If Default: Permitted Values: |
set_values_to |
Variables to be set The specified variables are set to the specified values for the new observations. Set a list of variables to some specified value for the new records
For example: set_values_to = exprs( AVAL = sum(AVAL), DTYPE = "AVERAGE", ) |
keep_source_vars |
Variables to keep from the source dataset For each event the specified variables are kept from the selected
observations. The variables specified for Permitted Values: A list of expressions where each element is
a symbol or a tidyselect expression, e.g., |
For each event select the observations to consider:
If the event is of class event
, the observations of the source dataset
are restricted by condition
and then the first or last (mode
)
observation per by group (by_vars
) is selected.
If the event is of class event_joined
, filter_joined()
is called to
select the observations.
The variables specified by the set_values_to
field of the event
are added to the selected observations.
The variable specified for tmp_event_nr_var
is added and set to
the number of the event.
Only the variables specified for the keep_source_vars
field of the
event, and the by variables (by_vars
) and the variables created by
set_values_to
are kept. If keep_source_vars = NULL
is used for an event
in derive_extreme_event()
the value of the keep_source_vars
argument of
derive_extreme_event()
is used.
All selected observations are bound together.
For each group (with respect to the variables specified for the
by_vars
parameter) the first or last observation (with respect to the
order specified for the order
parameter and the mode specified for the
mode
parameter) is selected.
The variables specified by the set_values_to
parameter are added to
the selected observations.
The observations are added to input dataset.
The input dataset with the best or worst observation of each by group added as new observations.
event()
, event_joined()
, derive_vars_extreme_event()
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(tibble) library(dplyr) library(lubridate) adqs <- tribble( ~USUBJID, ~PARAMCD, ~AVALC, ~ADY, "1", "NO SLEEP", "N", 1, "1", "WAKE UP", "N", 2, "1", "FALL ASLEEP", "N", 3, "2", "NO SLEEP", "N", 1, "2", "WAKE UP", "Y", 2, "2", "WAKE UP", "Y", 3, "2", "FALL ASLEEP", "N", 4, "3", "NO SLEEP", NA_character_, 1 ) # Add a new record for each USUBJID storing the the worst sleeping problem. derive_extreme_event( adqs, by_vars = exprs(USUBJID), events = list( event( condition = PARAMCD == "NO SLEEP" & AVALC == "Y", set_values_to = exprs(AVALC = "No sleep", AVAL = 1) ), event( condition = PARAMCD == "WAKE UP" & AVALC == "Y", set_values_to = exprs(AVALC = "Waking up more than three times", AVAL = 2) ), event( condition = PARAMCD == "FALL ASLEEP" & AVALC == "Y", set_values_to = exprs(AVALC = "More than 30 mins to fall asleep", AVAL = 3) ), event( condition = all(AVALC == "N"), set_values_to = exprs( AVALC = "No sleeping problems", AVAL = 4 ) ), event( condition = TRUE, set_values_to = exprs(AVALC = "Missing", AVAL = 99) ) ), tmp_event_nr_var = event_nr, order = exprs(event_nr, desc(ADY)), mode = "first", set_values_to = exprs( PARAMCD = "WSP", PARAM = "Worst Sleeping Problems" ) ) # Use different mode by event adhy <- tribble( ~USUBJID, ~AVISITN, ~CRIT1FL, "1", 1, "Y", "1", 2, "Y", "2", 1, "Y", "2", 2, NA_character_, "2", 3, "Y", "2", 4, NA_character_ ) %>% mutate( PARAMCD = "ALKPH", PARAM = "Alkaline Phosphatase (U/L)" ) derive_extreme_event( adhy, by_vars = exprs(USUBJID), events = list( event( condition = is.na(CRIT1FL), set_values_to = exprs(AVALC = "N") ), event( condition = CRIT1FL == "Y", mode = "last", set_values_to = exprs(AVALC = "Y") ) ), tmp_event_nr_var = event_nr, order = exprs(event_nr, AVISITN), mode = "first", keep_source_vars = exprs(AVISITN), set_values_to = exprs( PARAMCD = "ALK2", PARAM = "ALKPH <= 2 times ULN" ) ) # Derive confirmed best overall response (using event_joined()) # CR - complete response, PR - partial response, SD - stable disease # NE - not evaluable, PD - progressive disease adsl <- tribble( ~USUBJID, ~TRTSDTC, "1", "2020-01-01", "2", "2019-12-12", "3", "2019-11-11", "4", "2019-12-30", "5", "2020-01-01", "6", "2020-02-02", "7", "2020-02-02", "8", "2020-02-01" ) %>% mutate(TRTSDT = ymd(TRTSDTC)) adrs <- tribble( ~USUBJID, ~ADTC, ~AVALC, "1", "2020-01-01", "PR", "1", "2020-02-01", "CR", "1", "2020-02-16", "NE", "1", "2020-03-01", "CR", "1", "2020-04-01", "SD", "2", "2020-01-01", "SD", "2", "2020-02-01", "PR", "2", "2020-03-01", "SD", "2", "2020-03-13", "CR", "4", "2020-01-01", "PR", "4", "2020-03-01", "NE", "4", "2020-04-01", "NE", "4", "2020-05-01", "PR", "5", "2020-01-01", "PR", "5", "2020-01-10", "PR", "5", "2020-01-20", "PR", "6", "2020-02-06", "PR", "6", "2020-02-16", "CR", "6", "2020-03-30", "PR", "7", "2020-02-06", "PR", "7", "2020-02-16", "CR", "7", "2020-04-01", "NE", "8", "2020-02-16", "PD" ) %>% mutate( ADT = ymd(ADTC), PARAMCD = "OVR", PARAM = "Overall Response by Investigator" ) %>% derive_vars_merged( dataset_add = adsl, by_vars = exprs(USUBJID), new_vars = exprs(TRTSDT) ) derive_extreme_event( adrs, by_vars = exprs(USUBJID), tmp_event_nr_var = event_nr, order = exprs(event_nr, ADT), mode = "first", source_datasets = list(adsl = adsl), events = list( event_joined( description = paste( "CR needs to be confirmed by a second CR at least 28 days later", "at most one NE is acceptable between the two assessments" ), join_vars = exprs(AVALC, ADT), join_type = "after", first_cond_upper = AVALC.join == "CR" & ADT.join >= ADT + 28, condition = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1, set_values_to = exprs( AVALC = "CR" ) ), event_joined( description = paste( "PR needs to be confirmed by a second CR or PR at least 28 days later,", "at most one NE is acceptable between the two assessments" ), join_vars = exprs(AVALC, ADT), join_type = "after", first_cond_upper = AVALC.join %in% c("CR", "PR") & ADT.join >= ADT + 28, condition = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1, set_values_to = exprs( AVALC = "PR" ) ), event( description = paste( "CR, PR, or SD are considered as SD if occurring at least 28", "after treatment start" ), condition = AVALC %in% c("CR", "PR", "SD") & ADT >= TRTSDT + 28, set_values_to = exprs( AVALC = "SD" ) ), event( condition = AVALC == "PD", set_values_to = exprs( AVALC = "PD" ) ), event( condition = AVALC %in% c("CR", "PR", "SD", "NE"), set_values_to = exprs( AVALC = "NE" ) ), event( description = "set response to MISSING for patients without records in ADRS", dataset_name = "adsl", condition = TRUE, set_values_to = exprs( AVALC = "MISSING" ), keep_source_vars = exprs(TRTSDT) ) ), set_values_to = exprs( PARAMCD = "CBOR", PARAM = "Best Confirmed Overall Response by Investigator" ) ) %>% filter(PARAMCD == "CBOR")
library(tibble) library(dplyr) library(lubridate) adqs <- tribble( ~USUBJID, ~PARAMCD, ~AVALC, ~ADY, "1", "NO SLEEP", "N", 1, "1", "WAKE UP", "N", 2, "1", "FALL ASLEEP", "N", 3, "2", "NO SLEEP", "N", 1, "2", "WAKE UP", "Y", 2, "2", "WAKE UP", "Y", 3, "2", "FALL ASLEEP", "N", 4, "3", "NO SLEEP", NA_character_, 1 ) # Add a new record for each USUBJID storing the the worst sleeping problem. derive_extreme_event( adqs, by_vars = exprs(USUBJID), events = list( event( condition = PARAMCD == "NO SLEEP" & AVALC == "Y", set_values_to = exprs(AVALC = "No sleep", AVAL = 1) ), event( condition = PARAMCD == "WAKE UP" & AVALC == "Y", set_values_to = exprs(AVALC = "Waking up more than three times", AVAL = 2) ), event( condition = PARAMCD == "FALL ASLEEP" & AVALC == "Y", set_values_to = exprs(AVALC = "More than 30 mins to fall asleep", AVAL = 3) ), event( condition = all(AVALC == "N"), set_values_to = exprs( AVALC = "No sleeping problems", AVAL = 4 ) ), event( condition = TRUE, set_values_to = exprs(AVALC = "Missing", AVAL = 99) ) ), tmp_event_nr_var = event_nr, order = exprs(event_nr, desc(ADY)), mode = "first", set_values_to = exprs( PARAMCD = "WSP", PARAM = "Worst Sleeping Problems" ) ) # Use different mode by event adhy <- tribble( ~USUBJID, ~AVISITN, ~CRIT1FL, "1", 1, "Y", "1", 2, "Y", "2", 1, "Y", "2", 2, NA_character_, "2", 3, "Y", "2", 4, NA_character_ ) %>% mutate( PARAMCD = "ALKPH", PARAM = "Alkaline Phosphatase (U/L)" ) derive_extreme_event( adhy, by_vars = exprs(USUBJID), events = list( event( condition = is.na(CRIT1FL), set_values_to = exprs(AVALC = "N") ), event( condition = CRIT1FL == "Y", mode = "last", set_values_to = exprs(AVALC = "Y") ) ), tmp_event_nr_var = event_nr, order = exprs(event_nr, AVISITN), mode = "first", keep_source_vars = exprs(AVISITN), set_values_to = exprs( PARAMCD = "ALK2", PARAM = "ALKPH <= 2 times ULN" ) ) # Derive confirmed best overall response (using event_joined()) # CR - complete response, PR - partial response, SD - stable disease # NE - not evaluable, PD - progressive disease adsl <- tribble( ~USUBJID, ~TRTSDTC, "1", "2020-01-01", "2", "2019-12-12", "3", "2019-11-11", "4", "2019-12-30", "5", "2020-01-01", "6", "2020-02-02", "7", "2020-02-02", "8", "2020-02-01" ) %>% mutate(TRTSDT = ymd(TRTSDTC)) adrs <- tribble( ~USUBJID, ~ADTC, ~AVALC, "1", "2020-01-01", "PR", "1", "2020-02-01", "CR", "1", "2020-02-16", "NE", "1", "2020-03-01", "CR", "1", "2020-04-01", "SD", "2", "2020-01-01", "SD", "2", "2020-02-01", "PR", "2", "2020-03-01", "SD", "2", "2020-03-13", "CR", "4", "2020-01-01", "PR", "4", "2020-03-01", "NE", "4", "2020-04-01", "NE", "4", "2020-05-01", "PR", "5", "2020-01-01", "PR", "5", "2020-01-10", "PR", "5", "2020-01-20", "PR", "6", "2020-02-06", "PR", "6", "2020-02-16", "CR", "6", "2020-03-30", "PR", "7", "2020-02-06", "PR", "7", "2020-02-16", "CR", "7", "2020-04-01", "NE", "8", "2020-02-16", "PD" ) %>% mutate( ADT = ymd(ADTC), PARAMCD = "OVR", PARAM = "Overall Response by Investigator" ) %>% derive_vars_merged( dataset_add = adsl, by_vars = exprs(USUBJID), new_vars = exprs(TRTSDT) ) derive_extreme_event( adrs, by_vars = exprs(USUBJID), tmp_event_nr_var = event_nr, order = exprs(event_nr, ADT), mode = "first", source_datasets = list(adsl = adsl), events = list( event_joined( description = paste( "CR needs to be confirmed by a second CR at least 28 days later", "at most one NE is acceptable between the two assessments" ), join_vars = exprs(AVALC, ADT), join_type = "after", first_cond_upper = AVALC.join == "CR" & ADT.join >= ADT + 28, condition = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1, set_values_to = exprs( AVALC = "CR" ) ), event_joined( description = paste( "PR needs to be confirmed by a second CR or PR at least 28 days later,", "at most one NE is acceptable between the two assessments" ), join_vars = exprs(AVALC, ADT), join_type = "after", first_cond_upper = AVALC.join %in% c("CR", "PR") & ADT.join >= ADT + 28, condition = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1, set_values_to = exprs( AVALC = "PR" ) ), event( description = paste( "CR, PR, or SD are considered as SD if occurring at least 28", "after treatment start" ), condition = AVALC %in% c("CR", "PR", "SD") & ADT >= TRTSDT + 28, set_values_to = exprs( AVALC = "SD" ) ), event( condition = AVALC == "PD", set_values_to = exprs( AVALC = "PD" ) ), event( condition = AVALC %in% c("CR", "PR", "SD", "NE"), set_values_to = exprs( AVALC = "NE" ) ), event( description = "set response to MISSING for patients without records in ADRS", dataset_name = "adsl", condition = TRUE, set_values_to = exprs( AVALC = "MISSING" ), keep_source_vars = exprs(TRTSDT) ) ), set_values_to = exprs( PARAMCD = "CBOR", PARAM = "Best Confirmed Overall Response by Investigator" ) ) %>% filter(PARAMCD == "CBOR")
Add the first or last observation for each by group as new observations. The
new observations can be selected from the additional dataset. This function can
be used for adding the maximum or minimum value as a separate visit.
All variables of the selected observation are kept. This distinguishes
derive_extreme_records()
from derive_summary_records()
,
where only the by variables are populated for the new records.
derive_extreme_records( dataset = NULL, dataset_add, dataset_ref = NULL, by_vars = NULL, order = NULL, mode = NULL, filter_add = NULL, check_type = "warning", exist_flag = NULL, true_value = "Y", false_value = NA_character_, keep_source_vars = exprs(everything()), set_values_to )
derive_extreme_records( dataset = NULL, dataset_add, dataset_ref = NULL, by_vars = NULL, order = NULL, mode = NULL, filter_add = NULL, check_type = "warning", exist_flag = NULL, true_value = "Y", false_value = NA_character_, keep_source_vars = exprs(everything()), set_values_to )
dataset |
Input dataset |
dataset_add |
Additional dataset The additional dataset, which determines the by groups returned in the input dataset,
based on the groups that exist in this dataset after being subset by The variables specified in the |
dataset_ref |
Reference dataset The variables specified for |
by_vars |
Grouping variables If Permitted Values: list of variables created by |
order |
Sort order Within each by group the observations are ordered by the specified order. Permitted Values: list of expressions created by |
mode |
Selection mode (first or last) If Permitted Values: |
filter_add |
Filter for additional dataset ( Only observations in |
check_type |
Check uniqueness? If Permitted Values: |
exist_flag |
Existence flag The specified variable is added to the output dataset. For by groups with at least one observation in the additional dataset
( For all other by groups Permitted Values: Variable name |
true_value |
True value For new observations selected from the additional dataset ( |
false_value |
False value For new observations not selected from the additional dataset
( |
keep_source_vars |
Variables to be kept in the new records A named list or tidyselect expressions created by |
set_values_to |
Variables to be set The specified variables are set to the specified values for the new observations. Set a list of variables to some specified value for the new records
For example: set_values_to = exprs( AVAL = sum(AVAL), DTYPE = "AVERAGE", ) |
The additional dataset (dataset_add
) is restricted as specified by the
filter_add
argument.
For each group (with respect to the variables specified for the
by_vars
argument) the first or last observation (with respect to the
order specified for the order
argument and the mode specified for the
mode
argument) is selected.
If dataset_ref
is specified, observations which are in dataset_ref
but not in the selected records are added.
The variables specified by the set_values_to
argument are added to
the selected observations.
The variables specified by the keep_source_vars
argument are selected
along with the variables specified in by_vars
and set_values_to
arguments.
The observations are added to input dataset.
The input dataset with the first or last observation of each by group added as new observations.
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) adlb <- tribble( ~USUBJID, ~AVISITN, ~AVAL, ~LBSEQ, "1", 1, 113, 1, "1", 2, 113, 2, "1", 3, 117, 3, "2", 1, 101, 1, "2", 2, 101, 2, "2", 3, 95, 3 ) # Add a new record for each USUBJID storing the minimum value (first AVAL). # If multiple records meet the minimum criterion, take the first value by # AVISITN. Set AVISITN = 97 and DTYPE = MINIMUM for these new records. # Specify the variables that need to be kept in the new records. derive_extreme_records( adlb, dataset_add = adlb, by_vars = exprs(USUBJID), order = exprs(AVAL, AVISITN), mode = "first", filter_add = !is.na(AVAL), keep_source_vars = exprs(AVAL), set_values_to = exprs( AVISITN = 97, DTYPE = "MINIMUM" ) ) # Add a new record for each USUBJID storing the maximum value (last AVAL). # If multiple records meet the maximum criterion, take the first value by # AVISITN. Set AVISITN = 98 and DTYPE = MAXIMUM for these new records. derive_extreme_records( adlb, dataset_add = adlb, by_vars = exprs(USUBJID), order = exprs(desc(AVAL), AVISITN), mode = "first", filter_add = !is.na(AVAL), set_values_to = exprs( AVISITN = 98, DTYPE = "MAXIMUM" ) ) # Add a new record for each USUBJID storing for the last value. # Set AVISITN = 99 and DTYPE = LOV for these new records. derive_extreme_records( adlb, dataset_add = adlb, by_vars = exprs(USUBJID), order = exprs(AVISITN), mode = "last", set_values_to = exprs( AVISITN = 99, DTYPE = "LOV" ) ) # Derive a new parameter for the first disease progression (PD) adsl <- tribble( ~USUBJID, ~DTHDT, "1", ymd("2022-05-13"), "2", ymd(""), "3", ymd("") ) %>% mutate(STUDYID = "XX1234") adrs <- tribble( ~USUBJID, ~ADTC, ~AVALC, "1", "2020-01-02", "PR", "1", "2020-02-01", "CR", "1", "2020-03-01", "CR", "1", "2020-04-01", "SD", "2", "2021-06-15", "SD", "2", "2021-07-16", "PD", "2", "2021-09-14", "PD" ) %>% mutate( STUDYID = "XX1234", ADT = ymd(ADTC), PARAMCD = "OVR", PARAM = "Overall Response", ANL01FL = "Y" ) %>% select(-ADTC) derive_extreme_records( adrs, dataset_ref = adsl, dataset_add = adrs, by_vars = exprs(STUDYID, USUBJID), filter_add = PARAMCD == "OVR" & AVALC == "PD", order = exprs(ADT), exist_flag = AVALC, true_value = "Y", false_value = "N", mode = "first", set_values_to = exprs( PARAMCD = "PD", PARAM = "Disease Progression", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y", ADT = ADT ) ) # derive parameter indicating death derive_extreme_records( dataset_ref = adsl, dataset_add = adsl, by_vars = exprs(STUDYID, USUBJID), filter_add = !is.na(DTHDT), exist_flag = AVALC, true_value = "Y", false_value = "N", mode = "first", set_values_to = exprs( PARAMCD = "DEATH", PARAM = "Death", ANL01FL = "Y", ADT = DTHDT ) )
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) adlb <- tribble( ~USUBJID, ~AVISITN, ~AVAL, ~LBSEQ, "1", 1, 113, 1, "1", 2, 113, 2, "1", 3, 117, 3, "2", 1, 101, 1, "2", 2, 101, 2, "2", 3, 95, 3 ) # Add a new record for each USUBJID storing the minimum value (first AVAL). # If multiple records meet the minimum criterion, take the first value by # AVISITN. Set AVISITN = 97 and DTYPE = MINIMUM for these new records. # Specify the variables that need to be kept in the new records. derive_extreme_records( adlb, dataset_add = adlb, by_vars = exprs(USUBJID), order = exprs(AVAL, AVISITN), mode = "first", filter_add = !is.na(AVAL), keep_source_vars = exprs(AVAL), set_values_to = exprs( AVISITN = 97, DTYPE = "MINIMUM" ) ) # Add a new record for each USUBJID storing the maximum value (last AVAL). # If multiple records meet the maximum criterion, take the first value by # AVISITN. Set AVISITN = 98 and DTYPE = MAXIMUM for these new records. derive_extreme_records( adlb, dataset_add = adlb, by_vars = exprs(USUBJID), order = exprs(desc(AVAL), AVISITN), mode = "first", filter_add = !is.na(AVAL), set_values_to = exprs( AVISITN = 98, DTYPE = "MAXIMUM" ) ) # Add a new record for each USUBJID storing for the last value. # Set AVISITN = 99 and DTYPE = LOV for these new records. derive_extreme_records( adlb, dataset_add = adlb, by_vars = exprs(USUBJID), order = exprs(AVISITN), mode = "last", set_values_to = exprs( AVISITN = 99, DTYPE = "LOV" ) ) # Derive a new parameter for the first disease progression (PD) adsl <- tribble( ~USUBJID, ~DTHDT, "1", ymd("2022-05-13"), "2", ymd(""), "3", ymd("") ) %>% mutate(STUDYID = "XX1234") adrs <- tribble( ~USUBJID, ~ADTC, ~AVALC, "1", "2020-01-02", "PR", "1", "2020-02-01", "CR", "1", "2020-03-01", "CR", "1", "2020-04-01", "SD", "2", "2021-06-15", "SD", "2", "2021-07-16", "PD", "2", "2021-09-14", "PD" ) %>% mutate( STUDYID = "XX1234", ADT = ymd(ADTC), PARAMCD = "OVR", PARAM = "Overall Response", ANL01FL = "Y" ) %>% select(-ADTC) derive_extreme_records( adrs, dataset_ref = adsl, dataset_add = adrs, by_vars = exprs(STUDYID, USUBJID), filter_add = PARAMCD == "OVR" & AVALC == "PD", order = exprs(ADT), exist_flag = AVALC, true_value = "Y", false_value = "N", mode = "first", set_values_to = exprs( PARAMCD = "PD", PARAM = "Disease Progression", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y", ADT = ADT ) ) # derive parameter indicating death derive_extreme_records( dataset_ref = adsl, dataset_add = adsl, by_vars = exprs(STUDYID, USUBJID), filter_add = !is.na(DTHDT), exist_flag = AVALC, true_value = "Y", false_value = "N", mode = "first", set_values_to = exprs( PARAMCD = "DEATH", PARAM = "Death", ANL01FL = "Y", ADT = DTHDT ) )
Adds LOCF records as new observations for each 'by group' when the dataset does not contain observations for missed visits/time points.
derive_locf_records( dataset, dataset_ref, by_vars, analysis_var = AVAL, order, keep_vars = NULL )
derive_locf_records( dataset, dataset_ref, by_vars, analysis_var = AVAL, order, keep_vars = NULL )
dataset |
Input dataset The variables specified by the |
dataset_ref |
Expected observations dataset Data frame with all the combinations of |
by_vars |
Grouping variables For each group defined by Permitted Values: list of variables created by |
analysis_var |
Analysis variable. Default: Permitted Values: a variable |
order |
Sort order The dataset is sorted by For handling of |
keep_vars |
Variables that need carrying the last observation forward Keep variables that need carrying the last observation forward other than |
For each group (with respect to the variables specified for the
by_vars parameter) those observations from dataset_ref
are added to
the output dataset
which do not have a corresponding observation in the input dataset or
for which analysis_var
is NA for the corresponding observation in the input dataset.
For the new observations, analysis_var
is set to the non-missing analysis_var
of the
previous observation in the input dataset (when sorted by order
) and
DTYPE
is set to "LOCF".
The input dataset with the new "LOCF" observations added for each
by_vars
. Note, a variable will only be populated in the new parameter rows
if it is specified in by_vars
.
G Gayatri
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(dplyr) library(tibble) advs <- tribble( ~STUDYID, ~USUBJID, ~PARAMCD, ~PARAMN, ~AVAL, ~AVISITN, ~AVISIT, "CDISC01", "01-701-1015", "PULSE", 1, 65, 0, "BASELINE", "CDISC01", "01-701-1015", "DIABP", 2, 79, 0, "BASELINE", "CDISC01", "01-701-1015", "DIABP", 2, 80, 2, "WEEK 2", "CDISC01", "01-701-1015", "DIABP", 2, NA, 4, "WEEK 4", "CDISC01", "01-701-1015", "DIABP", 2, NA, 6, "WEEK 6", "CDISC01", "01-701-1015", "SYSBP", 3, 130, 0, "BASELINE", "CDISC01", "01-701-1015", "SYSBP", 3, 132, 2, "WEEK 2", "CDISC01", "01-701-1028", "PULSE", 1, 61, 0, "BASELINE", "CDISC01", "01-701-1028", "PULSE", 1, 60, 6, "WEEK 6", "CDISC01", "01-701-1028", "DIABP", 2, 51, 0, "BASELINE", "CDISC01", "01-701-1028", "DIABP", 2, 50, 2, "WEEK 2", "CDISC01", "01-701-1028", "DIABP", 2, 51, 4, "WEEK 4", "CDISC01", "01-701-1028", "DIABP", 2, 50, 6, "WEEK 6", "CDISC01", "01-701-1028", "SYSBP", 3, 121, 0, "BASELINE", "CDISC01", "01-701-1028", "SYSBP", 3, 121, 2, "WEEK 2", "CDISC01", "01-701-1028", "SYSBP", 3, 121, 4, "WEEK 4", "CDISC01", "01-701-1028", "SYSBP", 3, 121, 6, "WEEK 6" ) # A dataset with all the combinations of PARAMCD, PARAM, AVISIT, AVISITN, ... which are expected. advs_expected_obsv <- tribble( ~PARAMCD, ~AVISITN, ~AVISIT, "PULSE", 0, "BASELINE", "PULSE", 6, "WEEK 6", "DIABP", 0, "BASELINE", "DIABP", 2, "WEEK 2", "DIABP", 4, "WEEK 4", "DIABP", 6, "WEEK 6", "SYSBP", 0, "BASELINE", "SYSBP", 2, "WEEK 2", "SYSBP", 4, "WEEK 4", "SYSBP", 6, "WEEK 6" ) derive_locf_records( dataset = advs, dataset_ref = advs_expected_obsv, by_vars = exprs(STUDYID, USUBJID, PARAMCD), order = exprs(AVISITN, AVISIT), keep_vars = exprs(PARAMN) ) |> arrange(USUBJID, PARAMCD, AVISIT)
library(dplyr) library(tibble) advs <- tribble( ~STUDYID, ~USUBJID, ~PARAMCD, ~PARAMN, ~AVAL, ~AVISITN, ~AVISIT, "CDISC01", "01-701-1015", "PULSE", 1, 65, 0, "BASELINE", "CDISC01", "01-701-1015", "DIABP", 2, 79, 0, "BASELINE", "CDISC01", "01-701-1015", "DIABP", 2, 80, 2, "WEEK 2", "CDISC01", "01-701-1015", "DIABP", 2, NA, 4, "WEEK 4", "CDISC01", "01-701-1015", "DIABP", 2, NA, 6, "WEEK 6", "CDISC01", "01-701-1015", "SYSBP", 3, 130, 0, "BASELINE", "CDISC01", "01-701-1015", "SYSBP", 3, 132, 2, "WEEK 2", "CDISC01", "01-701-1028", "PULSE", 1, 61, 0, "BASELINE", "CDISC01", "01-701-1028", "PULSE", 1, 60, 6, "WEEK 6", "CDISC01", "01-701-1028", "DIABP", 2, 51, 0, "BASELINE", "CDISC01", "01-701-1028", "DIABP", 2, 50, 2, "WEEK 2", "CDISC01", "01-701-1028", "DIABP", 2, 51, 4, "WEEK 4", "CDISC01", "01-701-1028", "DIABP", 2, 50, 6, "WEEK 6", "CDISC01", "01-701-1028", "SYSBP", 3, 121, 0, "BASELINE", "CDISC01", "01-701-1028", "SYSBP", 3, 121, 2, "WEEK 2", "CDISC01", "01-701-1028", "SYSBP", 3, 121, 4, "WEEK 4", "CDISC01", "01-701-1028", "SYSBP", 3, 121, 6, "WEEK 6" ) # A dataset with all the combinations of PARAMCD, PARAM, AVISIT, AVISITN, ... which are expected. advs_expected_obsv <- tribble( ~PARAMCD, ~AVISITN, ~AVISIT, "PULSE", 0, "BASELINE", "PULSE", 6, "WEEK 6", "DIABP", 0, "BASELINE", "DIABP", 2, "WEEK 2", "DIABP", 4, "WEEK 4", "DIABP", 6, "WEEK 6", "SYSBP", 0, "BASELINE", "SYSBP", 2, "WEEK 2", "SYSBP", 4, "WEEK 4", "SYSBP", 6, "WEEK 6" ) derive_locf_records( dataset = advs, dataset_ref = advs_expected_obsv, by_vars = exprs(STUDYID, USUBJID, PARAMCD), order = exprs(AVISITN, AVISIT), keep_vars = exprs(PARAMN) ) |> arrange(USUBJID, PARAMCD, AVISIT)
Adds a record for BMI/Body Mass Index using Weight and Height each by group (e.g., subject and visit) where the source parameters are available.
Note: This is a wrapper function for the more generic derive_param_computed()
.
derive_param_bmi( dataset, by_vars, set_values_to = exprs(PARAMCD = "BMI"), weight_code = "WEIGHT", height_code = "HEIGHT", get_unit_expr, filter = NULL, constant_by_vars = NULL )
derive_param_bmi( dataset, by_vars, set_values_to = exprs(PARAMCD = "BMI"), weight_code = "WEIGHT", height_code = "HEIGHT", get_unit_expr, filter = NULL, constant_by_vars = NULL )
dataset |
Input dataset The variables specified by the The variable specified by |
by_vars |
Grouping variables For each group defined by Permitted Values: list of variables created by |
set_values_to |
Variables to be set The specified variables are set to the specified values for the new
observations. For example Permitted Values: List of variable-value pairs |
weight_code |
WEIGHT parameter code The observations where Permitted Values: character value |
height_code |
HEIGHT parameter code The observations where Permitted Values: character value Permitted Values: logical scalar |
get_unit_expr |
An expression providing the unit of the parameter The result is used to check the units of the input parameters. Permitted Values: A variable of the input dataset or a function call |
filter |
Filter condition The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account. Permitted Values: a condition |
constant_by_vars |
By variables for when HEIGHT is constant When HEIGHT is constant, the HEIGHT parameters (measured only once) are merged to the other parameters using the specified variables. If height is constant (e.g. only measured once at screening or baseline) then
use Permitted Values: list of variables created by |
The analysis value of the new parameter is derived as
The input dataset with the new parameter added. Note, a variable will only
be populated in the new parameter rows if it is specified in by_vars
.
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
# Example 1: Derive BMI where height is measured only once using constant_by_vars advs <- tibble::tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVISIT, "01-701-1015", "HEIGHT", "Height (cm)", 147, "SCREENING", "01-701-1015", "WEIGHT", "Weight (kg)", 54.0, "SCREENING", "01-701-1015", "WEIGHT", "Weight (kg)", 54.4, "BASELINE", "01-701-1015", "WEIGHT", "Weight (kg)", 53.1, "WEEK 2", "01-701-1028", "HEIGHT", "Height (cm)", 163, "SCREENING", "01-701-1028", "WEIGHT", "Weight (kg)", 78.5, "SCREENING", "01-701-1028", "WEIGHT", "Weight (kg)", 80.3, "BASELINE", "01-701-1028", "WEIGHT", "Weight (kg)", 80.7, "WEEK 2" ) derive_param_bmi( advs, by_vars = exprs(USUBJID, AVISIT), weight_code = "WEIGHT", height_code = "HEIGHT", set_values_to = exprs( PARAMCD = "BMI", PARAM = "Body Mass Index (kg/m^2)" ), get_unit_expr = extract_unit(PARAM), constant_by_vars = exprs(USUBJID) ) # Example 2: Derive BMI where height is measured only once and keep only one record # where both height and weight are measured. derive_param_bmi( advs, by_vars = exprs(USUBJID, AVISIT), weight_code = "WEIGHT", height_code = "HEIGHT", set_values_to = exprs( PARAMCD = "BMI", PARAM = "Body Mass Index (kg/m^2)" ), get_unit_expr = extract_unit(PARAM) ) # Example 3: Pediatric study where height and weight are measured multiple times advs <- tibble::tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~VISIT, "01-101-1001", "HEIGHT", "Height (cm)", 47.1, "BASELINE", "01-101-1001", "HEIGHT", "Height (cm)", 59.1, "WEEK 12", "01-101-1001", "HEIGHT", "Height (cm)", 64.7, "WEEK 24", "01-101-1001", "HEIGHT", "Height (cm)", 68.2, "WEEK 48", "01-101-1001", "WEIGHT", "Weight (kg)", 2.6, "BASELINE", "01-101-1001", "WEIGHT", "Weight (kg)", 5.3, "WEEK 12", "01-101-1001", "WEIGHT", "Weight (kg)", 6.7, "WEEK 24", "01-101-1001", "WEIGHT", "Weight (kg)", 7.4, "WEEK 48", ) derive_param_bmi( advs, by_vars = exprs(USUBJID, VISIT), weight_code = "WEIGHT", height_code = "HEIGHT", set_values_to = exprs( PARAMCD = "BMI", PARAM = "Body Mass Index (kg/m^2)" ), get_unit_expr = extract_unit(PARAM) )
# Example 1: Derive BMI where height is measured only once using constant_by_vars advs <- tibble::tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVISIT, "01-701-1015", "HEIGHT", "Height (cm)", 147, "SCREENING", "01-701-1015", "WEIGHT", "Weight (kg)", 54.0, "SCREENING", "01-701-1015", "WEIGHT", "Weight (kg)", 54.4, "BASELINE", "01-701-1015", "WEIGHT", "Weight (kg)", 53.1, "WEEK 2", "01-701-1028", "HEIGHT", "Height (cm)", 163, "SCREENING", "01-701-1028", "WEIGHT", "Weight (kg)", 78.5, "SCREENING", "01-701-1028", "WEIGHT", "Weight (kg)", 80.3, "BASELINE", "01-701-1028", "WEIGHT", "Weight (kg)", 80.7, "WEEK 2" ) derive_param_bmi( advs, by_vars = exprs(USUBJID, AVISIT), weight_code = "WEIGHT", height_code = "HEIGHT", set_values_to = exprs( PARAMCD = "BMI", PARAM = "Body Mass Index (kg/m^2)" ), get_unit_expr = extract_unit(PARAM), constant_by_vars = exprs(USUBJID) ) # Example 2: Derive BMI where height is measured only once and keep only one record # where both height and weight are measured. derive_param_bmi( advs, by_vars = exprs(USUBJID, AVISIT), weight_code = "WEIGHT", height_code = "HEIGHT", set_values_to = exprs( PARAMCD = "BMI", PARAM = "Body Mass Index (kg/m^2)" ), get_unit_expr = extract_unit(PARAM) ) # Example 3: Pediatric study where height and weight are measured multiple times advs <- tibble::tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~VISIT, "01-101-1001", "HEIGHT", "Height (cm)", 47.1, "BASELINE", "01-101-1001", "HEIGHT", "Height (cm)", 59.1, "WEEK 12", "01-101-1001", "HEIGHT", "Height (cm)", 64.7, "WEEK 24", "01-101-1001", "HEIGHT", "Height (cm)", 68.2, "WEEK 48", "01-101-1001", "WEIGHT", "Weight (kg)", 2.6, "BASELINE", "01-101-1001", "WEIGHT", "Weight (kg)", 5.3, "WEEK 12", "01-101-1001", "WEIGHT", "Weight (kg)", 6.7, "WEEK 24", "01-101-1001", "WEIGHT", "Weight (kg)", 7.4, "WEEK 48", ) derive_param_bmi( advs, by_vars = exprs(USUBJID, VISIT), weight_code = "WEIGHT", height_code = "HEIGHT", set_values_to = exprs( PARAMCD = "BMI", PARAM = "Body Mass Index (kg/m^2)" ), get_unit_expr = extract_unit(PARAM) )
Adds a record for BSA (Body Surface Area) using the specified derivation method for each by group (e.g., subject and visit) where the source parameters are available.
Note: This is a wrapper function for the more generic derive_param_computed()
.
derive_param_bsa( dataset, by_vars, method, set_values_to = exprs(PARAMCD = "BSA"), height_code = "HEIGHT", weight_code = "WEIGHT", get_unit_expr, filter = NULL, constant_by_vars = NULL )
derive_param_bsa( dataset, by_vars, method, set_values_to = exprs(PARAMCD = "BSA"), height_code = "HEIGHT", weight_code = "WEIGHT", get_unit_expr, filter = NULL, constant_by_vars = NULL )
dataset |
Input dataset The variables specified by the The variable specified by |
by_vars |
Grouping variables For each group defined by Permitted Values: list of variables created by |
method |
Derivation method to use. Note that Mosteller: DuBois-DuBois: Haycock: Gehan-George: Boyd: Fujimoto: Takahira: Permitted Values: character value |
set_values_to |
Variables to be set The specified variables are set to the specified values for the new
observations. For example Permitted Values: List of variable-value pairs |
height_code |
HEIGHT parameter code The observations where Permitted Values: character value |
weight_code |
WEIGHT parameter code The observations where Permitted Values: character value |
get_unit_expr |
An expression providing the unit of the parameter The result is used to check the units of the input parameters. Permitted Values: A variable of the input dataset or a function call |
filter |
Filter condition The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account. Permitted Values: a condition |
constant_by_vars |
By variables for when HEIGHT is constant When HEIGHT is constant, the HEIGHT parameters (measured only once) are merged to the other parameters using the specified variables. If height is constant (e.g. only measured once at screening or baseline) then
use Permitted Values: list of variables created by |
The input dataset with the new parameter added. Note, a variable will only
be populated in the new parameter rows if it is specified in by_vars
.
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(tibble) # Example 1: Derive BSA where height is measured only once using constant_by_vars advs <- tibble::tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~VISIT, "01-701-1015", "HEIGHT", "Height (cm)", 170, "BASELINE", "01-701-1015", "WEIGHT", "Weight (kg)", 75, "BASELINE", "01-701-1015", "WEIGHT", "Weight (kg)", 78, "MONTH 1", "01-701-1015", "WEIGHT", "Weight (kg)", 80, "MONTH 2", "01-701-1028", "HEIGHT", "Height (cm)", 185, "BASELINE", "01-701-1028", "WEIGHT", "Weight (kg)", 90, "BASELINE", "01-701-1028", "WEIGHT", "Weight (kg)", 88, "MONTH 1", "01-701-1028", "WEIGHT", "Weight (kg)", 85, "MONTH 2", ) derive_param_bsa( advs, by_vars = exprs(USUBJID, VISIT), method = "Mosteller", set_values_to = exprs( PARAMCD = "BSA", PARAM = "Body Surface Area (m^2)" ), get_unit_expr = extract_unit(PARAM), constant_by_vars = exprs(USUBJID) ) derive_param_bsa( advs, by_vars = exprs(USUBJID, VISIT), method = "Fujimoto", set_values_to = exprs( PARAMCD = "BSA", PARAM = "Body Surface Area (m^2)" ), get_unit_expr = extract_unit(PARAM), constant_by_vars = exprs(USUBJID) ) # Example 2: Derive BSA where height is measured only once and keep only one record # where both height and weight are measured. derive_param_bsa( advs, by_vars = exprs(USUBJID, VISIT), method = "Mosteller", set_values_to = exprs( PARAMCD = "BSA", PARAM = "Body Surface Area (m^2)" ), get_unit_expr = extract_unit(PARAM) ) # Example 3: Pediatric study where height and weight are measured multiple times advs <- tibble::tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~VISIT, "01-101-1001", "HEIGHT", "Height (cm)", 47.1, "BASELINE", "01-101-1001", "HEIGHT", "Height (cm)", 59.1, "WEEK 12", "01-101-1001", "HEIGHT", "Height (cm)", 64.7, "WEEK 24", "01-101-1001", "HEIGHT", "Height (cm)", 68.2, "WEEK 48", "01-101-1001", "WEIGHT", "Weight (kg)", 2.6, "BASELINE", "01-101-1001", "WEIGHT", "Weight (kg)", 5.3, "WEEK 12", "01-101-1001", "WEIGHT", "Weight (kg)", 6.7, "WEEK 24", "01-101-1001", "WEIGHT", "Weight (kg)", 7.4, "WEEK 48", ) derive_param_bsa( advs, by_vars = exprs(USUBJID, VISIT), method = "Mosteller", set_values_to = exprs( PARAMCD = "BSA", PARAM = "Body Surface Area (m^2)" ), get_unit_expr = extract_unit(PARAM) )
library(tibble) # Example 1: Derive BSA where height is measured only once using constant_by_vars advs <- tibble::tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~VISIT, "01-701-1015", "HEIGHT", "Height (cm)", 170, "BASELINE", "01-701-1015", "WEIGHT", "Weight (kg)", 75, "BASELINE", "01-701-1015", "WEIGHT", "Weight (kg)", 78, "MONTH 1", "01-701-1015", "WEIGHT", "Weight (kg)", 80, "MONTH 2", "01-701-1028", "HEIGHT", "Height (cm)", 185, "BASELINE", "01-701-1028", "WEIGHT", "Weight (kg)", 90, "BASELINE", "01-701-1028", "WEIGHT", "Weight (kg)", 88, "MONTH 1", "01-701-1028", "WEIGHT", "Weight (kg)", 85, "MONTH 2", ) derive_param_bsa( advs, by_vars = exprs(USUBJID, VISIT), method = "Mosteller", set_values_to = exprs( PARAMCD = "BSA", PARAM = "Body Surface Area (m^2)" ), get_unit_expr = extract_unit(PARAM), constant_by_vars = exprs(USUBJID) ) derive_param_bsa( advs, by_vars = exprs(USUBJID, VISIT), method = "Fujimoto", set_values_to = exprs( PARAMCD = "BSA", PARAM = "Body Surface Area (m^2)" ), get_unit_expr = extract_unit(PARAM), constant_by_vars = exprs(USUBJID) ) # Example 2: Derive BSA where height is measured only once and keep only one record # where both height and weight are measured. derive_param_bsa( advs, by_vars = exprs(USUBJID, VISIT), method = "Mosteller", set_values_to = exprs( PARAMCD = "BSA", PARAM = "Body Surface Area (m^2)" ), get_unit_expr = extract_unit(PARAM) ) # Example 3: Pediatric study where height and weight are measured multiple times advs <- tibble::tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~VISIT, "01-101-1001", "HEIGHT", "Height (cm)", 47.1, "BASELINE", "01-101-1001", "HEIGHT", "Height (cm)", 59.1, "WEEK 12", "01-101-1001", "HEIGHT", "Height (cm)", 64.7, "WEEK 24", "01-101-1001", "HEIGHT", "Height (cm)", 68.2, "WEEK 48", "01-101-1001", "WEIGHT", "Weight (kg)", 2.6, "BASELINE", "01-101-1001", "WEIGHT", "Weight (kg)", 5.3, "WEEK 12", "01-101-1001", "WEIGHT", "Weight (kg)", 6.7, "WEEK 24", "01-101-1001", "WEIGHT", "Weight (kg)", 7.4, "WEEK 48", ) derive_param_bsa( advs, by_vars = exprs(USUBJID, VISIT), method = "Mosteller", set_values_to = exprs( PARAMCD = "BSA", PARAM = "Body Surface Area (m^2)" ), get_unit_expr = extract_unit(PARAM) )
Adds a parameter computed from the analysis value of other parameters. It is expected that the analysis value of the new parameter is defined by an expression using the analysis values of other parameters. For example mean arterial pressure (MAP) can be derived from systolic (SYSBP) and diastolic blood pressure (DIABP) with the formula
derive_param_computed( dataset = NULL, dataset_add = NULL, by_vars, parameters, set_values_to, filter = NULL, constant_by_vars = NULL, constant_parameters = NULL, keep_nas = FALSE )
derive_param_computed( dataset = NULL, dataset_add = NULL, by_vars, parameters, set_values_to, filter = NULL, constant_by_vars = NULL, constant_parameters = NULL, keep_nas = FALSE )
dataset |
Input dataset The variables specified by the The variable specified by |
dataset_add |
Additional dataset The variables specified by the The variable specified by If the argument is specified, the observations of the additional dataset
are considered in addition to the observations from the input dataset
( |
by_vars |
Grouping variables For each group defined by Permitted Values: list of variables created by |
parameters |
Required parameter codes It is expected that all parameter codes ( If observations should be considered which do not have a parameter code,
e.g., if an SDTM dataset is used, temporary parameter codes can be derived
by specifying a list of expressions. The name of the element defines the
temporary parameter code and the expression the condition for selecting the
records. For example Unnamed elements in the list of expressions are considered as parameter
codes. For example, Permitted Values: A character vector of |
set_values_to |
Variables to be set The specified variables are set to the specified values for the new
observations. The values of variables of the parameters specified by
exprs( AVAL = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3, PARAMCD = "MAP" ) defines the analysis value and parameter code for the new parameter. Variable names in the expression must not contain more than one dot. Permitted Values: List of variable-value pairs |
filter |
Filter condition The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account. Permitted Values: a condition |
constant_by_vars |
By variables for constant parameters The constant parameters (parameters that are measured only once) are merged to the other parameters using the specified variables. (Refer to Example 2) Permitted Values: list of variables created by |
constant_parameters |
Required constant parameter codes It is expected that all the parameter codes ( If observations should be considered which do not have a parameter code,
e.g., if an SDTM dataset is used, temporary parameter codes can be derived
by specifying a list of expressions. The name of the element defines the
temporary parameter code and the expression the condition for selecting the
records. For example Unnamed elements in the list of expressions are considered as parameter
codes. For example, Permitted Values: A character vector of |
keep_nas |
Keep observations with If the argument is set to |
For each group (with respect to the variables specified for the
by_vars
parameter) an observation is added to the output dataset if the
filtered input dataset (dataset
) or the additional dataset
(dataset_add
) contains exactly one observation for each parameter code
specified for parameters
.
For the new observations the variables specified for set_values_to
are
set to the provided values. The values of the other variables of the input
dataset are set to NA
.
The input dataset with the new parameter added. Note, a variable will only
be populated in the new parameter rows if it is specified in by_vars
.
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(tibble) library(dplyr) library(lubridate) # Example 1a: Derive MAP advs <- tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT, "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 51, "mmHg", "BASELINE", "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 50, "mmHg", "WEEK 2", "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "mmHg", "BASELINE", "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "mmHg", "WEEK 2", "01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 79, "mmHg", "BASELINE", "01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 80, "mmHg", "WEEK 2", "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 130, "mmHg", "BASELINE", "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 132, "mmHg", "WEEK 2" ) %>% mutate( ADT = case_when( VISIT == "BASELINE" ~ as.Date("2024-01-10"), VISIT == "WEEK 2" ~ as.Date("2024-01-24") ), ADTF = NA_character_ ) derive_param_computed( advs, by_vars = exprs(USUBJID, VISIT), parameters = c("SYSBP", "DIABP"), set_values_to = exprs( AVAL = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3, PARAMCD = "MAP", PARAM = "Mean Arterial Pressure (mmHg)", AVALU = "mmHg", ADT = ADT.SYSBP ) ) # Example 1b: Using option `keep_nas = TRUE` to derive MAP in the case where some/all values # of a variable used in the computation are missing derive_param_computed( advs, by_vars = exprs(USUBJID, VISIT), parameters = c("SYSBP", "DIABP"), set_values_to = exprs( AVAL = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3, PARAMCD = "MAP", PARAM = "Mean Arterial Pressure (mmHg)", AVALU = "mmHg", ADT = ADT.SYSBP, ADTF = ADTF.SYSBP ), keep_nas = TRUE ) # Example 2: Derive BMI where height is measured only once advs <- tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT, "01-701-1015", "HEIGHT", "Height (cm)", 147.0, "cm", "SCREENING", "01-701-1015", "WEIGHT", "Weight (kg)", 54.0, "kg", "SCREENING", "01-701-1015", "WEIGHT", "Weight (kg)", 54.4, "kg", "BASELINE", "01-701-1015", "WEIGHT", "Weight (kg)", 53.1, "kg", "WEEK 2", "01-701-1028", "HEIGHT", "Height (cm)", 163.0, "cm", "SCREENING", "01-701-1028", "WEIGHT", "Weight (kg)", 78.5, "kg", "SCREENING", "01-701-1028", "WEIGHT", "Weight (kg)", 80.3, "kg", "BASELINE", "01-701-1028", "WEIGHT", "Weight (kg)", 80.7, "kg", "WEEK 2" ) derive_param_computed( advs, by_vars = exprs(USUBJID, VISIT), parameters = "WEIGHT", set_values_to = exprs( AVAL = AVAL.WEIGHT / (AVAL.HEIGHT / 100)^2, PARAMCD = "BMI", PARAM = "Body Mass Index (kg/m^2)", AVALU = "kg/m^2" ), constant_parameters = c("HEIGHT"), constant_by_vars = exprs(USUBJID) ) # Example 3: Using data from an additional dataset and other variables than AVAL qs <- tribble( ~USUBJID, ~AVISIT, ~QSTESTCD, ~QSORRES, ~QSSTRESN, "1", "WEEK 2", "CHSF112", NA, 1, "1", "WEEK 2", "CHSF113", "Yes", NA, "1", "WEEK 2", "CHSF114", NA, 1, "1", "WEEK 4", "CHSF112", NA, 2, "1", "WEEK 4", "CHSF113", "No", NA, "1", "WEEK 4", "CHSF114", NA, 1 ) adchsf <- tribble( ~USUBJID, ~AVISIT, ~PARAMCD, ~QSSTRESN, ~AVAL, "1", "WEEK 2", "CHSF12", 1, 6, "1", "WEEK 2", "CHSF14", 1, 6, "1", "WEEK 4", "CHSF12", 2, 12, "1", "WEEK 4", "CHSF14", 1, 6 ) %>% mutate(QSORRES = NA_character_) derive_param_computed( adchsf, dataset_add = qs, by_vars = exprs(USUBJID, AVISIT), parameters = exprs(CHSF12, CHSF13 = QSTESTCD %in% c("CHSF113", "CHSF213"), CHSF14), set_values_to = exprs( AVAL = case_when( QSORRES.CHSF13 == "Not applicable" ~ 0, QSORRES.CHSF13 == "Yes" ~ 38, QSORRES.CHSF13 == "No" ~ if_else( QSSTRESN.CHSF12 > QSSTRESN.CHSF14, 25, 0 ) ), PARAMCD = "CHSF13" ) ) # Example 4: Computing more than one variable adlb_tbilialk <- tribble( ~USUBJID, ~PARAMCD, ~AVALC, ~ADTM, ~ADTF, "1", "ALK2", "Y", "2021-05-13", NA_character_, "1", "TBILI2", "Y", "2021-06-30", "D", "2", "ALK2", "Y", "2021-12-31", "M", "2", "TBILI2", "N", "2021-11-11", NA_character_, "3", "ALK2", "N", "2021-04-03", NA_character_, "3", "TBILI2", "N", "2021-04-04", NA_character_ ) %>% mutate(ADTM = ymd(ADTM)) derive_param_computed( dataset_add = adlb_tbilialk, by_vars = exprs(USUBJID), parameters = c("ALK2", "TBILI2"), set_values_to = exprs( AVALC = if_else(AVALC.TBILI2 == "Y" & AVALC.ALK2 == "Y", "Y", "N"), ADTM = pmax(ADTM.TBILI2, ADTM.ALK2), ADTF = if_else(ADTM == ADTM.TBILI2, ADTF.TBILI2, ADTF.ALK2), PARAMCD = "TB2AK2", PARAM = "TBILI > 2 times ULN and ALKPH <= 2 times ULN" ), keep_nas = TRUE )
library(tibble) library(dplyr) library(lubridate) # Example 1a: Derive MAP advs <- tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT, "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 51, "mmHg", "BASELINE", "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 50, "mmHg", "WEEK 2", "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "mmHg", "BASELINE", "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "mmHg", "WEEK 2", "01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 79, "mmHg", "BASELINE", "01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 80, "mmHg", "WEEK 2", "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 130, "mmHg", "BASELINE", "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 132, "mmHg", "WEEK 2" ) %>% mutate( ADT = case_when( VISIT == "BASELINE" ~ as.Date("2024-01-10"), VISIT == "WEEK 2" ~ as.Date("2024-01-24") ), ADTF = NA_character_ ) derive_param_computed( advs, by_vars = exprs(USUBJID, VISIT), parameters = c("SYSBP", "DIABP"), set_values_to = exprs( AVAL = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3, PARAMCD = "MAP", PARAM = "Mean Arterial Pressure (mmHg)", AVALU = "mmHg", ADT = ADT.SYSBP ) ) # Example 1b: Using option `keep_nas = TRUE` to derive MAP in the case where some/all values # of a variable used in the computation are missing derive_param_computed( advs, by_vars = exprs(USUBJID, VISIT), parameters = c("SYSBP", "DIABP"), set_values_to = exprs( AVAL = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3, PARAMCD = "MAP", PARAM = "Mean Arterial Pressure (mmHg)", AVALU = "mmHg", ADT = ADT.SYSBP, ADTF = ADTF.SYSBP ), keep_nas = TRUE ) # Example 2: Derive BMI where height is measured only once advs <- tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT, "01-701-1015", "HEIGHT", "Height (cm)", 147.0, "cm", "SCREENING", "01-701-1015", "WEIGHT", "Weight (kg)", 54.0, "kg", "SCREENING", "01-701-1015", "WEIGHT", "Weight (kg)", 54.4, "kg", "BASELINE", "01-701-1015", "WEIGHT", "Weight (kg)", 53.1, "kg", "WEEK 2", "01-701-1028", "HEIGHT", "Height (cm)", 163.0, "cm", "SCREENING", "01-701-1028", "WEIGHT", "Weight (kg)", 78.5, "kg", "SCREENING", "01-701-1028", "WEIGHT", "Weight (kg)", 80.3, "kg", "BASELINE", "01-701-1028", "WEIGHT", "Weight (kg)", 80.7, "kg", "WEEK 2" ) derive_param_computed( advs, by_vars = exprs(USUBJID, VISIT), parameters = "WEIGHT", set_values_to = exprs( AVAL = AVAL.WEIGHT / (AVAL.HEIGHT / 100)^2, PARAMCD = "BMI", PARAM = "Body Mass Index (kg/m^2)", AVALU = "kg/m^2" ), constant_parameters = c("HEIGHT"), constant_by_vars = exprs(USUBJID) ) # Example 3: Using data from an additional dataset and other variables than AVAL qs <- tribble( ~USUBJID, ~AVISIT, ~QSTESTCD, ~QSORRES, ~QSSTRESN, "1", "WEEK 2", "CHSF112", NA, 1, "1", "WEEK 2", "CHSF113", "Yes", NA, "1", "WEEK 2", "CHSF114", NA, 1, "1", "WEEK 4", "CHSF112", NA, 2, "1", "WEEK 4", "CHSF113", "No", NA, "1", "WEEK 4", "CHSF114", NA, 1 ) adchsf <- tribble( ~USUBJID, ~AVISIT, ~PARAMCD, ~QSSTRESN, ~AVAL, "1", "WEEK 2", "CHSF12", 1, 6, "1", "WEEK 2", "CHSF14", 1, 6, "1", "WEEK 4", "CHSF12", 2, 12, "1", "WEEK 4", "CHSF14", 1, 6 ) %>% mutate(QSORRES = NA_character_) derive_param_computed( adchsf, dataset_add = qs, by_vars = exprs(USUBJID, AVISIT), parameters = exprs(CHSF12, CHSF13 = QSTESTCD %in% c("CHSF113", "CHSF213"), CHSF14), set_values_to = exprs( AVAL = case_when( QSORRES.CHSF13 == "Not applicable" ~ 0, QSORRES.CHSF13 == "Yes" ~ 38, QSORRES.CHSF13 == "No" ~ if_else( QSSTRESN.CHSF12 > QSSTRESN.CHSF14, 25, 0 ) ), PARAMCD = "CHSF13" ) ) # Example 4: Computing more than one variable adlb_tbilialk <- tribble( ~USUBJID, ~PARAMCD, ~AVALC, ~ADTM, ~ADTF, "1", "ALK2", "Y", "2021-05-13", NA_character_, "1", "TBILI2", "Y", "2021-06-30", "D", "2", "ALK2", "Y", "2021-12-31", "M", "2", "TBILI2", "N", "2021-11-11", NA_character_, "3", "ALK2", "N", "2021-04-03", NA_character_, "3", "TBILI2", "N", "2021-04-04", NA_character_ ) %>% mutate(ADTM = ymd(ADTM)) derive_param_computed( dataset_add = adlb_tbilialk, by_vars = exprs(USUBJID), parameters = c("ALK2", "TBILI2"), set_values_to = exprs( AVALC = if_else(AVALC.TBILI2 == "Y" & AVALC.ALK2 == "Y", "Y", "N"), ADTM = pmax(ADTM.TBILI2, ADTM.ALK2), ADTF = if_else(ADTM == ADTM.TBILI2, ADTF.TBILI2, ADTF.ALK2), PARAMCD = "TB2AK2", PARAM = "TBILI > 2 times ULN and ALKPH <= 2 times ULN" ), keep_nas = TRUE )
Adds a record for the dose intensity for each by group (e.g., subject and visit) where the source parameters are available.
Note: This is a wrapper function for the more generic derive_param_computed()
.
The analysis value of the new parameter is derived as Total Dose / Planned Dose * 100
derive_param_doseint( dataset, by_vars, set_values_to = exprs(PARAMCD = "TNDOSINT"), tadm_code = "TNDOSE", tpadm_code = "TSNDOSE", zero_doses = "Inf", filter = NULL )
derive_param_doseint( dataset, by_vars, set_values_to = exprs(PARAMCD = "TNDOSINT"), tadm_code = "TNDOSE", tpadm_code = "TSNDOSE", zero_doses = "Inf", filter = NULL )
dataset |
Input dataset The variables specified by the The variable specified by |
by_vars |
Grouping variables Only variables specified in Permitted Values: list of variables created by |
set_values_to |
Variables to be set The specified variables are set to the specified values for the new
observations. For example Permitted Values: List of variable-value pairs |
tadm_code |
Total Doses Administered parameter code The observations where Permitted Values: character value |
tpadm_code |
Total Doses Planned parameter code The observations where Permitted Values: character value |
zero_doses |
Flag indicating logic for handling 0 planned or
administered doses for a Default: Permitted Values: No record is returned if either the planned ( If
If
|
filter |
Filter condition The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account. Permitted Values: a condition |
The input dataset with the new parameter rows added. Note, a variable will only
be populated in the new parameter rows if it is specified in by_vars
.
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(tibble) library(lubridate, warn.conflicts = FALSE) adex <- tribble( ~USUBJID, ~PARAMCD, ~VISIT, ~ANL01FL, ~ASTDT, ~AENDT, ~AVAL, "P001", "TNDOSE", "V1", "Y", ymd("2020-01-01"), ymd("2020-01-30"), 59, "P001", "TSNDOSE", "V1", "Y", ymd("2020-01-01"), ymd("2020-02-01"), 96, "P001", "TNDOSE", "V2", "Y", ymd("2020-02-01"), ymd("2020-03-15"), 88, "P001", "TSNDOSE", "V2", "Y", ymd("2020-02-05"), ymd("2020-03-01"), 88, "P002", "TNDOSE", "V1", "Y", ymd("2021-01-01"), ymd("2021-01-30"), 0, "P002", "TSNDOSE", "V1", "Y", ymd("2021-01-01"), ymd("2021-02-01"), 0, "P002", "TNDOSE", "V2", "Y", ymd("2021-02-01"), ymd("2021-03-15"), 52, "P002", "TSNDOSE", "V2", "Y", ymd("2021-02-05"), ymd("2021-03-01"), 0 ) derive_param_doseint( adex, by_vars = exprs(USUBJID, VISIT), set_values_to = exprs(PARAMCD = "TNDOSINT"), tadm_code = "TNDOSE", tpadm_code = "TSNDOSE" ) derive_param_doseint( adex, by_vars = exprs(USUBJID, VISIT), set_values_to = exprs(PARAMCD = "TDOSINT2"), tadm_code = "TNDOSE", tpadm_code = "TSNDOSE", zero_doses = "100" )
library(tibble) library(lubridate, warn.conflicts = FALSE) adex <- tribble( ~USUBJID, ~PARAMCD, ~VISIT, ~ANL01FL, ~ASTDT, ~AENDT, ~AVAL, "P001", "TNDOSE", "V1", "Y", ymd("2020-01-01"), ymd("2020-01-30"), 59, "P001", "TSNDOSE", "V1", "Y", ymd("2020-01-01"), ymd("2020-02-01"), 96, "P001", "TNDOSE", "V2", "Y", ymd("2020-02-01"), ymd("2020-03-15"), 88, "P001", "TSNDOSE", "V2", "Y", ymd("2020-02-05"), ymd("2020-03-01"), 88, "P002", "TNDOSE", "V1", "Y", ymd("2021-01-01"), ymd("2021-01-30"), 0, "P002", "TSNDOSE", "V1", "Y", ymd("2021-01-01"), ymd("2021-02-01"), 0, "P002", "TNDOSE", "V2", "Y", ymd("2021-02-01"), ymd("2021-03-15"), 52, "P002", "TSNDOSE", "V2", "Y", ymd("2021-02-05"), ymd("2021-03-01"), 0 ) derive_param_doseint( adex, by_vars = exprs(USUBJID, VISIT), set_values_to = exprs(PARAMCD = "TNDOSINT"), tadm_code = "TNDOSE", tpadm_code = "TSNDOSE" ) derive_param_doseint( adex, by_vars = exprs(USUBJID, VISIT), set_values_to = exprs(PARAMCD = "TDOSINT2"), tadm_code = "TNDOSE", tpadm_code = "TSNDOSE", zero_doses = "100" )
Add a new parameter indicating that a certain event exists in a dataset.
AVALC
and AVAL
indicate if an event occurred or not. For example, the
function can derive a parameter indicating if there is measurable disease at
baseline.
derive_param_exist_flag( dataset = NULL, dataset_ref, dataset_add, condition, true_value = "Y", false_value = NA_character_, missing_value = NA_character_, filter_add = NULL, by_vars = get_admiral_option("subject_keys"), set_values_to )
derive_param_exist_flag( dataset = NULL, dataset_ref, dataset_add, condition, true_value = "Y", false_value = NA_character_, missing_value = NA_character_, filter_add = NULL, by_vars = get_admiral_option("subject_keys"), set_values_to )
dataset |
Input dataset The variables specified by the |
dataset_ref |
Reference dataset, e.g., ADSL The variables specified in |
dataset_add |
Additional dataset The variables specified by the This dataset is used to check if an event occurred or not. Any observation
in the dataset fulfilling the event condition ( |
condition |
Event condition The condition is evaluated at the additional dataset ( For all groups where it evaluates as For all groups where it evaluates as For all groups not present in the additional dataset |
true_value |
True value For all groups with at least one observations in the additional dataset
( Default: Permitted Value: A character scalar |
false_value |
False value For all groups with at least one observations in the additional dataset
( Default: Permitted Value: A character scalar |
missing_value |
Values used for missing information For all groups without an observation in the additional dataset
( Default: Permitted Value: A character scalar |
filter_add |
Filter for additional data Only observations fulfilling the specified condition are taken into account for flagging. If the parameter is not specified, all observations are considered. Permitted Values: a condition |
by_vars |
Grouping variables Permitted Values: list of variables created by |
set_values_to |
Variables to set A named list returned by |
The additional dataset (dataset_add
) is restricted to the observations
matching the filter_add
condition.
For each group in dataset_ref
a new observation is created.
The AVALC
variable is added and set to the true value (true_value
)
if for the group at least one observation exists in the (restricted)
additional dataset where the condition evaluates to TRUE
.
It is set to the false value (false_value
) if for the group at least
one observation exists and for all observations the condition evaluates
to FALSE
or NA
.
Otherwise, it is set to the missing value (missing_value
), i.e., for
those groups not in dataset_add
.
The variables specified by the set_values_to
parameter are added to
the new observations.
The new observations are added to input dataset.
The input dataset with a new parameter indicating if an event
occurred (AVALC
and the variables specified by by_vars
and set_value_to
are populated for the new parameter).
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) # Derive a new parameter for measurable disease at baseline adsl <- tribble( ~USUBJID, "1", "2", "3" ) %>% mutate(STUDYID = "XX1234") tu <- tribble( ~USUBJID, ~VISIT, ~TUSTRESC, "1", "SCREENING", "TARGET", "1", "WEEK 1", "TARGET", "1", "WEEK 5", "TARGET", "1", "WEEK 9", "NON-TARGET", "2", "SCREENING", "NON-TARGET", "2", "SCREENING", "NON-TARGET" ) %>% mutate( STUDYID = "XX1234", TUTESTCD = "TUMIDENT" ) derive_param_exist_flag( dataset_ref = adsl, dataset_add = tu, filter_add = TUTESTCD == "TUMIDENT" & VISIT == "SCREENING", condition = TUSTRESC == "TARGET", false_value = "N", missing_value = "N", set_values_to = exprs( AVAL = yn_to_numeric(AVALC), PARAMCD = "MDIS", PARAM = "Measurable Disease at Baseline" ) )
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) # Derive a new parameter for measurable disease at baseline adsl <- tribble( ~USUBJID, "1", "2", "3" ) %>% mutate(STUDYID = "XX1234") tu <- tribble( ~USUBJID, ~VISIT, ~TUSTRESC, "1", "SCREENING", "TARGET", "1", "WEEK 1", "TARGET", "1", "WEEK 5", "TARGET", "1", "WEEK 9", "NON-TARGET", "2", "SCREENING", "NON-TARGET", "2", "SCREENING", "NON-TARGET" ) %>% mutate( STUDYID = "XX1234", TUTESTCD = "TUMIDENT" ) derive_param_exist_flag( dataset_ref = adsl, dataset_add = tu, filter_add = TUTESTCD == "TUMIDENT" & VISIT == "SCREENING", condition = TUSTRESC == "TARGET", false_value = "N", missing_value = "N", set_values_to = exprs( AVAL = yn_to_numeric(AVALC), PARAMCD = "MDIS", PARAM = "Measurable Disease at Baseline" ) )
Add a record computed from the aggregated analysis value of another parameter and compute the
start (ASTDT(M)
)and end date (AENDT(M)
) as the minimum and maximum date by by_vars
.
derive_param_exposure( dataset = NULL, dataset_add, by_vars, input_code, filter_add = NULL, set_values_to = NULL )
derive_param_exposure( dataset = NULL, dataset_add, by_vars, input_code, filter_add = NULL, set_values_to = NULL )
dataset |
Input dataset The variables specified by the |
dataset_add |
Additional dataset The variables specified for |
by_vars |
Grouping variables For each group defined by Permitted Values: list of variables created by |
input_code |
Required parameter code The observations where Permitted Values: A character of |
filter_add |
Filter condition as logical expression to apply during
summary calculation. By default, filtering expressions are computed within
For example,
|
set_values_to |
Variable-value pairs Set a list of variables to some specified value for the new observation(s)
Permitted Values: List of variable-value pairs |
For each group (with respect to the variables specified for the by_vars
parameter),
an observation is added to the output dataset and the defined values are set to the defined
variables
The input dataset with a new record added for each group (with respect to the variables
specified for the by_vars
parameter). That is, a variable will only
be populated in this new record if it is specified in by_vars
.
For each new record,
the variable specified analysis_var
is computed as defined by summary_fun
,
the variable(s) specified on the LHS of set_values_to
are set to their paired value (RHS).
In addition, the start and end date are computed as the minimum/maximum dates by by_vars
.
If the input datasets contains
both AxxDTM
and AxxDT
then all ASTDTM
,AENDTM
, ASTDT
, AENDT
are computed
only AxxDTM
then ASTDTM
,AENDTM
are computed
only AxxDT
then ASTDT
,AENDT
are computed.
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate, warn.conflicts = FALSE) library(stringr, warn.conflicts = FALSE) adex <- tribble( ~USUBJID, ~PARAMCD, ~AVAL, ~AVALC, ~VISIT, ~ASTDT, ~AENDT, "1015", "DOSE", 80, NA_character_, "BASELINE", ymd("2014-01-02"), ymd("2014-01-16"), "1015", "DOSE", 85, NA_character_, "WEEK 2", ymd("2014-01-17"), ymd("2014-06-18"), "1015", "DOSE", 82, NA_character_, "WEEK 24", ymd("2014-06-19"), ymd("2014-07-02"), "1015", "ADJ", NA, NA_character_, "BASELINE", ymd("2014-01-02"), ymd("2014-01-16"), "1015", "ADJ", NA, NA_character_, "WEEK 2", ymd("2014-01-17"), ymd("2014-06-18"), "1015", "ADJ", NA, NA_character_, "WEEK 24", ymd("2014-06-19"), ymd("2014-07-02"), "1017", "DOSE", 80, NA_character_, "BASELINE", ymd("2014-01-05"), ymd("2014-01-19"), "1017", "DOSE", 50, NA_character_, "WEEK 2", ymd("2014-01-20"), ymd("2014-05-10"), "1017", "DOSE", 65, NA_character_, "WEEK 24", ymd("2014-05-10"), ymd("2014-07-02"), "1017", "ADJ", NA, NA_character_, "BASELINE", ymd("2014-01-05"), ymd("2014-01-19"), "1017", "ADJ", NA, "ADVERSE EVENT", "WEEK 2", ymd("2014-01-20"), ymd("2014-05-10"), "1017", "ADJ", NA, NA_character_, "WEEK 24", ymd("2014-05-10"), ymd("2014-07-02") ) %>% mutate(ASTDTM = ymd_hms(paste(ASTDT, "00:00:00")), AENDTM = ymd_hms(paste(AENDT, "00:00:00"))) # Cumulative dose adex %>% derive_param_exposure( dataset_add = adex, by_vars = exprs(USUBJID), set_values_to = exprs( PARAMCD = "TDOSE", PARCAT1 = "OVERALL", AVAL = sum(AVAL, na.rm = TRUE) ), input_code = "DOSE" ) %>% select(-ASTDTM, -AENDTM) # average dose in w2-24 adex %>% derive_param_exposure( dataset_add = adex, by_vars = exprs(USUBJID), filter_add = VISIT %in% c("WEEK 2", "WEEK 24"), set_values_to = exprs( PARAMCD = "AVDW224", PARCAT1 = "WEEK2-24", AVAL = mean(AVAL, na.rm = TRUE) ), input_code = "DOSE" ) %>% select(-ASTDTM, -AENDTM) # Any dose adjustment? adex %>% derive_param_exposure( dataset_add = adex, by_vars = exprs(USUBJID), set_values_to = exprs( PARAMCD = "TADJ", PARCAT1 = "OVERALL", AVALC = if_else(sum(!is.na(AVALC)) > 0, "Y", NA_character_) ), input_code = "ADJ" ) %>% select(-ASTDTM, -AENDTM)
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate, warn.conflicts = FALSE) library(stringr, warn.conflicts = FALSE) adex <- tribble( ~USUBJID, ~PARAMCD, ~AVAL, ~AVALC, ~VISIT, ~ASTDT, ~AENDT, "1015", "DOSE", 80, NA_character_, "BASELINE", ymd("2014-01-02"), ymd("2014-01-16"), "1015", "DOSE", 85, NA_character_, "WEEK 2", ymd("2014-01-17"), ymd("2014-06-18"), "1015", "DOSE", 82, NA_character_, "WEEK 24", ymd("2014-06-19"), ymd("2014-07-02"), "1015", "ADJ", NA, NA_character_, "BASELINE", ymd("2014-01-02"), ymd("2014-01-16"), "1015", "ADJ", NA, NA_character_, "WEEK 2", ymd("2014-01-17"), ymd("2014-06-18"), "1015", "ADJ", NA, NA_character_, "WEEK 24", ymd("2014-06-19"), ymd("2014-07-02"), "1017", "DOSE", 80, NA_character_, "BASELINE", ymd("2014-01-05"), ymd("2014-01-19"), "1017", "DOSE", 50, NA_character_, "WEEK 2", ymd("2014-01-20"), ymd("2014-05-10"), "1017", "DOSE", 65, NA_character_, "WEEK 24", ymd("2014-05-10"), ymd("2014-07-02"), "1017", "ADJ", NA, NA_character_, "BASELINE", ymd("2014-01-05"), ymd("2014-01-19"), "1017", "ADJ", NA, "ADVERSE EVENT", "WEEK 2", ymd("2014-01-20"), ymd("2014-05-10"), "1017", "ADJ", NA, NA_character_, "WEEK 24", ymd("2014-05-10"), ymd("2014-07-02") ) %>% mutate(ASTDTM = ymd_hms(paste(ASTDT, "00:00:00")), AENDTM = ymd_hms(paste(AENDT, "00:00:00"))) # Cumulative dose adex %>% derive_param_exposure( dataset_add = adex, by_vars = exprs(USUBJID), set_values_to = exprs( PARAMCD = "TDOSE", PARCAT1 = "OVERALL", AVAL = sum(AVAL, na.rm = TRUE) ), input_code = "DOSE" ) %>% select(-ASTDTM, -AENDTM) # average dose in w2-24 adex %>% derive_param_exposure( dataset_add = adex, by_vars = exprs(USUBJID), filter_add = VISIT %in% c("WEEK 2", "WEEK 24"), set_values_to = exprs( PARAMCD = "AVDW224", PARCAT1 = "WEEK2-24", AVAL = mean(AVAL, na.rm = TRUE) ), input_code = "DOSE" ) %>% select(-ASTDTM, -AENDTM) # Any dose adjustment? adex %>% derive_param_exposure( dataset_add = adex, by_vars = exprs(USUBJID), set_values_to = exprs( PARAMCD = "TADJ", PARCAT1 = "OVERALL", AVALC = if_else(sum(!is.na(AVALC)) > 0, "Y", NA_character_) ), input_code = "ADJ" ) %>% select(-ASTDTM, -AENDTM)
The derive_param_extreme_record()
function has been superseded in favor of derive_extreme_event()
.
Generates parameter based on the first or last observation from multiple source datasets, based on user-defined filter, order and by group criteria. All variables of the selected observation are kept.
derive_param_extreme_record( dataset = NULL, sources, source_datasets, by_vars = NULL, order, mode, set_values_to )
derive_param_extreme_record( dataset = NULL, sources, source_datasets, by_vars = NULL, order, mode, set_values_to )
dataset |
Input dataset |
sources |
Sources A list of |
source_datasets |
Source datasets A named list of datasets is expected. The |
by_vars |
Grouping variables If the argument is specified, for each by group the observations are selected separately. Permitted Values: list of variables created by |
order |
Sort order If the argument is set to a non-null value, for each by group the first or
last observation from the source datasets is selected with respect to
the specified order. Variables created via Please note that Permitted Values: list of expressions created by |
mode |
Selection mode (first or last) If Permitted Values: |
set_values_to |
Variables to be set The specified variables are set to the specified values for the new observations. A list of variable name-value pairs is expected.
|
The following steps are performed to create the output dataset:
For each source dataset the observations as specified by
the filter
element are selected.
Variables specified by new_vars
are created for each source dataset.
The first or last observation (with respect to the
order
variable) for each by group (specified by by_vars
) from multiple sources
is selected and added to the input dataset.
The input dataset with the first or last observation of each by group added as new observations.
Other superseded:
date_source()
,
derive_var_dthcaus()
,
derive_var_extreme_dt()
,
derive_var_extreme_dtm()
,
dthcaus_source()
,
get_summary_records()
aevent_samp <- tibble::tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~RSSTDTC, "1", "PD", "First Progressive Disease", "2022-04-01", "2", "PD", "First Progressive Disease", "2021-04-01", "3", "PD", "First Progressive Disease", "2023-04-01" ) cm <- tibble::tribble( ~STUDYID, ~USUBJID, ~CMDECOD, ~CMSTDTC, "1001", "1", "ACT", "2021-12-25" ) pr <- tibble::tribble( ~STUDYID, ~USUBJID, ~PRDECOD, ~PRSTDTC, "1001", "1", "ACS", "2021-12-27", "1001", "2", "ACS", "2020-12-25", "1001", "3", "ACS", "2022-12-25", ) derive_param_extreme_record( dataset = aevent_samp, sources = list( records_source( dataset_name = "cm", filter = CMDECOD == "ACT", new_vars = exprs( ADT = convert_dtc_to_dt(CMSTDTC), AVALC = CMDECOD ) ), records_source( dataset_name = "pr", filter = PRDECOD == "ACS", new_vars = exprs( ADT = convert_dtc_to_dt(PRSTDTC), AVALC = PRDECOD ) ) ), source_datasets = list(cm = cm, pr = pr), by_vars = exprs(USUBJID), order = exprs(ADT), mode = "first", set_values_to = exprs( PARAMCD = "FIRSTACT", PARAM = "First Anti-Cancer Therapy" ) )
aevent_samp <- tibble::tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~RSSTDTC, "1", "PD", "First Progressive Disease", "2022-04-01", "2", "PD", "First Progressive Disease", "2021-04-01", "3", "PD", "First Progressive Disease", "2023-04-01" ) cm <- tibble::tribble( ~STUDYID, ~USUBJID, ~CMDECOD, ~CMSTDTC, "1001", "1", "ACT", "2021-12-25" ) pr <- tibble::tribble( ~STUDYID, ~USUBJID, ~PRDECOD, ~PRSTDTC, "1001", "1", "ACS", "2021-12-27", "1001", "2", "ACS", "2020-12-25", "1001", "3", "ACS", "2022-12-25", ) derive_param_extreme_record( dataset = aevent_samp, sources = list( records_source( dataset_name = "cm", filter = CMDECOD == "ACT", new_vars = exprs( ADT = convert_dtc_to_dt(CMSTDTC), AVALC = CMDECOD ) ), records_source( dataset_name = "pr", filter = PRDECOD == "ACS", new_vars = exprs( ADT = convert_dtc_to_dt(PRSTDTC), AVALC = PRDECOD ) ) ), source_datasets = list(cm = cm, pr = pr), by_vars = exprs(USUBJID), order = exprs(ADT), mode = "first", set_values_to = exprs( PARAMCD = "FIRSTACT", PARAM = "First Anti-Cancer Therapy" ) )
Adds a record for framingham score (FCVD101) for each by group (e.g., subject and visit) where the source parameters are available.
derive_param_framingham( dataset, by_vars, set_values_to = exprs(PARAMCD = "FCVD101"), sysbp_code = "SYSBP", chol_code = "CHOL", cholhdl_code = "CHOLHDL", age = AGE, sex = SEX, smokefl = SMOKEFL, diabetfl = DIABETFL, trthypfl = TRTHYPFL, get_unit_expr, filter = NULL )
derive_param_framingham( dataset, by_vars, set_values_to = exprs(PARAMCD = "FCVD101"), sysbp_code = "SYSBP", chol_code = "CHOL", cholhdl_code = "CHOLHDL", age = AGE, sex = SEX, smokefl = SMOKEFL, diabetfl = DIABETFL, trthypfl = TRTHYPFL, get_unit_expr, filter = NULL )
dataset |
Input dataset The variables specified by the The variable specified by |
by_vars |
Grouping variables Only variables specified in Permitted Values: list of variables created by |
set_values_to |
Variables to be set The specified variables are set to the specified values for the new
observations. For example Permitted Values: List of variable-value pairs |
sysbp_code |
Systolic blood pressure parameter code The observations where Permitted Values: character value |
chol_code |
Total serum cholesterol code The observations where Permitted Values: character value |
cholhdl_code |
HDL serum cholesterol code The observations where Permitted Values: character value |
age |
Subject age A variable containing the subject's age. Permitted Values: A numeric variable name that refers to a subject age column of the input dataset |
sex |
Subject sex A variable containing the subject's sex. Permitted Values: A character variable name that refers to a subject sex column of the input dataset |
smokefl |
Smoking status flag A flag indicating smoking status. Permitted Values: A character variable name that refers to a smoking status column of the input dataset. |
diabetfl |
Diabetic flag A flag indicating diabetic status. Permitted Values: A character variable name that refers to a diabetic status column of the input dataset |
trthypfl |
Treated with hypertension medication flag A flag indicating if a subject was treated with hypertension medication. Permitted Values: A character variable name that refers to a column that indicates whether a subject is treated for high blood pressure |
get_unit_expr |
An expression providing the unit of the parameter The result is used to check the units of the input parameters. Permitted Values: A variable of the input dataset or a function call |
filter |
Filter condition The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account. Permitted Values: a condition |
The values of age
, sex
, smokefl
, diabetfl
and trthypfl
will be
added to the by_vars
list.
The predicted probability of having cardiovascular disease (CVD)
within 10-years according to Framingham formula. See AHA Journal article
General Cardiovascular Risk Profile for Use in Primary Care for reference.
For Women:
Factor | Amount |
Age | 2.32888 |
Total Chol | 1.20904 |
HDL Chol | -0.70833 |
Sys BP | 2.76157 |
Sys BP + Hypertension Meds | 2.82263 |
Smoker | 0.52873 |
Non-Smoker | 0 |
Diabetic | 0.69154 |
Not Diabetic | 0 |
Average Risk | 26.1931 |
Risk Period | 0.95012 |
For Men:
Factor | Amount |
Age | 3.06117 |
Total Chol | 1.12370 |
HDL Chol | -0.93263 |
Sys BP | 1.93303 |
Sys BP + Hypertension Meds | 2.99881 |
Smoker | .65451 |
Non-Smoker | 0 |
Diabetic | 0.57367 |
Not Diabetic | 0 |
Average Risk | 23.9802 |
Risk Period | 0.88936 |
The equation for calculating risk:
The input dataset with the new parameter added
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(tibble) adcvrisk <- tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT, ~AGE, ~SEX, ~SMOKEFL, ~DIABETFL, ~TRTHYPFL, "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "mmHg", "BASELINE", 44, "F", "N", "N", "N", "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 115, "mmHg", "WEEK 2", 44, "F", "N", "N", "Y", "01-701-1015", "CHOL", "Total Cholesterol (mg/dL)", 216.16, "mg/dL", "BASELINE", 44, "F", "N", "N", "N", "01-701-1015", "CHOL", "Total Cholesterol (mg/dL)", 210.78, "mg/dL", "WEEK 2", 44, "F", "N", "N", "Y", "01-701-1015", "CHOLHDL", "Cholesterol/HDL-Cholesterol (mg/dL)", 54.91, "mg/dL", "BASELINE", 44, "F", "N", "N", "N", "01-701-1015", "CHOLHDL", "Cholesterol/HDL-Cholesterol (mg/dL)", 26.72, "mg/dL", "WEEK 2", 44, "F", "N", "N", "Y", "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 119, "mmHg", "BASELINE", 55, "M", "Y", "Y", "Y", "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 101, "mmHg", "WEEK 2", 55, "M", "Y", "Y", "Y", "01-701-1028", "CHOL", "Total Cholesterol (mg/dL)", 292.01, "mg/dL", "BASELINE", 55, "M", "Y", "Y", "Y", "01-701-1028", "CHOL", "Total Cholesterol (mg/dL)", 246.73, "mg/dL", "WEEK 2", 55, "M", "Y", "Y", "Y", "01-701-1028", "CHOLHDL", "Cholesterol/HDL-Cholesterol (mg/dL)", 65.55, "mg/dL", "BASELINE", 55, "M", "Y", "Y", "Y", "01-701-1028", "CHOLHDL", "Cholesterol/HDL-Cholesterol (mg/dL)", 44.62, "mg/dL", "WEEK 2", 55, "M", "Y", "Y", "Y" ) adcvrisk %>% derive_param_framingham( by_vars = exprs(USUBJID, VISIT), set_values_to = exprs( PARAMCD = "FCVD101", PARAM = "FCVD1-Framingham CVD 10-Year Risk Score (%)" ), get_unit_expr = AVALU ) derive_param_framingham( adcvrisk, by_vars = exprs(USUBJID, VISIT), set_values_to = exprs( PARAMCD = "FCVD101", PARAM = "FCVD1-Framingham CVD 10-Year Risk Score (%)" ), get_unit_expr = extract_unit(PARAM) )
library(tibble) adcvrisk <- tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT, ~AGE, ~SEX, ~SMOKEFL, ~DIABETFL, ~TRTHYPFL, "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "mmHg", "BASELINE", 44, "F", "N", "N", "N", "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 115, "mmHg", "WEEK 2", 44, "F", "N", "N", "Y", "01-701-1015", "CHOL", "Total Cholesterol (mg/dL)", 216.16, "mg/dL", "BASELINE", 44, "F", "N", "N", "N", "01-701-1015", "CHOL", "Total Cholesterol (mg/dL)", 210.78, "mg/dL", "WEEK 2", 44, "F", "N", "N", "Y", "01-701-1015", "CHOLHDL", "Cholesterol/HDL-Cholesterol (mg/dL)", 54.91, "mg/dL", "BASELINE", 44, "F", "N", "N", "N", "01-701-1015", "CHOLHDL", "Cholesterol/HDL-Cholesterol (mg/dL)", 26.72, "mg/dL", "WEEK 2", 44, "F", "N", "N", "Y", "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 119, "mmHg", "BASELINE", 55, "M", "Y", "Y", "Y", "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 101, "mmHg", "WEEK 2", 55, "M", "Y", "Y", "Y", "01-701-1028", "CHOL", "Total Cholesterol (mg/dL)", 292.01, "mg/dL", "BASELINE", 55, "M", "Y", "Y", "Y", "01-701-1028", "CHOL", "Total Cholesterol (mg/dL)", 246.73, "mg/dL", "WEEK 2", 55, "M", "Y", "Y", "Y", "01-701-1028", "CHOLHDL", "Cholesterol/HDL-Cholesterol (mg/dL)", 65.55, "mg/dL", "BASELINE", 55, "M", "Y", "Y", "Y", "01-701-1028", "CHOLHDL", "Cholesterol/HDL-Cholesterol (mg/dL)", 44.62, "mg/dL", "WEEK 2", 55, "M", "Y", "Y", "Y" ) adcvrisk %>% derive_param_framingham( by_vars = exprs(USUBJID, VISIT), set_values_to = exprs( PARAMCD = "FCVD101", PARAM = "FCVD1-Framingham CVD 10-Year Risk Score (%)" ), get_unit_expr = AVALU ) derive_param_framingham( adcvrisk, by_vars = exprs(USUBJID, VISIT), set_values_to = exprs( PARAMCD = "FCVD101", PARAM = "FCVD1-Framingham CVD 10-Year Risk Score (%)" ), get_unit_expr = extract_unit(PARAM) )
Adds a record for mean arterial pressure (MAP) for each by group (e.g., subject and visit) where the source parameters are available.
Note: This is a wrapper function for the more generic derive_param_computed()
.
derive_param_map( dataset, by_vars, set_values_to = exprs(PARAMCD = "MAP"), sysbp_code = "SYSBP", diabp_code = "DIABP", hr_code = NULL, get_unit_expr, filter = NULL )
derive_param_map( dataset, by_vars, set_values_to = exprs(PARAMCD = "MAP"), sysbp_code = "SYSBP", diabp_code = "DIABP", hr_code = NULL, get_unit_expr, filter = NULL )
dataset |
Input dataset The variables specified by the The variable specified by |
by_vars |
Grouping variables For each group defined by Permitted Values: list of variables created by |
set_values_to |
Variables to be set The specified variables are set to the specified values for the new
observations. For example Permitted Values: List of variable-value pairs |
sysbp_code |
Systolic blood pressure parameter code The observations where Permitted Values: character value |
diabp_code |
Diastolic blood pressure parameter code The observations where Permitted Values: character value |
hr_code |
Heart rate parameter code The observations where Permitted Values: character value |
get_unit_expr |
An expression providing the unit of the parameter The result is used to check the units of the input parameters. Permitted Values: A variable of the input dataset or a function call |
filter |
Filter condition The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account. Permitted Values: a condition |
The analysis value of the new parameter is derived as
if it is based on diastolic and systolic blood pressure and
if it is based on diastolic, systolic blood pressure, and heart rate.
The input dataset with the new parameter added. Note, a variable will only
be populated in the new parameter rows if it is specified in by_vars
.
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(tibble) library(dplyr, warn.conflicts = FALSE) advs <- tibble::tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~VISIT, "01-701-1015", "PULSE", "Pulse (beats/min)", 59, "BASELINE", "01-701-1015", "PULSE", "Pulse (beats/min)", 61, "WEEK 2", "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 51, "BASELINE", "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 50, "WEEK 2", "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "BASELINE", "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "WEEK 2", "01-701-1028", "PULSE", "Pulse (beats/min)", 62, "BASELINE", "01-701-1028", "PULSE", "Pulse (beats/min)", 77, "WEEK 2", "01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 79, "BASELINE", "01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 80, "WEEK 2", "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 130, "BASELINE", "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 132, "WEEK 2" ) # Derive MAP based on diastolic and systolic blood pressure advs %>% derive_param_map( by_vars = exprs(USUBJID, VISIT), set_values_to = exprs( PARAMCD = "MAP", PARAM = "Mean Arterial Pressure (mmHg)" ), get_unit_expr = extract_unit(PARAM) ) %>% filter(PARAMCD != "PULSE") # Derive MAP based on diastolic and systolic blood pressure and heart rate derive_param_map( advs, by_vars = exprs(USUBJID, VISIT), hr_code = "PULSE", set_values_to = exprs( PARAMCD = "MAP", PARAM = "Mean Arterial Pressure (mmHg)" ), get_unit_expr = extract_unit(PARAM) )
library(tibble) library(dplyr, warn.conflicts = FALSE) advs <- tibble::tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~VISIT, "01-701-1015", "PULSE", "Pulse (beats/min)", 59, "BASELINE", "01-701-1015", "PULSE", "Pulse (beats/min)", 61, "WEEK 2", "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 51, "BASELINE", "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 50, "WEEK 2", "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "BASELINE", "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "WEEK 2", "01-701-1028", "PULSE", "Pulse (beats/min)", 62, "BASELINE", "01-701-1028", "PULSE", "Pulse (beats/min)", 77, "WEEK 2", "01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 79, "BASELINE", "01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 80, "WEEK 2", "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 130, "BASELINE", "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 132, "WEEK 2" ) # Derive MAP based on diastolic and systolic blood pressure advs %>% derive_param_map( by_vars = exprs(USUBJID, VISIT), set_values_to = exprs( PARAMCD = "MAP", PARAM = "Mean Arterial Pressure (mmHg)" ), get_unit_expr = extract_unit(PARAM) ) %>% filter(PARAMCD != "PULSE") # Derive MAP based on diastolic and systolic blood pressure and heart rate derive_param_map( advs, by_vars = exprs(USUBJID, VISIT), hr_code = "PULSE", set_values_to = exprs( PARAMCD = "MAP", PARAM = "Mean Arterial Pressure (mmHg)" ), get_unit_expr = extract_unit(PARAM) )
Adds a record for corrected QT using either Bazett's, Fridericia's or Sagie's formula for each by group (e.g., subject and visit) where the source parameters are available.
Note: This is a wrapper function for the more generic derive_param_computed()
.
derive_param_qtc( dataset, by_vars, method, set_values_to = default_qtc_paramcd(method), qt_code = "QT", rr_code = "RR", get_unit_expr, filter = NULL )
derive_param_qtc( dataset, by_vars, method, set_values_to = default_qtc_paramcd(method), qt_code = "QT", rr_code = "RR", get_unit_expr, filter = NULL )
dataset |
Input dataset The variables specified by the The variable specified by |
by_vars |
Grouping variables Only variables specified in Permitted Values: list of variables created by |
method |
Method used to QT correction Permitted Values: |
set_values_to |
Variables to be set The specified variables are set to the specified values for the new
observations. For example Permitted Values: List of variable-value pairs |
qt_code |
QT parameter code The observations where Permitted Values: character value |
rr_code |
RR parameter code The observations where Permitted Values: character value |
get_unit_expr |
An expression providing the unit of the parameter The result is used to check the units of the input parameters. Permitted Values: A variable of the input dataset or a function call |
filter |
Filter condition The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account. Permitted Values: a condition |
The input dataset with the new parameter added. Note, a variable will only
be populated in the new parameter rows if it is specified in by_vars
.
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_rr()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(tibble) adeg <- tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT, "01-701-1015", "HR", "Heart Rate (beats/min)", 70.14, "beats/min", "BASELINE", "01-701-1015", "QT", "QT Duration (msec)", 370, "msec", "WEEK 2", "01-701-1015", "HR", "Heart Rate (beats/min)", 62.66, "beats/min", "WEEK 1", "01-701-1015", "RR", "RR Duration (msec)", 710, "msec", "WEEK 2", "01-701-1028", "HR", "Heart Rate (beats/min)", 85.45, "beats/min", "BASELINE", "01-701-1028", "QT", "QT Duration (msec)", 480, "msec", "WEEK 2", "01-701-1028", "QT", "QT Duration (msec)", 350, "msec", "WEEK 3", "01-701-1028", "HR", "Heart Rate (beats/min)", 56.54, "beats/min", "WEEK 3", "01-701-1028", "RR", "RR Duration (msec)", 842, "msec", "WEEK 2", ) derive_param_qtc( adeg, by_vars = exprs(USUBJID, VISIT), method = "Bazett", set_values_to = exprs( PARAMCD = "QTCBR", PARAM = "QTcB - Bazett's Correction Formula Rederived (msec)", AVALU = "msec" ), get_unit_expr = AVALU ) derive_param_qtc( adeg, by_vars = exprs(USUBJID, VISIT), method = "Fridericia", set_values_to = exprs( PARAMCD = "QTCFR", PARAM = "QTcF - Fridericia's Correction Formula Rederived (msec)", AVALU = "msec" ), get_unit_expr = extract_unit(PARAM) ) derive_param_qtc( adeg, by_vars = exprs(USUBJID, VISIT), method = "Sagie", set_values_to = exprs( PARAMCD = "QTLCR", PARAM = "QTlc - Sagie's Correction Formula Rederived (msec)", AVALU = "msec" ), get_unit_expr = extract_unit(PARAM) )
library(tibble) adeg <- tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT, "01-701-1015", "HR", "Heart Rate (beats/min)", 70.14, "beats/min", "BASELINE", "01-701-1015", "QT", "QT Duration (msec)", 370, "msec", "WEEK 2", "01-701-1015", "HR", "Heart Rate (beats/min)", 62.66, "beats/min", "WEEK 1", "01-701-1015", "RR", "RR Duration (msec)", 710, "msec", "WEEK 2", "01-701-1028", "HR", "Heart Rate (beats/min)", 85.45, "beats/min", "BASELINE", "01-701-1028", "QT", "QT Duration (msec)", 480, "msec", "WEEK 2", "01-701-1028", "QT", "QT Duration (msec)", 350, "msec", "WEEK 3", "01-701-1028", "HR", "Heart Rate (beats/min)", 56.54, "beats/min", "WEEK 3", "01-701-1028", "RR", "RR Duration (msec)", 842, "msec", "WEEK 2", ) derive_param_qtc( adeg, by_vars = exprs(USUBJID, VISIT), method = "Bazett", set_values_to = exprs( PARAMCD = "QTCBR", PARAM = "QTcB - Bazett's Correction Formula Rederived (msec)", AVALU = "msec" ), get_unit_expr = AVALU ) derive_param_qtc( adeg, by_vars = exprs(USUBJID, VISIT), method = "Fridericia", set_values_to = exprs( PARAMCD = "QTCFR", PARAM = "QTcF - Fridericia's Correction Formula Rederived (msec)", AVALU = "msec" ), get_unit_expr = extract_unit(PARAM) ) derive_param_qtc( adeg, by_vars = exprs(USUBJID, VISIT), method = "Sagie", set_values_to = exprs( PARAMCD = "QTLCR", PARAM = "QTlc - Sagie's Correction Formula Rederived (msec)", AVALU = "msec" ), get_unit_expr = extract_unit(PARAM) )
Adds a record for derived RR based on heart rate for each by group (e.g., subject and visit) where the source parameters are available.
Note: This is a wrapper function for the more generic derive_param_computed()
.
The analysis value of the new parameter is derived as
derive_param_rr( dataset, by_vars, set_values_to = exprs(PARAMCD = "RRR"), hr_code = "HR", get_unit_expr, filter = NULL )
derive_param_rr( dataset, by_vars, set_values_to = exprs(PARAMCD = "RRR"), hr_code = "HR", get_unit_expr, filter = NULL )
dataset |
Input dataset The variables specified by the The variable specified by |
by_vars |
Grouping variables For each group defined by Permitted Values: list of variables created by |
set_values_to |
Variables to be set The specified variables are set to the specified values for the new
observations. For example Permitted Values: List of variable-value pairs |
hr_code |
HR parameter code The observations where Permitted Values: character value |
get_unit_expr |
An expression providing the unit of the parameter The result is used to check the units of the input parameters. Permitted Values: A variable of the input dataset or a function call |
filter |
Filter condition The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account. Permitted Values: a condition |
The input dataset with the new parameter added. Note, a variable will only
be populated in the new parameter rows if it is specified in by_vars
.
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_wbc_abs()
,
derive_summary_records()
library(tibble) adeg <- tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT, "01-701-1015", "HR", "Heart Rate", 70.14, "beats/min", "BASELINE", "01-701-1015", "QT", "QT Duration", 370, "msec", "WEEK 2", "01-701-1015", "HR", "Heart Rate", 62.66, "beats/min", "WEEK 1", "01-701-1015", "RR", "RR Duration", 710, "msec", "WEEK 2", "01-701-1028", "HR", "Heart Rate", 85.45, "beats/min", "BASELINE", "01-701-1028", "QT", "QT Duration", 480, "msec", "WEEK 2", "01-701-1028", "QT", "QT Duration", 350, "msec", "WEEK 3", "01-701-1028", "HR", "Heart Rate", 56.54, "beats/min", "WEEK 3", "01-701-1028", "RR", "RR Duration", 842, "msec", "WEEK 2" ) derive_param_rr( adeg, by_vars = exprs(USUBJID, VISIT), set_values_to = exprs( PARAMCD = "RRR", PARAM = "RR Duration Rederived (msec)", AVALU = "msec" ), get_unit_expr = AVALU )
library(tibble) adeg <- tribble( ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT, "01-701-1015", "HR", "Heart Rate", 70.14, "beats/min", "BASELINE", "01-701-1015", "QT", "QT Duration", 370, "msec", "WEEK 2", "01-701-1015", "HR", "Heart Rate", 62.66, "beats/min", "WEEK 1", "01-701-1015", "RR", "RR Duration", 710, "msec", "WEEK 2", "01-701-1028", "HR", "Heart Rate", 85.45, "beats/min", "BASELINE", "01-701-1028", "QT", "QT Duration", 480, "msec", "WEEK 2", "01-701-1028", "QT", "QT Duration", 350, "msec", "WEEK 3", "01-701-1028", "HR", "Heart Rate", 56.54, "beats/min", "WEEK 3", "01-701-1028", "RR", "RR Duration", 842, "msec", "WEEK 2" ) derive_param_rr( adeg, by_vars = exprs(USUBJID, VISIT), set_values_to = exprs( PARAMCD = "RRR", PARAM = "RR Duration Rederived (msec)", AVALU = "msec" ), get_unit_expr = AVALU )
Add a time-to-event parameter to the input dataset.
derive_param_tte( dataset = NULL, dataset_adsl, source_datasets, by_vars = NULL, start_date = TRTSDT, event_conditions, censor_conditions, create_datetime = FALSE, set_values_to, subject_keys = get_admiral_option("subject_keys") )
derive_param_tte( dataset = NULL, dataset_adsl, source_datasets, by_vars = NULL, start_date = TRTSDT, event_conditions, censor_conditions, create_datetime = FALSE, set_values_to, subject_keys = get_admiral_option("subject_keys") )
dataset |
Input dataset
|
dataset_adsl |
ADSL input dataset The variables specified for |
source_datasets |
Source datasets A named list of datasets is expected. The |
by_vars |
By variables If the parameter is specified, separate time to event parameters are derived for each by group. The by variables must be in at least one of the source datasets. Each source dataset must contain either all by variables or none of the by variables. The by variables are not included in the output dataset. Permitted Values: list of variables created by |
start_date |
Time to event origin date The variable If the event or censoring date is before the origin date, |
event_conditions |
Sources and conditions defining events A list of |
censor_conditions |
Sources and conditions defining censorings A list of |
create_datetime |
Create datetime variables? If set to |
set_values_to |
Variables to set A named list returned by |
subject_keys |
Variables to uniquely identify a subject A list of symbols created using |
The following steps are performed to create the observations of the new parameter:
Deriving the events:
For each event source dataset the observations as
specified by the filter
element are selected. Then for each patient the
first observation (with respect to date
) is selected.
The ADT
variable is set to the variable specified by the
date
element. If the date variable is a datetime variable, only
the datepart is copied.
The CNSR
variable is added and set to the censor
element.
The variables specified by the set_values_to
element are
added.
The selected observations of all event source datasets are combined into a single dataset.
For each patient the first observation (with respect to the ADT
variable) from the single dataset is selected.
Deriving the censoring observations:
For each censoring source dataset the observations as
specified by the filter
element are selected. Then for each patient the
last observation (with respect to date
) is selected.
The ADT
variable is set to the variable specified by the
date
element. If the date variable is a datetime variable, only
the datepart is copied.
The CNSR
variable is added and set to the censor
element.
The variables specified by the set_values_to
element are
added.
The selected observations of all censoring source datasets are combined into a single dataset.
For each patient the last observation (with respect to the ADT
variable) from the single dataset is selected.
For each subject (as defined by the subject_keys
parameter) an
observation is selected. If an event is available, the event observation is
selected. Otherwise the censoring observation is selected.
Finally:
The variable specified for start_date
is joined from the
ADSL dataset. Only subjects in both datasets are kept,
i.e., subjects with both an event or censoring and an observation in
dataset_adsl
.
The variables as defined by the set_values_to
parameter are added.
The ADT
/ADTM
variable is set to the maximum of ADT
/ADTM
and
STARTDT
/STARTDTM
(depending on the create_datetime
parameter).
The new observations are added to the output dataset.
The input dataset with the new parameter added
event_source()
, censor_source()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) data("admiral_adsl") adsl <- admiral_adsl # derive overall survival parameter death <- event_source( dataset_name = "adsl", filter = DTHFL == "Y", date = DTHDT, set_values_to = exprs( EVNTDESC = "DEATH", SRCDOM = "ADSL", SRCVAR = "DTHDT" ) ) last_alive_dt <- censor_source( dataset_name = "adsl", date = LSTALVDT, set_values_to = exprs( EVNTDESC = "LAST DATE KNOWN ALIVE", SRCDOM = "ADSL", SRCVAR = "LSTALVDT" ) ) derive_param_tte( dataset_adsl = adsl, event_conditions = list(death), censor_conditions = list(last_alive_dt), source_datasets = list(adsl = adsl), set_values_to = exprs( PARAMCD = "OS", PARAM = "Overall Survival" ) ) %>% select(-STUDYID) %>% filter(row_number() %in% 20:30) # derive duration of response # only observations for subjects in dataset_adsl are created adsl <- tribble( ~USUBJID, ~DTHFL, ~DTHDT, ~RSPDT, "01", "Y", ymd("2021-06-12"), ymd("2021-03-04"), "02", "N", NA, NA, "03", "Y", ymd("2021-08-21"), NA, "04", "N", NA, ymd("2021-04-14") ) %>% mutate(STUDYID = "AB42") adrs <- tribble( ~USUBJID, ~AVALC, ~ADT, ~ASEQ, "01", "SD", ymd("2021-01-03"), 1, "01", "PR", ymd("2021-03-04"), 2, "01", "PD", ymd("2021-05-05"), 3, "02", "PD", ymd("2021-02-03"), 1, "04", "SD", ymd("2021-02-13"), 1, "04", "PR", ymd("2021-04-14"), 2, "04", "CR", ymd("2021-05-15"), 3 ) %>% mutate(STUDYID = "AB42", PARAMCD = "OVR") pd <- event_source( dataset_name = "adrs", filter = AVALC == "PD", date = ADT, set_values_to = exprs( EVENTDESC = "PD", SRCDOM = "ADRS", SRCVAR = "ADTM", SRCSEQ = ASEQ ) ) death <- event_source( dataset_name = "adsl", filter = DTHFL == "Y", date = DTHDT, set_values_to = exprs( EVENTDESC = "DEATH", SRCDOM = "ADSL", SRCVAR = "DTHDT" ) ) lastvisit <- censor_source( dataset_name = "adrs", date = ADT, censor = 1, set_values_to = exprs( EVENTDESC = "LAST TUMOR ASSESSMENT", SRCDOM = "ADRS", SRCVAR = "ADTM", SRCSEQ = ASEQ ) ) first_response <- censor_source( dataset_name = "adsl", date = RSPDT, censor = 1, set_values_to = exprs( EVENTDESC = "FIRST RESPONSE", SRCDOM = "ADSL", SRCVAR = "RSPDT" ) ) derive_param_tte( dataset_adsl = filter(adsl, !is.na(RSPDT)), start_date = RSPDT, event_conditions = list(pd, death), censor_conditions = list(lastvisit, first_response), source_datasets = list(adsl = adsl, adrs = adrs), set_values_to = exprs( PARAMCD = "DURRSP", PARAM = "Duration of Response" ) ) # derive time to adverse event for each preferred term adsl <- tribble( ~USUBJID, ~TRTSDT, ~EOSDT, "01", ymd("2020-12-06"), ymd("2021-03-06"), "02", ymd("2021-01-16"), ymd("2021-02-03") ) %>% mutate(STUDYID = "AB42") ae <- tribble( ~USUBJID, ~AESTDTC, ~AESEQ, ~AEDECOD, "01", "2021-01-03T10:56", 1, "Flu", "01", "2021-03-04", 2, "Cough", "01", "2021", 3, "Flu" ) %>% mutate(STUDYID = "AB42") ae_ext <- derive_vars_dt( ae, dtc = AESTDTC, new_vars_prefix = "AEST", highest_imputation = "M", flag_imputation = "none" ) ttae <- event_source( dataset_name = "ae", date = AESTDT, set_values_to = exprs( EVNTDESC = "AE", SRCDOM = "AE", SRCVAR = "AESTDTC", SRCSEQ = AESEQ ) ) eos <- censor_source( dataset_name = "adsl", date = EOSDT, set_values_to = exprs( EVNTDESC = "END OF STUDY", SRCDOM = "ADSL", SRCVAR = "EOSDT" ) ) derive_param_tte( dataset_adsl = adsl, by_vars = exprs(AEDECOD), start_date = TRTSDT, event_conditions = list(ttae), censor_conditions = list(eos), source_datasets = list(adsl = adsl, ae = ae_ext), set_values_to = exprs( PARAMCD = paste0("TTAE", as.numeric(as.factor(AEDECOD))), PARAM = paste("Time to First", AEDECOD, "Adverse Event"), PARCAT1 = "TTAE", PARCAT2 = AEDECOD ) ) %>% select(USUBJID, STARTDT, PARAMCD, PARAM, ADT, CNSR, SRCSEQ)
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) data("admiral_adsl") adsl <- admiral_adsl # derive overall survival parameter death <- event_source( dataset_name = "adsl", filter = DTHFL == "Y", date = DTHDT, set_values_to = exprs( EVNTDESC = "DEATH", SRCDOM = "ADSL", SRCVAR = "DTHDT" ) ) last_alive_dt <- censor_source( dataset_name = "adsl", date = LSTALVDT, set_values_to = exprs( EVNTDESC = "LAST DATE KNOWN ALIVE", SRCDOM = "ADSL", SRCVAR = "LSTALVDT" ) ) derive_param_tte( dataset_adsl = adsl, event_conditions = list(death), censor_conditions = list(last_alive_dt), source_datasets = list(adsl = adsl), set_values_to = exprs( PARAMCD = "OS", PARAM = "Overall Survival" ) ) %>% select(-STUDYID) %>% filter(row_number() %in% 20:30) # derive duration of response # only observations for subjects in dataset_adsl are created adsl <- tribble( ~USUBJID, ~DTHFL, ~DTHDT, ~RSPDT, "01", "Y", ymd("2021-06-12"), ymd("2021-03-04"), "02", "N", NA, NA, "03", "Y", ymd("2021-08-21"), NA, "04", "N", NA, ymd("2021-04-14") ) %>% mutate(STUDYID = "AB42") adrs <- tribble( ~USUBJID, ~AVALC, ~ADT, ~ASEQ, "01", "SD", ymd("2021-01-03"), 1, "01", "PR", ymd("2021-03-04"), 2, "01", "PD", ymd("2021-05-05"), 3, "02", "PD", ymd("2021-02-03"), 1, "04", "SD", ymd("2021-02-13"), 1, "04", "PR", ymd("2021-04-14"), 2, "04", "CR", ymd("2021-05-15"), 3 ) %>% mutate(STUDYID = "AB42", PARAMCD = "OVR") pd <- event_source( dataset_name = "adrs", filter = AVALC == "PD", date = ADT, set_values_to = exprs( EVENTDESC = "PD", SRCDOM = "ADRS", SRCVAR = "ADTM", SRCSEQ = ASEQ ) ) death <- event_source( dataset_name = "adsl", filter = DTHFL == "Y", date = DTHDT, set_values_to = exprs( EVENTDESC = "DEATH", SRCDOM = "ADSL", SRCVAR = "DTHDT" ) ) lastvisit <- censor_source( dataset_name = "adrs", date = ADT, censor = 1, set_values_to = exprs( EVENTDESC = "LAST TUMOR ASSESSMENT", SRCDOM = "ADRS", SRCVAR = "ADTM", SRCSEQ = ASEQ ) ) first_response <- censor_source( dataset_name = "adsl", date = RSPDT, censor = 1, set_values_to = exprs( EVENTDESC = "FIRST RESPONSE", SRCDOM = "ADSL", SRCVAR = "RSPDT" ) ) derive_param_tte( dataset_adsl = filter(adsl, !is.na(RSPDT)), start_date = RSPDT, event_conditions = list(pd, death), censor_conditions = list(lastvisit, first_response), source_datasets = list(adsl = adsl, adrs = adrs), set_values_to = exprs( PARAMCD = "DURRSP", PARAM = "Duration of Response" ) ) # derive time to adverse event for each preferred term adsl <- tribble( ~USUBJID, ~TRTSDT, ~EOSDT, "01", ymd("2020-12-06"), ymd("2021-03-06"), "02", ymd("2021-01-16"), ymd("2021-02-03") ) %>% mutate(STUDYID = "AB42") ae <- tribble( ~USUBJID, ~AESTDTC, ~AESEQ, ~AEDECOD, "01", "2021-01-03T10:56", 1, "Flu", "01", "2021-03-04", 2, "Cough", "01", "2021", 3, "Flu" ) %>% mutate(STUDYID = "AB42") ae_ext <- derive_vars_dt( ae, dtc = AESTDTC, new_vars_prefix = "AEST", highest_imputation = "M", flag_imputation = "none" ) ttae <- event_source( dataset_name = "ae", date = AESTDT, set_values_to = exprs( EVNTDESC = "AE", SRCDOM = "AE", SRCVAR = "AESTDTC", SRCSEQ = AESEQ ) ) eos <- censor_source( dataset_name = "adsl", date = EOSDT, set_values_to = exprs( EVNTDESC = "END OF STUDY", SRCDOM = "ADSL", SRCVAR = "EOSDT" ) ) derive_param_tte( dataset_adsl = adsl, by_vars = exprs(AEDECOD), start_date = TRTSDT, event_conditions = list(ttae), censor_conditions = list(eos), source_datasets = list(adsl = adsl, ae = ae_ext), set_values_to = exprs( PARAMCD = paste0("TTAE", as.numeric(as.factor(AEDECOD))), PARAM = paste("Time to First", AEDECOD, "Adverse Event"), PARCAT1 = "TTAE", PARCAT2 = AEDECOD ) ) %>% select(USUBJID, STARTDT, PARAMCD, PARAM, ADT, CNSR, SRCSEQ)
Add a parameter by converting lab differentials from fraction or percentage to absolute values
derive_param_wbc_abs( dataset, by_vars, set_values_to, get_unit_expr, wbc_unit = "10^9/L", wbc_code = "WBC", diff_code, diff_type = "fraction" )
derive_param_wbc_abs( dataset, by_vars, set_values_to, get_unit_expr, wbc_unit = "10^9/L", wbc_code = "WBC", diff_code, diff_type = "fraction" )
dataset |
Input dataset The variables specified by the The variable specified by |
by_vars |
Grouping variables Permitted Values: list of variables created by |
set_values_to |
Variables to set A named list returned by |
get_unit_expr |
An expression providing the unit of the parameter The result is used to check the units of the input parameters. Permitted Values: a variable containing unit from the input dataset, or a function call,
for example, |
wbc_unit |
A string containing the required unit of the WBC parameter Default: |
wbc_code |
White Blood Cell (WBC) parameter The observations where Default: Permitted Values: character value |
diff_code |
white blood differential parameter The observations where |
diff_type |
A string specifying the type of differential Permitted Values: |
If diff_type
is "percent"
, the analysis value of the new parameter is derived as
If diff_type
is "fraction"
, the analysis value of the new parameter is derived as
New records are created for each group of records (grouped by by_vars
) if 1) the white blood
cell component in absolute value is not already available from the input dataset, and 2) the
white blood cell absolute value (identified by wbc_code
) and the white blood cell differential
(identified by diff_code
) are both present.
The input dataset with the new parameter added
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_summary_records()
library(tibble) test_lb <- tribble( ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT, "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1", "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1", "P01", "LYMLE", 0.90, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1", "P01", "LYMLE", 0.70, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1", "P01", "ALB", 36, "Albumin (g/dL)", "CYCLE 2 DAY 1", "P02", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1", "P02", "LYMPH", 29, "Lymphocytes Abs (10^9/L)", "CYCLE 1 DAY 1", "P02", "LYMLE", 0.87, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1", "P03", "LYMLE", 0.89, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1" ) derive_param_wbc_abs( dataset = test_lb, by_vars = exprs(USUBJID, VISIT), set_values_to = exprs( PARAMCD = "LYMPH", PARAM = "Lymphocytes Abs (10^9/L)", DTYPE = "CALCULATION" ), get_unit_expr = extract_unit(PARAM), wbc_code = "WBC", diff_code = "LYMLE", diff_type = "fraction" )
library(tibble) test_lb <- tribble( ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT, "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1", "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1", "P01", "LYMLE", 0.90, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1", "P01", "LYMLE", 0.70, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1", "P01", "ALB", 36, "Albumin (g/dL)", "CYCLE 2 DAY 1", "P02", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1", "P02", "LYMPH", 29, "Lymphocytes Abs (10^9/L)", "CYCLE 1 DAY 1", "P02", "LYMLE", 0.87, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1", "P03", "LYMLE", 0.89, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1" ) derive_param_wbc_abs( dataset = test_lb, by_vars = exprs(USUBJID, VISIT), set_values_to = exprs( PARAMCD = "LYMPH", PARAM = "Lymphocytes Abs (10^9/L)", DTYPE = "CALCULATION" ), get_unit_expr = extract_unit(PARAM), wbc_code = "WBC", diff_code = "LYMLE", diff_type = "fraction" )
It is not uncommon to have an analysis need whereby one needs to derive an
analysis value (AVAL
) from multiple records. The ADaM basic dataset
structure variable DTYPE
is available to indicate when a new derived
records has been added to a dataset.
derive_summary_records( dataset = NULL, dataset_add, dataset_ref = NULL, by_vars, filter_add = NULL, set_values_to, missing_values = NULL )
derive_summary_records( dataset = NULL, dataset_add, dataset_ref = NULL, by_vars, filter_add = NULL, set_values_to, missing_values = NULL )
dataset |
Input dataset The variables specified by the |
dataset_add |
Additional dataset The variables specified for |
dataset_ref |
Reference dataset The variables specified for |
by_vars |
Grouping variables Variables to consider for generation of groupwise summary
records. Providing the names of variables in Permitted Values: list of variables created by |
filter_add |
Filter condition as logical expression to apply during
summary calculation. By default, filtering expressions are computed within
For example,
|
set_values_to |
Variables to be set The specified variables are set to the specified values for the new observations. Set a list of variables to some specified value for the new records
For example: set_values_to = exprs( AVAL = sum(AVAL), DTYPE = "AVERAGE", ) |
missing_values |
Values for missing summary values For observations of the reference dataset ( Permitted Values: named list of expressions, e.g.,
|
When all records have same values within by_vars
then this function will
retain those common values in the newly derived records. Otherwise new value
will be set to NA
.
A data frame with derived records appended to original dataset.
get_summary_records()
, derive_var_merged_summary()
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd()
,
derive_expected_records()
,
derive_extreme_event()
,
derive_extreme_records()
,
derive_locf_records()
,
derive_param_bmi()
,
derive_param_bsa()
,
derive_param_computed()
,
derive_param_doseint()
,
derive_param_exist_flag()
,
derive_param_exposure()
,
derive_param_framingham()
,
derive_param_map()
,
derive_param_qtc()
,
derive_param_rr()
,
derive_param_wbc_abs()
library(tibble) library(dplyr) adeg <- tribble( ~USUBJID, ~EGSEQ, ~PARAM, ~AVISIT, ~EGDTC, ~AVAL, ~TRTA, "XYZ-1001", 1, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385, NA_character_, "XYZ-1001", 2, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:52", 399, NA_character_, "XYZ-1001", 3, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:56", 396, NA_character_, "XYZ-1001", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:45", 384, "Placebo", "XYZ-1001", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:48", 393, "Placebo", "XYZ-1001", 6, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:51", 388, "Placebo", "XYZ-1001", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:45", 385, "Placebo", "XYZ-1001", 8, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:48", 394, "Placebo", "XYZ-1001", 9, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:51", 402, "Placebo", "XYZ-1002", 1, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 399, NA_character_, "XYZ-1002", 2, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 410, NA_character_, "XYZ-1002", 3, "QTcF Int. (msec)", "Baseline", "2016-02-22T08:01", 392, NA_character_, "XYZ-1002", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:50", 401, "Active 20mg", "XYZ-1002", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:53", 407, "Active 20mg", "XYZ-1002", 6, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:56", 400, "Active 20mg", "XYZ-1002", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:50", 412, "Active 20mg", "XYZ-1002", 8, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:53", 414, "Active 20mg", "XYZ-1002", 9, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:56", 402, "Active 20mg" ) %>% mutate( ADTM = convert_dtc_to_dtm(EGDTC) ) # Summarize the average of the triplicate ECG interval values (AVAL) derive_summary_records( adeg, dataset_add = adeg, by_vars = exprs(USUBJID, PARAM, AVISIT), set_values_to = exprs( AVAL = mean(AVAL, na.rm = TRUE), DTYPE = "AVERAGE" ) ) %>% arrange(USUBJID, AVISIT) # Derive more than one summary variable derive_summary_records( adeg, dataset_add = adeg, by_vars = exprs(USUBJID, PARAM, AVISIT), set_values_to = exprs( AVAL = mean(AVAL), ADTM = max(ADTM), DTYPE = "AVERAGE" ) ) %>% arrange(USUBJID, AVISIT) %>% select(-EGSEQ, -TRTA) # Sample ADEG dataset with triplicate record for only AVISIT = 'Baseline' adeg <- tribble( ~USUBJID, ~EGSEQ, ~PARAM, ~AVISIT, ~EGDTC, ~AVAL, ~TRTA, "XYZ-1001", 1, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385, NA_character_, "XYZ-1001", 2, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:52", 399, NA_character_, "XYZ-1001", 3, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:56", 396, NA_character_, "XYZ-1001", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:48", 393, "Placebo", "XYZ-1001", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:51", 388, "Placebo", "XYZ-1001", 6, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:48", 394, "Placebo", "XYZ-1001", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:51", 402, "Placebo", "XYZ-1002", 1, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 399, NA_character_, "XYZ-1002", 2, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 410, NA_character_, "XYZ-1002", 3, "QTcF Int. (msec)", "Baseline", "2016-02-22T08:01", 392, NA_character_, "XYZ-1002", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:53", 407, "Active 20mg", "XYZ-1002", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:56", 400, "Active 20mg", "XYZ-1002", 6, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:53", 414, "Active 20mg", "XYZ-1002", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:56", 402, "Active 20mg" ) # Compute the average of AVAL only if there are more than 2 records within the # by group derive_summary_records( adeg, dataset_add = adeg, by_vars = exprs(USUBJID, PARAM, AVISIT), filter_add = n() > 2, set_values_to = exprs( AVAL = mean(AVAL, na.rm = TRUE), DTYPE = "AVERAGE" ) ) %>% arrange(USUBJID, AVISIT)
library(tibble) library(dplyr) adeg <- tribble( ~USUBJID, ~EGSEQ, ~PARAM, ~AVISIT, ~EGDTC, ~AVAL, ~TRTA, "XYZ-1001", 1, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385, NA_character_, "XYZ-1001", 2, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:52", 399, NA_character_, "XYZ-1001", 3, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:56", 396, NA_character_, "XYZ-1001", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:45", 384, "Placebo", "XYZ-1001", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:48", 393, "Placebo", "XYZ-1001", 6, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:51", 388, "Placebo", "XYZ-1001", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:45", 385, "Placebo", "XYZ-1001", 8, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:48", 394, "Placebo", "XYZ-1001", 9, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:51", 402, "Placebo", "XYZ-1002", 1, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 399, NA_character_, "XYZ-1002", 2, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 410, NA_character_, "XYZ-1002", 3, "QTcF Int. (msec)", "Baseline", "2016-02-22T08:01", 392, NA_character_, "XYZ-1002", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:50", 401, "Active 20mg", "XYZ-1002", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:53", 407, "Active 20mg", "XYZ-1002", 6, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:56", 400, "Active 20mg", "XYZ-1002", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:50", 412, "Active 20mg", "XYZ-1002", 8, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:53", 414, "Active 20mg", "XYZ-1002", 9, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:56", 402, "Active 20mg" ) %>% mutate( ADTM = convert_dtc_to_dtm(EGDTC) ) # Summarize the average of the triplicate ECG interval values (AVAL) derive_summary_records( adeg, dataset_add = adeg, by_vars = exprs(USUBJID, PARAM, AVISIT), set_values_to = exprs( AVAL = mean(AVAL, na.rm = TRUE), DTYPE = "AVERAGE" ) ) %>% arrange(USUBJID, AVISIT) # Derive more than one summary variable derive_summary_records( adeg, dataset_add = adeg, by_vars = exprs(USUBJID, PARAM, AVISIT), set_values_to = exprs( AVAL = mean(AVAL), ADTM = max(ADTM), DTYPE = "AVERAGE" ) ) %>% arrange(USUBJID, AVISIT) %>% select(-EGSEQ, -TRTA) # Sample ADEG dataset with triplicate record for only AVISIT = 'Baseline' adeg <- tribble( ~USUBJID, ~EGSEQ, ~PARAM, ~AVISIT, ~EGDTC, ~AVAL, ~TRTA, "XYZ-1001", 1, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385, NA_character_, "XYZ-1001", 2, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:52", 399, NA_character_, "XYZ-1001", 3, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:56", 396, NA_character_, "XYZ-1001", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:48", 393, "Placebo", "XYZ-1001", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:51", 388, "Placebo", "XYZ-1001", 6, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:48", 394, "Placebo", "XYZ-1001", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:51", 402, "Placebo", "XYZ-1002", 1, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 399, NA_character_, "XYZ-1002", 2, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 410, NA_character_, "XYZ-1002", 3, "QTcF Int. (msec)", "Baseline", "2016-02-22T08:01", 392, NA_character_, "XYZ-1002", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:53", 407, "Active 20mg", "XYZ-1002", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:56", 400, "Active 20mg", "XYZ-1002", 6, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:53", 414, "Active 20mg", "XYZ-1002", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:56", 402, "Active 20mg" ) # Compute the average of AVAL only if there are more than 2 records within the # by group derive_summary_records( adeg, dataset_add = adeg, by_vars = exprs(USUBJID, PARAM, AVISIT), filter_add = n() > 2, set_values_to = exprs( AVAL = mean(AVAL, na.rm = TRUE), DTYPE = "AVERAGE" ) ) %>% arrange(USUBJID, AVISIT)
Converts the given age variable (age_var
) to the unit 'years' from the current
units given in the age_var+U
variable or age_unit
argument and stores
in a new variable (new_var
).
derive_var_age_years(dataset, age_var, age_unit = NULL, new_var)
derive_var_age_years(dataset, age_var, age_unit = NULL, new_var)
dataset |
Input dataset The variables specified by the |
age_var |
Age variable. A numeric object is expected. |
age_unit |
Age unit. The Default: NULL Permitted Values: 'years', 'months', 'weeks', 'days', 'hours', 'minutes', 'seconds' |
new_var |
New age variable to be created in years. The returned values are doubles and NOT integers. ' |
This function is used to convert an age variable into the unit 'years' which can then be used to create age groups. The resulting column contains the equivalent years as a double. Note, underlying computations assume an equal number of days in each year (365.25).
The input dataset (dataset
) with new_var
variable added in years.
ADSL Functions that returns variable appended to dataset:
derive_vars_aage()
,
derive_vars_extreme_event()
,
derive_vars_period()
library(tibble) # Derive age with age units specified data <- tribble( ~AGE, ~AGEU, 27, "days", 24, "months", 3, "years", 4, "weeks", 1, "years" ) derive_var_age_years(data, AGE, new_var = AAGE) # Derive age without age units variable specified data <- tribble( ~AGE, 12, 24, 36, 48 ) derive_var_age_years(data, AGE, age_unit = "months", new_var = AAGE)
library(tibble) # Derive age with age units specified data <- tribble( ~AGE, ~AGEU, 27, "days", 24, "months", 3, "years", 4, "weeks", 1, "years" ) derive_var_age_years(data, AGE, new_var = AAGE) # Derive age without age units variable specified data <- tribble( ~AGE, 12, 24, 36, 48 ) derive_var_age_years(data, AGE, age_unit = "months", new_var = AAGE)
Derives a ratio variable for a BDS dataset based on user specified variables.
derive_var_analysis_ratio(dataset, numer_var, denom_var, new_var = NULL)
derive_var_analysis_ratio(dataset, numer_var, denom_var, new_var = NULL)
dataset |
Input dataset The variables specified by the |
numer_var |
Variable containing numeric values to be used in the numerator of the ratio calculation. |
denom_var |
Variable containing numeric values to be used in the denominator of the ratio calculation. |
new_var |
A user-defined variable that will be appended to the dataset.
The default behavior will take the denominator variable and prefix it with Default is |
A user wishing to calculate a Ratio to Baseline, AVAL / BASE
will
have returned a new variable R2BASE
that will be appended to the input dataset.
Ratio to Analysis Range Lower Limit AVAL / ANRLO
will return a new variable
R2ANRLO
, and Ratio to Analysis Range Upper Limit AVAL / ANRHI
will return
a new variable R2ANRLO
. Please note how the denominator variable has the prefix
R2----
. A user can override the default returned variables by using the
new_var
argument. Also, values of 0 in the denominator will return NA
in
the derivation.
Reference CDISC ADaM Implementation Guide Version 1.1 Section 3.3.4 Analysis Parameter Variables for BDS Datasets
The input dataset with a ratio variable appended
BDS-Findings Functions that returns variable appended to dataset:
derive_basetype_records()
,
derive_var_anrind()
,
derive_var_atoxgr()
,
derive_var_atoxgr_dir()
,
derive_var_base()
,
derive_var_chg()
,
derive_var_ontrtfl()
,
derive_var_pchg()
,
derive_var_shift()
,
derive_vars_crit_flag()
library(tibble) data <- tribble( ~USUBJID, ~PARAMCD, ~SEQ, ~AVAL, ~BASE, ~ANRLO, ~ANRHI, "P01", "ALT", 1, 27, 27, 6, 34, "P01", "ALT", 2, 41, 27, 6, 34, "P01", "ALT", 3, 17, 27, 6, 34, "P02", "ALB", 1, 38, 38, 33, 49, "P02", "ALB", 2, 39, 38, 33, 49, "P02", "ALB", 3, 37, 38, 33, 49 ) # Returns "R2" prefixed variables data %>% derive_var_analysis_ratio(numer_var = AVAL, denom_var = BASE) %>% derive_var_analysis_ratio(numer_var = AVAL, denom_var = ANRLO) %>% derive_var_analysis_ratio(numer_var = AVAL, denom_var = ANRHI) # Returns user-defined variables data %>% derive_var_analysis_ratio(numer_var = AVAL, denom_var = BASE, new_var = R01BASE) %>% derive_var_analysis_ratio(numer_var = AVAL, denom_var = ANRLO, new_var = R01ANRLO) %>% derive_var_analysis_ratio(numer_var = AVAL, denom_var = ANRHI, new_var = R01ANRHI)
library(tibble) data <- tribble( ~USUBJID, ~PARAMCD, ~SEQ, ~AVAL, ~BASE, ~ANRLO, ~ANRHI, "P01", "ALT", 1, 27, 27, 6, 34, "P01", "ALT", 2, 41, 27, 6, 34, "P01", "ALT", 3, 17, 27, 6, 34, "P02", "ALB", 1, 38, 38, 33, 49, "P02", "ALB", 2, 39, 38, 33, 49, "P02", "ALB", 3, 37, 38, 33, 49 ) # Returns "R2" prefixed variables data %>% derive_var_analysis_ratio(numer_var = AVAL, denom_var = BASE) %>% derive_var_analysis_ratio(numer_var = AVAL, denom_var = ANRLO) %>% derive_var_analysis_ratio(numer_var = AVAL, denom_var = ANRHI) # Returns user-defined variables data %>% derive_var_analysis_ratio(numer_var = AVAL, denom_var = BASE, new_var = R01BASE) %>% derive_var_analysis_ratio(numer_var = AVAL, denom_var = ANRLO, new_var = R01ANRLO) %>% derive_var_analysis_ratio(numer_var = AVAL, denom_var = ANRHI, new_var = R01ANRHI)
Derive Reference Range Indicator
derive_var_anrind( dataset, signif_dig = get_admiral_option("signif_digits"), use_a1hia1lo = FALSE )
derive_var_anrind( dataset, signif_dig = get_admiral_option("signif_digits"), use_a1hia1lo = FALSE )
dataset |
Input dataset
|
signif_dig |
Number of significant digits to use when comparing values. Significant digits used to avoid floating point discrepancies when comparing numeric values. See blog: How admiral handles floating points |
use_a1hia1lo |
A logical value indicating whether to use |
In the case that A1H1
and A1LO
are to be used, ANRIND
is set to:
"NORMAL"
if AVAL
is greater or equal ANRLO
and less than
or equal ANRHI
; or if AVAL
is greater than or equal ANRLO
and ANRHI
is missing; or if AVAL
is less than or equal ANRHI
and ANRLO
is
missing
"LOW"
if AVAL
is less than ANRLO
and either A1LO
is missing or AVAL
is greater than or equal A1LO
"HIGH"
if AVAL
is greater than ANRHI
and either A1HI
is missing or AVAL
is less than or equal A1HI
"LOW LOW"
if AVAL
is less than A1LO
"HIGH HIGH"
if AVAL
is greater than A1HI
In the case that A1H1
and A1LO
are not to be used, ANRIND
is set to:
"NORMAL"
if AVAL
is greater or equal ANRLO
and less than
or equal ANRHI
; or if AVAL
is greater than or equal ANRLO
and ANRHI
is missing; or if AVAL
is less than or equal ANRHI
and ANRLO
is
missing
"LOW"
if AVAL
is less than ANRLO
"HIGH"
if AVAL
is greater than ANRHI
The input dataset with additional column ANRIND
BDS-Findings Functions that returns variable appended to dataset:
derive_basetype_records()
,
derive_var_analysis_ratio()
,
derive_var_atoxgr()
,
derive_var_atoxgr_dir()
,
derive_var_base()
,
derive_var_chg()
,
derive_var_ontrtfl()
,
derive_var_pchg()
,
derive_var_shift()
,
derive_vars_crit_flag()
library(tibble) library(dplyr, warn.conflicts = FALSE) vs <- tibble::tribble( ~USUBJID, ~PARAMCD, ~AVAL, ~ANRLO, ~ANRHI, ~A1LO, ~A1HI, "P01", "PUL", 70, 60, 100, 40, 110, "P01", "PUL", 57, 60, 100, 40, 110, "P01", "PUL", 60, 60, 100, 40, 110, "P01", "DIABP", 102, 60, 80, 40, 90, "P02", "PUL", 109, 60, 100, 40, 110, "P02", "PUL", 100, 60, 100, 40, 110, "P02", "DIABP", 80, 60, 80, 40, 90, "P03", "PUL", 39, 60, 100, 40, 110, "P03", "PUL", 40, 60, 100, 40, 110 ) vs %>% derive_var_anrind(use_a1hia1lo = TRUE) vs %>% derive_var_anrind(use_a1hia1lo = FALSE)
library(tibble) library(dplyr, warn.conflicts = FALSE) vs <- tibble::tribble( ~USUBJID, ~PARAMCD, ~AVAL, ~ANRLO, ~ANRHI, ~A1LO, ~A1HI, "P01", "PUL", 70, 60, 100, 40, 110, "P01", "PUL", 57, 60, 100, 40, 110, "P01", "PUL", 60, 60, 100, 40, 110, "P01", "DIABP", 102, 60, 80, 40, 90, "P02", "PUL", 109, 60, 100, 40, 110, "P02", "PUL", 100, 60, 100, 40, 110, "P02", "DIABP", 80, 60, 80, 40, 90, "P03", "PUL", 39, 60, 100, 40, 110, "P03", "PUL", 40, 60, 100, 40, 110 ) vs %>% derive_var_anrind(use_a1hia1lo = TRUE) vs %>% derive_var_anrind(use_a1hia1lo = FALSE)
Derives character lab grade based on high and low severity/toxicity grade(s).
derive_var_atoxgr( dataset, lotox_description_var = ATOXDSCL, hitox_description_var = ATOXDSCH )
derive_var_atoxgr( dataset, lotox_description_var = ATOXDSCL, hitox_description_var = ATOXDSCH )
dataset |
Input dataset The variables specified by the |
lotox_description_var |
Variable containing the toxicity grade description for low values, eg. "Anemia" |
hitox_description_var |
Variable containing the toxicity grade description for high values, eg. "Hemoglobin Increased". |
Created variable ATOXGR
will contain values "-4", "-3", "-2", "-1" for low values
and "1", "2", "3", "4" for high values, and will contain "0" if value is gradable
and does not satisfy any of the criteria for high or low values. ATOXGR is set to
missing if information not available to give a grade.
Function applies the following rules:
High and low missing - overall missing
Low grade not missing and > 0 - overall holds low grade
High grade not missing and > 0 - overall holds high grade
(Only high direction OR low direction is NORMAL) and high grade normal - overall NORMAL
(Only low direction OR high direction is NORMAL) and low grade normal - overall NORMAL
otherwise set to missing
The input data set with the character variable added
BDS-Findings Functions that returns variable appended to dataset:
derive_basetype_records()
,
derive_var_analysis_ratio()
,
derive_var_anrind()
,
derive_var_atoxgr_dir()
,
derive_var_base()
,
derive_var_chg()
,
derive_var_ontrtfl()
,
derive_var_pchg()
,
derive_var_shift()
,
derive_vars_crit_flag()
library(tibble) adlb <- tribble( ~ATOXDSCL, ~ATOXDSCH, ~ATOXGRL, ~ATOXGRH, "Hypoglycemia", "Hyperglycemia", NA_character_, "0", "Hypoglycemia", "Hyperglycemia", "0", "1", "Hypoglycemia", "Hyperglycemia", "0", "0", NA_character_, "INR Increased", NA_character_, "0", "Hypophosphatemia", NA_character_, "1", NA_character_ ) derive_var_atoxgr(adlb)
library(tibble) adlb <- tribble( ~ATOXDSCL, ~ATOXDSCH, ~ATOXGRL, ~ATOXGRH, "Hypoglycemia", "Hyperglycemia", NA_character_, "0", "Hypoglycemia", "Hyperglycemia", "0", "1", "Hypoglycemia", "Hyperglycemia", "0", "0", NA_character_, "INR Increased", NA_character_, "0", "Hypophosphatemia", NA_character_, "1", NA_character_ ) derive_var_atoxgr(adlb)
Derives a character lab grade based on severity/toxicity criteria.
derive_var_atoxgr_dir( dataset, new_var, tox_description_var, meta_criteria, criteria_direction, get_unit_expr, signif_dig = get_admiral_option("signif_digits") )
derive_var_atoxgr_dir( dataset, new_var, tox_description_var, meta_criteria, criteria_direction, get_unit_expr, signif_dig = get_admiral_option("signif_digits") )
dataset |
Input dataset The variables specified by the |
new_var |
Name of the character grade variable to create, for example, |
tox_description_var |
Variable containing the description of the grading criteria. For example: "Anemia" or "INR Increased". |
meta_criteria |
Metadata data set holding the criteria (normally a case statement) Permitted Values:
|
criteria_direction |
Direction (L= Low, H = High) of toxicity grade. Permitted Values: "L", "H" |
get_unit_expr |
An expression providing the unit of the parameter The result is used to check the units of the input parameters. Compared with
Permitted Values: A variable containing unit from the input dataset, or a function call,
for example, |
signif_dig |
Number of significant digits to use when comparing a lab value against another value. Significant digits used to avoid floating point discrepancies when comparing numeric values. See blog: How admiral handles floating points |
new_var
is derived with values NA, "0", "1", "2", "3", "4", where "4" is the most
severe grade
"4" is where the lab value satisfies the criteria for grade 4.
"3" is where the lab value satisfies the criteria for grade 3.
"2" is where the lab value satisfies the criteria for grade 2.
"1" is where the lab value satisfies the criteria for grade 1.
"0" is where a grade can be derived and is not grade "1", "2", "3" or "4".
NA is where a grade cannot be derived.
The input dataset with the character variable added
BDS-Findings Functions that returns variable appended to dataset:
derive_basetype_records()
,
derive_var_analysis_ratio()
,
derive_var_anrind()
,
derive_var_atoxgr()
,
derive_var_base()
,
derive_var_chg()
,
derive_var_ontrtfl()
,
derive_var_pchg()
,
derive_var_shift()
,
derive_vars_crit_flag()
library(tibble) data <- tribble( ~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~PARAM, "Hypoglycemia", 119, 4, 7, "Glucose (mmol/L)", "Lymphocyte count decreased", 0.7, 1, 4, "Lymphocytes Abs (10^9/L)", "Anemia", 129, 120, 180, "Hemoglobin (g/L)", "White blood cell decreased", 10, 5, 20, "White blood cell (10^9/L)", "White blood cell decreased", 15, 5, 20, "White blood cell (10^9/L)", "Anemia", 140, 120, 180, "Hemoglobin (g/L)" ) derive_var_atoxgr_dir(data, new_var = ATOXGRL, tox_description_var = ATOXDSCL, meta_criteria = atoxgr_criteria_ctcv5, criteria_direction = "L", get_unit_expr = extract_unit(PARAM) ) data <- tribble( ~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~PARAM, "CPK increased", 129, 0, 30, "Creatine Kinase (U/L)", "Lymphocyte count increased", 4, 1, 4, "Lymphocytes Abs (10^9/L)", "Lymphocyte count increased", 2, 1, 4, "Lymphocytes Abs (10^9/L)", "CPK increased", 140, 120, 180, "Creatine Kinase (U/L)" ) derive_var_atoxgr_dir(data, new_var = ATOXGRH, tox_description_var = ATOXDSCH, meta_criteria = atoxgr_criteria_ctcv5, criteria_direction = "H", get_unit_expr = extract_unit(PARAM) )
library(tibble) data <- tribble( ~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~PARAM, "Hypoglycemia", 119, 4, 7, "Glucose (mmol/L)", "Lymphocyte count decreased", 0.7, 1, 4, "Lymphocytes Abs (10^9/L)", "Anemia", 129, 120, 180, "Hemoglobin (g/L)", "White blood cell decreased", 10, 5, 20, "White blood cell (10^9/L)", "White blood cell decreased", 15, 5, 20, "White blood cell (10^9/L)", "Anemia", 140, 120, 180, "Hemoglobin (g/L)" ) derive_var_atoxgr_dir(data, new_var = ATOXGRL, tox_description_var = ATOXDSCL, meta_criteria = atoxgr_criteria_ctcv5, criteria_direction = "L", get_unit_expr = extract_unit(PARAM) ) data <- tribble( ~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~PARAM, "CPK increased", 129, 0, 30, "Creatine Kinase (U/L)", "Lymphocyte count increased", 4, 1, 4, "Lymphocytes Abs (10^9/L)", "Lymphocyte count increased", 2, 1, 4, "Lymphocytes Abs (10^9/L)", "CPK increased", 140, 120, 180, "Creatine Kinase (U/L)" ) derive_var_atoxgr_dir(data, new_var = ATOXGRH, tox_description_var = ATOXDSCH, meta_criteria = atoxgr_criteria_ctcv5, criteria_direction = "H", get_unit_expr = extract_unit(PARAM) )
Derive baseline variables, e.g. BASE
or BNRIND
, in a BDS dataset.
Note: This is a wrapper function for the more generic derive_vars_merged()
.
derive_var_base( dataset, by_vars, source_var = AVAL, new_var = BASE, filter = ABLFL == "Y" )
derive_var_base( dataset, by_vars, source_var = AVAL, new_var = BASE, filter = ABLFL == "Y" )
dataset |
Input dataset The variables specified by the |
by_vars |
Grouping variables Grouping variables uniquely identifying a set
of records for which to calculate Permitted Values: list of variables created by |
source_var |
The column from which to extract the baseline value, e.g. |
new_var |
The name of the newly created baseline column, e.g. |
filter |
The condition used to filter By default |
For each by_vars
group, the baseline record is identified by the
condition specified in filter
which defaults to ABLFL == "Y"
. Subsequently,
every value of the new_var
variable for the by_vars
group is set to the
value of the source_var
variable of the baseline record. In case there are
multiple baseline records within by_vars
an error is issued.
A new data.frame
containing all records and variables of the input
dataset plus the new_var
variable
BDS-Findings Functions that returns variable appended to dataset:
derive_basetype_records()
,
derive_var_analysis_ratio()
,
derive_var_anrind()
,
derive_var_atoxgr()
,
derive_var_atoxgr_dir()
,
derive_var_chg()
,
derive_var_ontrtfl()
,
derive_var_pchg()
,
derive_var_shift()
,
derive_vars_crit_flag()
library(tibble) dataset <- tribble( ~STUDYID, ~USUBJID, ~PARAMCD, ~AVAL, ~AVALC, ~AVISIT, ~ABLFL, ~ANRIND, "TEST01", "PAT01", "PARAM01", 10.12, NA, "Baseline", "Y", "NORMAL", "TEST01", "PAT01", "PARAM01", 9.700, NA, "Day 7", "N", "LOW", "TEST01", "PAT01", "PARAM01", 15.01, NA, "Day 14", "N", "HIGH", "TEST01", "PAT01", "PARAM02", 8.350, NA, "Baseline", "Y", "LOW", "TEST01", "PAT01", "PARAM02", NA, NA, "Day 7", "N", NA, "TEST01", "PAT01", "PARAM02", 8.350, NA, "Day 14", "N", "LOW", "TEST01", "PAT01", "PARAM03", NA, "LOW", "Baseline", "Y", NA, "TEST01", "PAT01", "PARAM03", NA, "LOW", "Day 7", "N", NA, "TEST01", "PAT01", "PARAM03", NA, "MEDIUM", "Day 14", "N", NA, "TEST01", "PAT01", "PARAM04", NA, "HIGH", "Baseline", "Y", NA, "TEST01", "PAT01", "PARAM04", NA, "HIGH", "Day 7", "N", NA, "TEST01", "PAT01", "PARAM04", NA, "MEDIUM", "Day 14", "N", NA ) ## Derive `BASE` variable from `AVAL` derive_var_base( dataset, by_vars = exprs(USUBJID, PARAMCD), source_var = AVAL, new_var = BASE ) ## Derive `BASEC` variable from `AVALC` derive_var_base( dataset, by_vars = exprs(USUBJID, PARAMCD), source_var = AVALC, new_var = BASEC ) ## Derive `BNRIND` variable from `ANRIND` derive_var_base( dataset, by_vars = exprs(USUBJID, PARAMCD), source_var = ANRIND, new_var = BNRIND )
library(tibble) dataset <- tribble( ~STUDYID, ~USUBJID, ~PARAMCD, ~AVAL, ~AVALC, ~AVISIT, ~ABLFL, ~ANRIND, "TEST01", "PAT01", "PARAM01", 10.12, NA, "Baseline", "Y", "NORMAL", "TEST01", "PAT01", "PARAM01", 9.700, NA, "Day 7", "N", "LOW", "TEST01", "PAT01", "PARAM01", 15.01, NA, "Day 14", "N", "HIGH", "TEST01", "PAT01", "PARAM02", 8.350, NA, "Baseline", "Y", "LOW", "TEST01", "PAT01", "PARAM02", NA, NA, "Day 7", "N", NA, "TEST01", "PAT01", "PARAM02", 8.350, NA, "Day 14", "N", "LOW", "TEST01", "PAT01", "PARAM03", NA, "LOW", "Baseline", "Y", NA, "TEST01", "PAT01", "PARAM03", NA, "LOW", "Day 7", "N", NA, "TEST01", "PAT01", "PARAM03", NA, "MEDIUM", "Day 14", "N", NA, "TEST01", "PAT01", "PARAM04", NA, "HIGH", "Baseline", "Y", NA, "TEST01", "PAT01", "PARAM04", NA, "HIGH", "Day 7", "N", NA, "TEST01", "PAT01", "PARAM04", NA, "MEDIUM", "Day 14", "N", NA ) ## Derive `BASE` variable from `AVAL` derive_var_base( dataset, by_vars = exprs(USUBJID, PARAMCD), source_var = AVAL, new_var = BASE ) ## Derive `BASEC` variable from `AVALC` derive_var_base( dataset, by_vars = exprs(USUBJID, PARAMCD), source_var = AVALC, new_var = BASEC ) ## Derive `BNRIND` variable from `ANRIND` derive_var_base( dataset, by_vars = exprs(USUBJID, PARAMCD), source_var = ANRIND, new_var = BNRIND )
Derive change from baseline (CHG
) in a BDS dataset
derive_var_chg(dataset)
derive_var_chg(dataset)
dataset |
Input dataset |
Change from baseline is calculated by subtracting the baseline value from the analysis value.
The input dataset with an additional column named CHG
BDS-Findings Functions that returns variable appended to dataset:
derive_basetype_records()
,
derive_var_analysis_ratio()
,
derive_var_anrind()
,
derive_var_atoxgr()
,
derive_var_atoxgr_dir()
,
derive_var_base()
,
derive_var_ontrtfl()
,
derive_var_pchg()
,
derive_var_shift()
,
derive_vars_crit_flag()
library(tibble) advs <- tribble( ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BASE, "P01", "WEIGHT", 80, "Y", 80, "P01", "WEIGHT", 80.8, "", 80, "P01", "WEIGHT", 81.4, "", 80, "P02", "WEIGHT", 75.3, "Y", 75.3, "P02", "WEIGHT", 76, "", 75.3 ) derive_var_chg(advs)
library(tibble) advs <- tribble( ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BASE, "P01", "WEIGHT", 80, "Y", 80, "P01", "WEIGHT", 80.8, "", 80, "P01", "WEIGHT", 81.4, "", 80, "P02", "WEIGHT", 75.3, "Y", 75.3, "P02", "WEIGHT", 76, "", 75.3 ) derive_var_chg(advs)
The derive_var_dthcaus()
function has been superseded in favor of derive_vars_extreme_event()
.
Derive death cause (DTHCAUS
) and add traceability variables if required.
derive_var_dthcaus( dataset, ..., source_datasets, subject_keys = get_admiral_option("subject_keys") )
derive_var_dthcaus( dataset, ..., source_datasets, subject_keys = get_admiral_option("subject_keys") )
dataset |
Input dataset The variables specified by the |
... |
Objects of class "dthcaus_source" created by |
source_datasets |
A named |
subject_keys |
Variables to uniquely identify a subject A list of expressions where the expressions are symbols as returned by
|
This function derives DTHCAUS
along with the user-defined traceability
variables, if required. If a subject has death info from multiple sources,
the one from the source with the earliest death date will be used. If dates are
equivalent, the first source will be kept, so the user should provide the inputs in
the preferred order.
The input dataset with DTHCAUS
variable added.
Other superseded:
date_source()
,
derive_param_extreme_record()
,
derive_var_extreme_dt()
,
derive_var_extreme_dtm()
,
dthcaus_source()
,
get_summary_records()
library(tibble) library(dplyr, warn.conflicts = FALSE) adsl <- tribble( ~STUDYID, ~USUBJID, "STUDY01", "PAT01", "STUDY01", "PAT02", "STUDY01", "PAT03" ) ae <- tribble( ~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC, "STUDY01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-04-04" ) ds <- tribble( ~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC, "STUDY01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03", "STUDY01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11", "STUDY01", "PAT02", 3, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-01", "STUDY01", "PAT03", 1, "DEATH", "POST STUDY REPORTING OF DEATH", "2022-03-03" ) # Derive `DTHCAUS` only - for on-study deaths only src_ae <- dthcaus_source( dataset_name = "ae", filter = AEOUT == "FATAL", date = convert_dtc_to_dt(AEDTHDTC), mode = "first", dthcaus = AEDECOD ) src_ds <- dthcaus_source( dataset_name = "ds", filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM), date = convert_dtc_to_dt(DSSTDTC), mode = "first", dthcaus = DSTERM ) derive_var_dthcaus(adsl, src_ae, src_ds, source_datasets = list(ae = ae, ds = ds)) # Derive `DTHCAUS` and add traceability variables - for on-study deaths only src_ae <- dthcaus_source( dataset_name = "ae", filter = AEOUT == "FATAL", date = convert_dtc_to_dt(AEDTHDTC), mode = "first", dthcaus = AEDECOD, set_values_to = exprs(DTHDOM = "AE", DTHSEQ = AESEQ) ) src_ds <- dthcaus_source( dataset_name = "ds", filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM), date = convert_dtc_to_dt(DSSTDTC), mode = "first", dthcaus = DSTERM, set_values_to = exprs(DTHDOM = "DS", DTHSEQ = DSSEQ) ) derive_var_dthcaus(adsl, src_ae, src_ds, source_datasets = list(ae = ae, ds = ds)) # Derive `DTHCAUS` as above - now including post-study deaths with different `DTHCAUS` value src_ae <- dthcaus_source( dataset_name = "ae", filter = AEOUT == "FATAL", date = convert_dtc_to_dt(AEDTHDTC), mode = "first", dthcaus = AEDECOD, set_values_to = exprs(DTHDOM = "AE", DTHSEQ = AESEQ) ) ds <- mutate( ds, DSSTDT = convert_dtc_to_dt(DSSTDTC) ) src_ds <- dthcaus_source( dataset_name = "ds", filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM), date = DSSTDT, mode = "first", dthcaus = DSTERM, set_values_to = exprs(DTHDOM = "DS", DTHSEQ = DSSEQ) ) src_ds_post <- dthcaus_source( dataset_name = "ds", filter = DSDECOD == "DEATH" & DSTERM == "POST STUDY REPORTING OF DEATH", date = DSSTDT, mode = "first", dthcaus = "POST STUDY: UNKNOWN CAUSE", set_values_to = exprs(DTHDOM = "DS", DTHSEQ = DSSEQ) ) derive_var_dthcaus( adsl, src_ae, src_ds, src_ds_post, source_datasets = list(ae = ae, ds = ds) )
library(tibble) library(dplyr, warn.conflicts = FALSE) adsl <- tribble( ~STUDYID, ~USUBJID, "STUDY01", "PAT01", "STUDY01", "PAT02", "STUDY01", "PAT03" ) ae <- tribble( ~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC, "STUDY01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-04-04" ) ds <- tribble( ~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC, "STUDY01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03", "STUDY01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11", "STUDY01", "PAT02", 3, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-01", "STUDY01", "PAT03", 1, "DEATH", "POST STUDY REPORTING OF DEATH", "2022-03-03" ) # Derive `DTHCAUS` only - for on-study deaths only src_ae <- dthcaus_source( dataset_name = "ae", filter = AEOUT == "FATAL", date = convert_dtc_to_dt(AEDTHDTC), mode = "first", dthcaus = AEDECOD ) src_ds <- dthcaus_source( dataset_name = "ds", filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM), date = convert_dtc_to_dt(DSSTDTC), mode = "first", dthcaus = DSTERM ) derive_var_dthcaus(adsl, src_ae, src_ds, source_datasets = list(ae = ae, ds = ds)) # Derive `DTHCAUS` and add traceability variables - for on-study deaths only src_ae <- dthcaus_source( dataset_name = "ae", filter = AEOUT == "FATAL", date = convert_dtc_to_dt(AEDTHDTC), mode = "first", dthcaus = AEDECOD, set_values_to = exprs(DTHDOM = "AE", DTHSEQ = AESEQ) ) src_ds <- dthcaus_source( dataset_name = "ds", filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM), date = convert_dtc_to_dt(DSSTDTC), mode = "first", dthcaus = DSTERM, set_values_to = exprs(DTHDOM = "DS", DTHSEQ = DSSEQ) ) derive_var_dthcaus(adsl, src_ae, src_ds, source_datasets = list(ae = ae, ds = ds)) # Derive `DTHCAUS` as above - now including post-study deaths with different `DTHCAUS` value src_ae <- dthcaus_source( dataset_name = "ae", filter = AEOUT == "FATAL", date = convert_dtc_to_dt(AEDTHDTC), mode = "first", dthcaus = AEDECOD, set_values_to = exprs(DTHDOM = "AE", DTHSEQ = AESEQ) ) ds <- mutate( ds, DSSTDT = convert_dtc_to_dt(DSSTDTC) ) src_ds <- dthcaus_source( dataset_name = "ds", filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM), date = DSSTDT, mode = "first", dthcaus = DSTERM, set_values_to = exprs(DTHDOM = "DS", DTHSEQ = DSSEQ) ) src_ds_post <- dthcaus_source( dataset_name = "ds", filter = DSDECOD == "DEATH" & DSTERM == "POST STUDY REPORTING OF DEATH", date = DSSTDT, mode = "first", dthcaus = "POST STUDY: UNKNOWN CAUSE", set_values_to = exprs(DTHDOM = "DS", DTHSEQ = DSSEQ) ) derive_var_dthcaus( adsl, src_ae, src_ds, src_ds_post, source_datasets = list(ae = ae, ds = ds) )
The derive_var_extreme_dt()
function has been superseded in favor of derive_vars_extreme_event()
.
Add the first or last date from multiple sources to the
dataset, e.g., the last known alive date (LSTALVDT
).
Note: This is a wrapper function for the function derive_var_extreme_dtm()
.
derive_var_extreme_dt( dataset, new_var, ..., source_datasets, mode, subject_keys = get_admiral_option("subject_keys") )
derive_var_extreme_dt( dataset, new_var, ..., source_datasets, mode, subject_keys = get_admiral_option("subject_keys") )
dataset |
Input dataset The variables specified by the |
new_var |
Name of variable to create |
... |
Source(s) of dates. One or more |
source_datasets |
A named |
mode |
Selection mode (first or last) If Permitted Values: |
subject_keys |
Variables to uniquely identify a subject A list of expressions where the expressions are symbols as returned by
|
The following steps are performed to create the output dataset:
For each source dataset the observations as specified by the filter
element are selected and observations where date
is NA
are removed.
Then for each patient the first or last observation (with respect to date
and mode
) is selected.
The new variable is set to the variable or expression specified by the
date
element.
The variables specified by the set_values_to
element are added.
The selected observations of all source datasets are combined into a single dataset.
For each patient the first or last observation (with respect to the new
variable and mode
) from the single dataset is selected and the new
variable is merged to the input dataset.
The time part is removed from the new variable.
The input dataset with the new variable added.
date_source()
, derive_var_extreme_dtm()
, derive_vars_merged()
Other superseded:
date_source()
,
derive_param_extreme_record()
,
derive_var_dthcaus()
,
derive_var_extreme_dtm()
,
dthcaus_source()
,
get_summary_records()
library(dplyr, warn.conflicts = FALSE) ae <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AESEQ, ~AESTDTC, ~AEENDTC, "PILOT01", "AE", "01-1130", 5, "2014-05-09", "2014-05-09", "PILOT01", "AE", "01-1130", 6, "2014-05-22", NA, "PILOT01", "AE", "01-1130", 4, "2014-05-09", "2014-05-09", "PILOT01", "AE", "01-1130", 8, "2014-05-22", NA, "PILOT01", "AE", "01-1130", 7, "2014-05-22", NA, "PILOT01", "AE", "01-1130", 2, "2014-03-09", "2014-03-09", "PILOT01", "AE", "01-1130", 1, "2014-03-09", "2014-03-16", "PILOT01", "AE", "01-1130", 3, "2014-03-09", "2014-03-16", "PILOT01", "AE", "01-1133", 1, "2012-12-27", NA, "PILOT01", "AE", "01-1133", 3, "2012-12-27", NA, "PILOT01", "AE", "01-1133", 2, "2012-12-27", NA, "PILOT01", "AE", "01-1133", 4, "2012-12-27", NA, "PILOT01", "AE", "01-1211", 5, "2012-11-29", NA, "PILOT01", "AE", "01-1211", 1, "2012-11-16", NA, "PILOT01", "AE", "01-1211", 7, "2013-01-11", NA, "PILOT01", "AE", "01-1211", 8, "2013-01-11", NA, "PILOT01", "AE", "01-1211", 4, "2012-11-22", NA, "PILOT01", "AE", "01-1211", 2, "2012-11-21", "2012-11-21", "PILOT01", "AE", "01-1211", 3, "2012-11-21", NA, "PILOT01", "AE", "01-1211", 6, "2012-12-09", NA, "PILOT01", "AE", "01-1211", 9, "2013-01-14", "2013-01-14", "PILOT01", "AE", "09-1081", 2, "2014-05-01", NA, "PILOT01", "AE", "09-1081", 1, "2014-04-07", NA, "PILOT01", "AE", "09-1088", 1, "2014-05-08", NA, "PILOT01", "AE", "09-1088", 2, "2014-08-02", NA ) adsl <- tribble( ~STUDYID, ~USUBJID, ~TRTEDTM, ~TRTEDT, "PILOT01", "01-1130", "2014-08-16 23:59:59", "2014-08-16", "PILOT01", "01-1133", "2013-04-28 23:59:59", "2013-04-28", "PILOT01", "01-1211", "2013-01-12 23:59:59", "2013-01-12", "PILOT01", "09-1081", "2014-04-27 23:59:59", "2014-04-27", "PILOT01", "09-1088", "2014-10-09 23:59:59", "2014-10-09" ) %>% mutate( across(TRTEDTM:TRTEDT, as.Date) ) lb <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~LBSEQ, ~LBDTC, "PILOT01", "LB", "01-1130", 219, "2014-06-07T13:20", "PILOT01", "LB", "01-1130", 322, "2014-08-16T13:10", "PILOT01", "LB", "01-1133", 268, "2013-04-18T15:30", "PILOT01", "LB", "01-1133", 304, "2013-04-29T10:13", "PILOT01", "LB", "01-1211", 8, "2012-10-30T14:26", "PILOT01", "LB", "01-1211", 162, "2013-01-08T12:13", "PILOT01", "LB", "09-1081", 47, "2014-02-01T10:55", "PILOT01", "LB", "09-1081", 219, "2014-05-10T11:15", "PILOT01", "LB", "09-1088", 283, "2014-09-27T12:13", "PILOT01", "LB", "09-1088", 322, "2014-10-09T13:25" ) dm <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "DM", "01-1130", 84, "YEARS", "PILOT01", "DM", "01-1133", 81, "YEARS", "PILOT01", "DM", "01-1211", 76, "YEARS", "PILOT01", "DM", "09-1081", 86, "YEARS", "PILOT01", "DM", "09-1088", 69, "YEARS" ) ae_start <- date_source( dataset_name = "ae", date = convert_dtc_to_dt(AESTDTC, highest_imputation = "M") ) ae_end <- date_source( dataset_name = "ae", date = convert_dtc_to_dt(AEENDTC, highest_imputation = "M") ) ae_ext <- ae %>% derive_vars_dt( dtc = AESTDTC, new_vars_prefix = "AEST", highest_imputation = "M" ) %>% derive_vars_dt( dtc = AEENDTC, new_vars_prefix = "AEEN", highest_imputation = "M" ) lb_date <- date_source( dataset_name = "lb", date = convert_dtc_to_dt(LBDTC) ) lb_ext <- derive_vars_dt( lb, dtc = LBDTC, new_vars_prefix = "LB" ) adsl_date <- date_source(dataset_name = "adsl", date = TRTEDT) dm %>% derive_var_extreme_dt( new_var = LSTALVDT, ae_start, ae_end, lb_date, adsl_date, source_datasets = list( adsl = adsl, ae = ae_ext, lb = lb_ext ), mode = "last" ) %>% select(USUBJID, LSTALVDT) # derive last alive date and traceability variables ae_start <- date_source( dataset_name = "ae", date = convert_dtc_to_dt(AESTDTC, highest_imputation = "M"), set_values_to = exprs( LALVDOM = "AE", LALVSEQ = AESEQ, LALVVAR = "AESTDTC" ) ) ae_end <- date_source( dataset_name = "ae", date = convert_dtc_to_dt(AEENDTC, highest_imputation = "M"), set_values_to = exprs( LALVDOM = "AE", LALVSEQ = AESEQ, LALVVAR = "AEENDTC" ) ) lb_date <- date_source( dataset_name = "lb", date = convert_dtc_to_dt(LBDTC), set_values_to = exprs( LALVDOM = "LB", LALVSEQ = LBSEQ, LALVVAR = "LBDTC" ) ) adsl_date <- date_source( dataset_name = "adsl", date = TRTEDT, set_values_to = exprs( LALVDOM = "ADSL", LALVSEQ = NA_integer_, LALVVAR = "TRTEDT" ) ) dm %>% derive_var_extreme_dt( new_var = LSTALVDT, ae_start, ae_end, lb_date, adsl_date, source_datasets = list( adsl = adsl, ae = ae_ext, lb = lb_ext ), mode = "last" ) %>% select(USUBJID, LSTALVDT, LALVDOM, LALVSEQ, LALVVAR)
library(dplyr, warn.conflicts = FALSE) ae <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AESEQ, ~AESTDTC, ~AEENDTC, "PILOT01", "AE", "01-1130", 5, "2014-05-09", "2014-05-09", "PILOT01", "AE", "01-1130", 6, "2014-05-22", NA, "PILOT01", "AE", "01-1130", 4, "2014-05-09", "2014-05-09", "PILOT01", "AE", "01-1130", 8, "2014-05-22", NA, "PILOT01", "AE", "01-1130", 7, "2014-05-22", NA, "PILOT01", "AE", "01-1130", 2, "2014-03-09", "2014-03-09", "PILOT01", "AE", "01-1130", 1, "2014-03-09", "2014-03-16", "PILOT01", "AE", "01-1130", 3, "2014-03-09", "2014-03-16", "PILOT01", "AE", "01-1133", 1, "2012-12-27", NA, "PILOT01", "AE", "01-1133", 3, "2012-12-27", NA, "PILOT01", "AE", "01-1133", 2, "2012-12-27", NA, "PILOT01", "AE", "01-1133", 4, "2012-12-27", NA, "PILOT01", "AE", "01-1211", 5, "2012-11-29", NA, "PILOT01", "AE", "01-1211", 1, "2012-11-16", NA, "PILOT01", "AE", "01-1211", 7, "2013-01-11", NA, "PILOT01", "AE", "01-1211", 8, "2013-01-11", NA, "PILOT01", "AE", "01-1211", 4, "2012-11-22", NA, "PILOT01", "AE", "01-1211", 2, "2012-11-21", "2012-11-21", "PILOT01", "AE", "01-1211", 3, "2012-11-21", NA, "PILOT01", "AE", "01-1211", 6, "2012-12-09", NA, "PILOT01", "AE", "01-1211", 9, "2013-01-14", "2013-01-14", "PILOT01", "AE", "09-1081", 2, "2014-05-01", NA, "PILOT01", "AE", "09-1081", 1, "2014-04-07", NA, "PILOT01", "AE", "09-1088", 1, "2014-05-08", NA, "PILOT01", "AE", "09-1088", 2, "2014-08-02", NA ) adsl <- tribble( ~STUDYID, ~USUBJID, ~TRTEDTM, ~TRTEDT, "PILOT01", "01-1130", "2014-08-16 23:59:59", "2014-08-16", "PILOT01", "01-1133", "2013-04-28 23:59:59", "2013-04-28", "PILOT01", "01-1211", "2013-01-12 23:59:59", "2013-01-12", "PILOT01", "09-1081", "2014-04-27 23:59:59", "2014-04-27", "PILOT01", "09-1088", "2014-10-09 23:59:59", "2014-10-09" ) %>% mutate( across(TRTEDTM:TRTEDT, as.Date) ) lb <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~LBSEQ, ~LBDTC, "PILOT01", "LB", "01-1130", 219, "2014-06-07T13:20", "PILOT01", "LB", "01-1130", 322, "2014-08-16T13:10", "PILOT01", "LB", "01-1133", 268, "2013-04-18T15:30", "PILOT01", "LB", "01-1133", 304, "2013-04-29T10:13", "PILOT01", "LB", "01-1211", 8, "2012-10-30T14:26", "PILOT01", "LB", "01-1211", 162, "2013-01-08T12:13", "PILOT01", "LB", "09-1081", 47, "2014-02-01T10:55", "PILOT01", "LB", "09-1081", 219, "2014-05-10T11:15", "PILOT01", "LB", "09-1088", 283, "2014-09-27T12:13", "PILOT01", "LB", "09-1088", 322, "2014-10-09T13:25" ) dm <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "DM", "01-1130", 84, "YEARS", "PILOT01", "DM", "01-1133", 81, "YEARS", "PILOT01", "DM", "01-1211", 76, "YEARS", "PILOT01", "DM", "09-1081", 86, "YEARS", "PILOT01", "DM", "09-1088", 69, "YEARS" ) ae_start <- date_source( dataset_name = "ae", date = convert_dtc_to_dt(AESTDTC, highest_imputation = "M") ) ae_end <- date_source( dataset_name = "ae", date = convert_dtc_to_dt(AEENDTC, highest_imputation = "M") ) ae_ext <- ae %>% derive_vars_dt( dtc = AESTDTC, new_vars_prefix = "AEST", highest_imputation = "M" ) %>% derive_vars_dt( dtc = AEENDTC, new_vars_prefix = "AEEN", highest_imputation = "M" ) lb_date <- date_source( dataset_name = "lb", date = convert_dtc_to_dt(LBDTC) ) lb_ext <- derive_vars_dt( lb, dtc = LBDTC, new_vars_prefix = "LB" ) adsl_date <- date_source(dataset_name = "adsl", date = TRTEDT) dm %>% derive_var_extreme_dt( new_var = LSTALVDT, ae_start, ae_end, lb_date, adsl_date, source_datasets = list( adsl = adsl, ae = ae_ext, lb = lb_ext ), mode = "last" ) %>% select(USUBJID, LSTALVDT) # derive last alive date and traceability variables ae_start <- date_source( dataset_name = "ae", date = convert_dtc_to_dt(AESTDTC, highest_imputation = "M"), set_values_to = exprs( LALVDOM = "AE", LALVSEQ = AESEQ, LALVVAR = "AESTDTC" ) ) ae_end <- date_source( dataset_name = "ae", date = convert_dtc_to_dt(AEENDTC, highest_imputation = "M"), set_values_to = exprs( LALVDOM = "AE", LALVSEQ = AESEQ, LALVVAR = "AEENDTC" ) ) lb_date <- date_source( dataset_name = "lb", date = convert_dtc_to_dt(LBDTC), set_values_to = exprs( LALVDOM = "LB", LALVSEQ = LBSEQ, LALVVAR = "LBDTC" ) ) adsl_date <- date_source( dataset_name = "adsl", date = TRTEDT, set_values_to = exprs( LALVDOM = "ADSL", LALVSEQ = NA_integer_, LALVVAR = "TRTEDT" ) ) dm %>% derive_var_extreme_dt( new_var = LSTALVDT, ae_start, ae_end, lb_date, adsl_date, source_datasets = list( adsl = adsl, ae = ae_ext, lb = lb_ext ), mode = "last" ) %>% select(USUBJID, LSTALVDT, LALVDOM, LALVSEQ, LALVVAR)
The derive_var_extreme_dtm()
function has been superseded in favor of derive_vars_extreme_event()
.
Add the first or last datetime from multiple sources to the dataset, e.g.,
the last known alive datetime (LSTALVDTM
).
derive_var_extreme_dtm( dataset, new_var, ..., source_datasets, mode, subject_keys = get_admiral_option("subject_keys") )
derive_var_extreme_dtm( dataset, new_var, ..., source_datasets, mode, subject_keys = get_admiral_option("subject_keys") )
dataset |
Input dataset The variables specified by the |
new_var |
Name of variable to create |
... |
Source(s) of dates. One or more |
source_datasets |
A named |
mode |
Selection mode (first or last) If Permitted Values: |
subject_keys |
Variables to uniquely identify a subject A list of expressions where the expressions are symbols as returned by
|
The following steps are performed to create the output dataset:
For each source dataset the observations as specified by the filter
element are selected and observations where date
is NA
are removed.
Then for each patient the first or last observation (with respect to date
and mode
) is selected.
The new variable is set to the variable or expression specified by the
date
element. If this is a date variable (rather than datetime), then the
time is imputed as "00:00:00"
.
The variables specified by the set_values_to
element are added.
The selected observations of all source datasets are combined into a single dataset.
For each patient the first or last observation (with respect to the new
variable and mode
) from the single dataset is selected and the new
variable is merged to the input dataset.
The input dataset with the new variable added.
date_source()
, derive_var_extreme_dt()
,
derive_vars_merged()
Other superseded:
date_source()
,
derive_param_extreme_record()
,
derive_var_dthcaus()
,
derive_var_extreme_dt()
,
dthcaus_source()
,
get_summary_records()
library(dplyr, warn.conflicts = FALSE) library(lubridate) dm <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "DM", "01-1130", 84, "YEARS", "PILOT01", "DM", "01-1133", 81, "YEARS", "PILOT01", "DM", "01-1211", 76, "YEARS", "PILOT01", "DM", "09-1081", 86, "YEARS", "PILOT01", "DM", "09-1088", 69, "YEARS" ) ae <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AESEQ, ~AESTDTC, ~AEENDTC, "PILOT01", "AE", "01-1130", 5, "2014-05-09", "2014-05-09", "PILOT01", "AE", "01-1130", 6, "2014-05-22", NA, "PILOT01", "AE", "01-1130", 4, "2014-05-09", "2014-05-09", "PILOT01", "AE", "01-1130", 8, "2014-05-22", NA, "PILOT01", "AE", "01-1130", 7, "2014-05-22", NA, "PILOT01", "AE", "01-1130", 2, "2014-03-09", "2014-03-09", "PILOT01", "AE", "01-1130", 1, "2014-03-09", "2014-03-16", "PILOT01", "AE", "01-1130", 3, "2014-03-09", "2014-03-16", "PILOT01", "AE", "01-1133", 1, "2012-12-27", NA, "PILOT01", "AE", "01-1133", 3, "2012-12-27", NA, "PILOT01", "AE", "01-1133", 2, "2012-12-27", NA, "PILOT01", "AE", "01-1133", 4, "2012-12-27", NA, "PILOT01", "AE", "01-1211", 5, "2012-11-29", NA, "PILOT01", "AE", "01-1211", 1, "2012-11-16", NA, "PILOT01", "AE", "01-1211", 7, "2013-01-11", NA, "PILOT01", "AE", "01-1211", 8, "2013-01-11", NA, "PILOT01", "AE", "01-1211", 4, "2012-11-22", NA, "PILOT01", "AE", "01-1211", 2, "2012-11-21", "2012-11-21", "PILOT01", "AE", "01-1211", 3, "2012-11-21", NA, "PILOT01", "AE", "01-1211", 6, "2012-12-09", NA, "PILOT01", "AE", "01-1211", 9, "2013-01-14", "2013-01-14", "PILOT01", "AE", "09-1081", 2, "2014-05-01", NA, "PILOT01", "AE", "09-1081", 1, "2014-04-07", NA, "PILOT01", "AE", "09-1088", 1, "2014-05-08", NA, "PILOT01", "AE", "09-1088", 2, "2014-08-02", NA ) lb <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~LBSEQ, ~LBDTC, "PILOT01", "LB", "01-1130", 219, "2014-06-07T13:20", "PILOT01", "LB", "01-1130", 322, "2014-08-16T13:10", "PILOT01", "LB", "01-1133", 268, "2013-04-18T15:30", "PILOT01", "LB", "01-1133", 304, "2013-04-29T10:13", "PILOT01", "LB", "01-1211", 8, "2012-10-30T14:26", "PILOT01", "LB", "01-1211", 162, "2013-01-08T12:13", "PILOT01", "LB", "09-1081", 47, "2014-02-01T10:55", "PILOT01", "LB", "09-1081", 219, "2014-05-10T11:15", "PILOT01", "LB", "09-1088", 283, "2014-09-27T12:13", "PILOT01", "LB", "09-1088", 322, "2014-10-09T13:25" ) adsl <- tribble( ~STUDYID, ~USUBJID, ~TRTEDTM, "PILOT01", "01-1130", "2014-08-16 23:59:59", "PILOT01", "01-1133", "2013-04-28 23:59:59", "PILOT01", "01-1211", "2013-01-12 23:59:59", "PILOT01", "09-1081", "2014-04-27 23:59:59", "PILOT01", "09-1088", "2014-10-09 23:59:59" ) %>% mutate( TRTEDTM = as_datetime(TRTEDTM) ) # derive last known alive datetime (LSTALVDTM) ae_start <- date_source( dataset_name = "ae", date = convert_dtc_to_dtm(AESTDTC, highest_imputation = "M"), ) ae_end <- date_source( dataset_name = "ae", date = convert_dtc_to_dtm(AEENDTC, highest_imputation = "M"), ) ae_ext <- ae %>% derive_vars_dtm( dtc = AESTDTC, new_vars_prefix = "AEST", highest_imputation = "M" ) %>% derive_vars_dtm( dtc = AEENDTC, new_vars_prefix = "AEEN", highest_imputation = "M" ) lb_date <- date_source( dataset_name = "lb", date = convert_dtc_to_dtm(LBDTC), ) lb_ext <- derive_vars_dtm( lb, dtc = LBDTC, new_vars_prefix = "LB" ) adsl_date <- date_source( dataset_name = "adsl", date = TRTEDTM ) dm %>% derive_var_extreme_dtm( new_var = LSTALVDTM, ae_start, ae_end, lb_date, adsl_date, source_datasets = list( adsl = adsl, ae = ae_ext, lb = lb_ext ), mode = "last" ) %>% select(USUBJID, LSTALVDTM) # derive last alive datetime and traceability variables ae_start <- date_source( dataset_name = "ae", date = convert_dtc_to_dtm(AESTDTC, highest_imputation = "M"), set_values_to = exprs( LALVDOM = "AE", LALVSEQ = AESEQ, LALVVAR = "AESTDTC" ) ) ae_end <- date_source( dataset_name = "ae", date = convert_dtc_to_dtm(AEENDTC, highest_imputation = "M"), set_values_to = exprs( LALVDOM = "AE", LALVSEQ = AESEQ, LALVVAR = "AEENDTC" ) ) lb_date <- date_source( dataset_name = "lb", date = convert_dtc_to_dtm(LBDTC), set_values_to = exprs( LALVDOM = "LB", LALVSEQ = LBSEQ, LALVVAR = "LBDTC" ) ) adsl_date <- date_source( dataset_name = "adsl", date = TRTEDTM, set_values_to = exprs( LALVDOM = "ADSL", LALVSEQ = NA_integer_, LALVVAR = "TRTEDTM" ) ) dm %>% derive_var_extreme_dtm( new_var = LSTALVDTM, ae_start, ae_end, lb_date, adsl_date, source_datasets = list( adsl = adsl, ae = ae_ext, lb = lb_ext ), mode = "last" ) %>% select(USUBJID, LSTALVDTM, LALVDOM, LALVSEQ, LALVVAR)
library(dplyr, warn.conflicts = FALSE) library(lubridate) dm <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "DM", "01-1130", 84, "YEARS", "PILOT01", "DM", "01-1133", 81, "YEARS", "PILOT01", "DM", "01-1211", 76, "YEARS", "PILOT01", "DM", "09-1081", 86, "YEARS", "PILOT01", "DM", "09-1088", 69, "YEARS" ) ae <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AESEQ, ~AESTDTC, ~AEENDTC, "PILOT01", "AE", "01-1130", 5, "2014-05-09", "2014-05-09", "PILOT01", "AE", "01-1130", 6, "2014-05-22", NA, "PILOT01", "AE", "01-1130", 4, "2014-05-09", "2014-05-09", "PILOT01", "AE", "01-1130", 8, "2014-05-22", NA, "PILOT01", "AE", "01-1130", 7, "2014-05-22", NA, "PILOT01", "AE", "01-1130", 2, "2014-03-09", "2014-03-09", "PILOT01", "AE", "01-1130", 1, "2014-03-09", "2014-03-16", "PILOT01", "AE", "01-1130", 3, "2014-03-09", "2014-03-16", "PILOT01", "AE", "01-1133", 1, "2012-12-27", NA, "PILOT01", "AE", "01-1133", 3, "2012-12-27", NA, "PILOT01", "AE", "01-1133", 2, "2012-12-27", NA, "PILOT01", "AE", "01-1133", 4, "2012-12-27", NA, "PILOT01", "AE", "01-1211", 5, "2012-11-29", NA, "PILOT01", "AE", "01-1211", 1, "2012-11-16", NA, "PILOT01", "AE", "01-1211", 7, "2013-01-11", NA, "PILOT01", "AE", "01-1211", 8, "2013-01-11", NA, "PILOT01", "AE", "01-1211", 4, "2012-11-22", NA, "PILOT01", "AE", "01-1211", 2, "2012-11-21", "2012-11-21", "PILOT01", "AE", "01-1211", 3, "2012-11-21", NA, "PILOT01", "AE", "01-1211", 6, "2012-12-09", NA, "PILOT01", "AE", "01-1211", 9, "2013-01-14", "2013-01-14", "PILOT01", "AE", "09-1081", 2, "2014-05-01", NA, "PILOT01", "AE", "09-1081", 1, "2014-04-07", NA, "PILOT01", "AE", "09-1088", 1, "2014-05-08", NA, "PILOT01", "AE", "09-1088", 2, "2014-08-02", NA ) lb <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~LBSEQ, ~LBDTC, "PILOT01", "LB", "01-1130", 219, "2014-06-07T13:20", "PILOT01", "LB", "01-1130", 322, "2014-08-16T13:10", "PILOT01", "LB", "01-1133", 268, "2013-04-18T15:30", "PILOT01", "LB", "01-1133", 304, "2013-04-29T10:13", "PILOT01", "LB", "01-1211", 8, "2012-10-30T14:26", "PILOT01", "LB", "01-1211", 162, "2013-01-08T12:13", "PILOT01", "LB", "09-1081", 47, "2014-02-01T10:55", "PILOT01", "LB", "09-1081", 219, "2014-05-10T11:15", "PILOT01", "LB", "09-1088", 283, "2014-09-27T12:13", "PILOT01", "LB", "09-1088", 322, "2014-10-09T13:25" ) adsl <- tribble( ~STUDYID, ~USUBJID, ~TRTEDTM, "PILOT01", "01-1130", "2014-08-16 23:59:59", "PILOT01", "01-1133", "2013-04-28 23:59:59", "PILOT01", "01-1211", "2013-01-12 23:59:59", "PILOT01", "09-1081", "2014-04-27 23:59:59", "PILOT01", "09-1088", "2014-10-09 23:59:59" ) %>% mutate( TRTEDTM = as_datetime(TRTEDTM) ) # derive last known alive datetime (LSTALVDTM) ae_start <- date_source( dataset_name = "ae", date = convert_dtc_to_dtm(AESTDTC, highest_imputation = "M"), ) ae_end <- date_source( dataset_name = "ae", date = convert_dtc_to_dtm(AEENDTC, highest_imputation = "M"), ) ae_ext <- ae %>% derive_vars_dtm( dtc = AESTDTC, new_vars_prefix = "AEST", highest_imputation = "M" ) %>% derive_vars_dtm( dtc = AEENDTC, new_vars_prefix = "AEEN", highest_imputation = "M" ) lb_date <- date_source( dataset_name = "lb", date = convert_dtc_to_dtm(LBDTC), ) lb_ext <- derive_vars_dtm( lb, dtc = LBDTC, new_vars_prefix = "LB" ) adsl_date <- date_source( dataset_name = "adsl", date = TRTEDTM ) dm %>% derive_var_extreme_dtm( new_var = LSTALVDTM, ae_start, ae_end, lb_date, adsl_date, source_datasets = list( adsl = adsl, ae = ae_ext, lb = lb_ext ), mode = "last" ) %>% select(USUBJID, LSTALVDTM) # derive last alive datetime and traceability variables ae_start <- date_source( dataset_name = "ae", date = convert_dtc_to_dtm(AESTDTC, highest_imputation = "M"), set_values_to = exprs( LALVDOM = "AE", LALVSEQ = AESEQ, LALVVAR = "AESTDTC" ) ) ae_end <- date_source( dataset_name = "ae", date = convert_dtc_to_dtm(AEENDTC, highest_imputation = "M"), set_values_to = exprs( LALVDOM = "AE", LALVSEQ = AESEQ, LALVVAR = "AEENDTC" ) ) lb_date <- date_source( dataset_name = "lb", date = convert_dtc_to_dtm(LBDTC), set_values_to = exprs( LALVDOM = "LB", LALVSEQ = LBSEQ, LALVVAR = "LBDTC" ) ) adsl_date <- date_source( dataset_name = "adsl", date = TRTEDTM, set_values_to = exprs( LALVDOM = "ADSL", LALVSEQ = NA_integer_, LALVVAR = "TRTEDTM" ) ) dm %>% derive_var_extreme_dtm( new_var = LSTALVDTM, ae_start, ae_end, lb_date, adsl_date, source_datasets = list( adsl = adsl, ae = ae_ext, lb = lb_ext ), mode = "last" ) %>% select(USUBJID, LSTALVDTM, LALVDOM, LALVSEQ, LALVVAR)
Add a variable flagging the first or last observation within each by group
derive_var_extreme_flag( dataset, by_vars, order, new_var, mode, true_value = "Y", false_value = NA_character_, flag_all = FALSE, check_type = "warning" )
derive_var_extreme_flag( dataset, by_vars, order, new_var, mode, true_value = "Y", false_value = NA_character_, flag_all = FALSE, check_type = "warning" )
dataset |
Input dataset The variables specified by the |
by_vars |
Grouping variables Permitted Values: list of variables created by |
order |
Sort order The first or last observation is determined with respect to the specified order. For handling of Permitted Values: list of variables or functions of variables |
new_var |
Variable to add The specified variable is added to the output dataset. It is set to the value
set in Permitted Values: list of name-value pairs |
mode |
Flag mode Determines of the first or last observation is flagged. Permitted Values: |
true_value |
True value The value for the specified variable Permitted Values: An atomic scalar |
false_value |
False value The value for the specified variable Permitted Values: An atomic scalar |
flag_all |
Flag setting A logical value where if set to |
check_type |
Check uniqueness? If Default: Permitted Values: |
For each group (with respect to the variables specified for the
by_vars
parameter), new_var
is set to "Y"
for the first or last observation
(with respect to the order specified for the order
parameter and the flag mode
specified for the mode
parameter). In the case where the user wants to flag multiple records
of a grouping, for example records that all happen on the same visit and time, the argument
flag_all
can be set to TRUE
.
Otherwise, new_var
is set to NA
. Thus, the direction of "worst" is considered fixed for
all parameters in the dataset depending on the order
and the mode
, i.e. for every
parameter the first or last record will be flagged across the whole dataset.
The input dataset with the new flag variable added
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_joined_exist_flag()
,
derive_var_merged_ef_msrc()
,
derive_var_merged_exist_flag()
,
derive_var_merged_summary()
,
derive_var_obs_number()
,
derive_var_relative_flag()
,
derive_vars_cat()
,
derive_vars_computed()
,
derive_vars_joined()
,
derive_vars_merged()
,
derive_vars_merged_lookup()
,
derive_vars_transposed()
library(tibble) library(dplyr, warn.conflicts = FALSE) example_vs <- tribble( ~USUBJID, ~VSTESTCD, ~VISIT, ~VISITNUM, ~VSTPTNUM, ~VSSTRESN, "1001", "DIABP", "SCREENING", 1, 10, 64, "1001", "DIABP", "SCREENING", 1, 11, 66, "1001", "DIABP", "BASELINE", 2, 100, 68, "1001", "DIABP", "BASELINE", 2, 101, 68, "1001", "DIABP", "WEEK 2", 3, 200, 72, "1001", "DIABP", "WEEK 2", 3, 201, 71, "1001", "DIABP", "WEEK 4", 4, 300, 70, "1001", "DIABP", "WEEK 4", 4, 301, 70 ) # Flag last value for each patient, test, and visit, baseline observations are ignored example_vs %>% restrict_derivation( derivation = derive_var_extreme_flag, args = params( by_vars = exprs(USUBJID, VSTESTCD, VISIT), order = exprs(VSTPTNUM), new_var = LASTFL, mode = "last" ), filter = VISIT != "BASELINE" ) %>% arrange(USUBJID, VSTESTCD, VISITNUM, VSTPTNUM) %>% select(USUBJID, VSTESTCD, VISIT, VSTPTNUM, VSSTRESN, LASTFL) # Baseline (ABLFL) examples: input <- tribble( ~STUDYID, ~USUBJID, ~PARAMCD, ~AVISIT, ~ADT, ~AVAL, ~DTYPE, "TEST01", "PAT01", "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0, NA, "TEST01", "PAT01", "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, NA, "TEST01", "PAT01", "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, "AVERAGE", "TEST01", "PAT01", "PARAM01", "WEEK 1", as.Date("2021-04-27"), 10.0, "AVERAGE", "TEST01", "PAT01", "PARAM01", "WEEK 2", as.Date("2021-04-30"), 12.0, NA, "TEST01", "PAT02", "PARAM01", "SCREENING", as.Date("2021-04-27"), 15.0, "AVERAGE", "TEST01", "PAT02", "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, "AVERAGE", "TEST01", "PAT02", "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, "AVERAGE", "TEST01", "PAT02", "PARAM01", "WEEK 1", as.Date("2021-04-27"), 10.0, "AVERAGE", "TEST01", "PAT02", "PARAM01", "WEEK 2", as.Date("2021-04-30"), 12.0, "AVERAGE", "TEST01", "PAT01", "PARAM02", "SCREENING", as.Date("2021-04-27"), 15.0, "AVERAGE", "TEST01", "PAT01", "PARAM02", "SCREENING", as.Date("2021-04-25"), 14.0, "AVERAGE", "TEST01", "PAT01", "PARAM02", "SCREENING", as.Date("2021-04-23"), 15.0, NA, "TEST01", "PAT01", "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0, "AVERAGE", "TEST01", "PAT01", "PARAM02", "WEEK 2", as.Date("2021-04-30"), 12.0, NA, "TEST01", "PAT02", "PARAM02", "SCREENING", as.Date("2021-04-27"), 15.0, NA, "TEST01", "PAT02", "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0, NA, "TEST01", "PAT02", "PARAM02", "WEEK 1", as.Date("2021-04-23"), 15.0, NA, "TEST01", "PAT02", "PARAM02", "WEEK 1", as.Date("2021-04-27"), 10.0, NA, "TEST01", "PAT02", "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0, NA ) # Last observation restrict_derivation( input, derivation = derive_var_extreme_flag, args = params( by_vars = exprs(USUBJID, PARAMCD), order = exprs(ADT), new_var = ABLFL, mode = "last" ), filter = AVISIT == "BASELINE" ) # Worst observation - Direction = High restrict_derivation( input, derivation = derive_var_extreme_flag, args = params( by_vars = exprs(USUBJID, PARAMCD), order = exprs(AVAL, ADT), new_var = ABLFL, mode = "last" ), filter = AVISIT == "BASELINE" ) # Worst observation - Direction = Lo restrict_derivation( input, derivation = derive_var_extreme_flag, args = params( by_vars = exprs(USUBJID, PARAMCD), order = exprs(desc(AVAL), ADT), new_var = ABLFL, mode = "last" ), filter = AVISIT == "BASELINE" ) # Average observation restrict_derivation( input, derivation = derive_var_extreme_flag, args = params( by_vars = exprs(USUBJID, PARAMCD), order = exprs(ADT, desc(AVAL)), new_var = ABLFL, mode = "last" ), filter = AVISIT == "BASELINE" & DTYPE == "AVERAGE" ) # OCCURDS Examples example_ae <- tribble( ~USUBJID, ~AEBODSYS, ~AEDECOD, ~AESEV, ~AESTDY, ~AESEQ, "1015", "GENERAL DISORDERS", "ERYTHEMA", "MILD", 2, 1, "1015", "GENERAL DISORDERS", "PRURITUS", "MILD", 2, 2, "1015", "GI DISORDERS", "DIARRHOEA", "MILD", 8, 3, "1023", "CARDIAC DISORDERS", "AV BLOCK", "MILD", 22, 4, "1023", "SKIN DISORDERS", "ERYTHEMA", "MILD", 3, 1, "1023", "SKIN DISORDERS", "ERYTHEMA", "SEVERE", 5, 2, "1023", "SKIN DISORDERS", "ERYTHEMA", "MILD", 8, 3 ) # Most severe AE first occurrence per patient example_ae %>% mutate( TEMP_AESEVN = as.integer(factor(AESEV, levels = c("SEVERE", "MODERATE", "MILD"))) ) %>% derive_var_extreme_flag( new_var = AOCCIFL, by_vars = exprs(USUBJID), order = exprs(TEMP_AESEVN, AESTDY, AESEQ), mode = "first" ) %>% arrange(USUBJID, AESTDY, AESEQ) %>% select(USUBJID, AEDECOD, AESEV, AESTDY, AESEQ, AOCCIFL) # Most severe AE first occurrence per patient (flag all cases) example_ae %>% mutate( TEMP_AESEVN = as.integer(factor(AESEV, levels = c("SEVERE", "MODERATE", "MILD"))) ) %>% derive_var_extreme_flag( new_var = AOCCIFL, by_vars = exprs(USUBJID), order = exprs(TEMP_AESEVN, AESTDY), mode = "first", flag_all = TRUE ) %>% arrange(USUBJID, AESTDY) %>% select(USUBJID, AEDECOD, AESEV, AESTDY, AOCCIFL) # Most severe AE first occurrence per patient per body system example_ae %>% mutate( TEMP_AESEVN = as.integer(factor(AESEV, levels = c("SEVERE", "MODERATE", "MILD"))) ) %>% derive_var_extreme_flag( new_var = AOCCSIFL, by_vars = exprs(USUBJID, AEBODSYS), order = exprs(TEMP_AESEVN, AESTDY, AESEQ), mode = "first" ) %>% arrange(USUBJID, AESTDY, AESEQ) %>% select(USUBJID, AEBODSYS, AESEV, AESTDY, AOCCSIFL)
library(tibble) library(dplyr, warn.conflicts = FALSE) example_vs <- tribble( ~USUBJID, ~VSTESTCD, ~VISIT, ~VISITNUM, ~VSTPTNUM, ~VSSTRESN, "1001", "DIABP", "SCREENING", 1, 10, 64, "1001", "DIABP", "SCREENING", 1, 11, 66, "1001", "DIABP", "BASELINE", 2, 100, 68, "1001", "DIABP", "BASELINE", 2, 101, 68, "1001", "DIABP", "WEEK 2", 3, 200, 72, "1001", "DIABP", "WEEK 2", 3, 201, 71, "1001", "DIABP", "WEEK 4", 4, 300, 70, "1001", "DIABP", "WEEK 4", 4, 301, 70 ) # Flag last value for each patient, test, and visit, baseline observations are ignored example_vs %>% restrict_derivation( derivation = derive_var_extreme_flag, args = params( by_vars = exprs(USUBJID, VSTESTCD, VISIT), order = exprs(VSTPTNUM), new_var = LASTFL, mode = "last" ), filter = VISIT != "BASELINE" ) %>% arrange(USUBJID, VSTESTCD, VISITNUM, VSTPTNUM) %>% select(USUBJID, VSTESTCD, VISIT, VSTPTNUM, VSSTRESN, LASTFL) # Baseline (ABLFL) examples: input <- tribble( ~STUDYID, ~USUBJID, ~PARAMCD, ~AVISIT, ~ADT, ~AVAL, ~DTYPE, "TEST01", "PAT01", "PARAM01", "BASELINE", as.Date("2021-04-27"), 15.0, NA, "TEST01", "PAT01", "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, NA, "TEST01", "PAT01", "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, "AVERAGE", "TEST01", "PAT01", "PARAM01", "WEEK 1", as.Date("2021-04-27"), 10.0, "AVERAGE", "TEST01", "PAT01", "PARAM01", "WEEK 2", as.Date("2021-04-30"), 12.0, NA, "TEST01", "PAT02", "PARAM01", "SCREENING", as.Date("2021-04-27"), 15.0, "AVERAGE", "TEST01", "PAT02", "PARAM01", "BASELINE", as.Date("2021-04-25"), 14.0, "AVERAGE", "TEST01", "PAT02", "PARAM01", "BASELINE", as.Date("2021-04-23"), 15.0, "AVERAGE", "TEST01", "PAT02", "PARAM01", "WEEK 1", as.Date("2021-04-27"), 10.0, "AVERAGE", "TEST01", "PAT02", "PARAM01", "WEEK 2", as.Date("2021-04-30"), 12.0, "AVERAGE", "TEST01", "PAT01", "PARAM02", "SCREENING", as.Date("2021-04-27"), 15.0, "AVERAGE", "TEST01", "PAT01", "PARAM02", "SCREENING", as.Date("2021-04-25"), 14.0, "AVERAGE", "TEST01", "PAT01", "PARAM02", "SCREENING", as.Date("2021-04-23"), 15.0, NA, "TEST01", "PAT01", "PARAM02", "BASELINE", as.Date("2021-04-27"), 10.0, "AVERAGE", "TEST01", "PAT01", "PARAM02", "WEEK 2", as.Date("2021-04-30"), 12.0, NA, "TEST01", "PAT02", "PARAM02", "SCREENING", as.Date("2021-04-27"), 15.0, NA, "TEST01", "PAT02", "PARAM02", "BASELINE", as.Date("2021-04-25"), 14.0, NA, "TEST01", "PAT02", "PARAM02", "WEEK 1", as.Date("2021-04-23"), 15.0, NA, "TEST01", "PAT02", "PARAM02", "WEEK 1", as.Date("2021-04-27"), 10.0, NA, "TEST01", "PAT02", "PARAM02", "BASELINE", as.Date("2021-04-30"), 12.0, NA ) # Last observation restrict_derivation( input, derivation = derive_var_extreme_flag, args = params( by_vars = exprs(USUBJID, PARAMCD), order = exprs(ADT), new_var = ABLFL, mode = "last" ), filter = AVISIT == "BASELINE" ) # Worst observation - Direction = High restrict_derivation( input, derivation = derive_var_extreme_flag, args = params( by_vars = exprs(USUBJID, PARAMCD), order = exprs(AVAL, ADT), new_var = ABLFL, mode = "last" ), filter = AVISIT == "BASELINE" ) # Worst observation - Direction = Lo restrict_derivation( input, derivation = derive_var_extreme_flag, args = params( by_vars = exprs(USUBJID, PARAMCD), order = exprs(desc(AVAL), ADT), new_var = ABLFL, mode = "last" ), filter = AVISIT == "BASELINE" ) # Average observation restrict_derivation( input, derivation = derive_var_extreme_flag, args = params( by_vars = exprs(USUBJID, PARAMCD), order = exprs(ADT, desc(AVAL)), new_var = ABLFL, mode = "last" ), filter = AVISIT == "BASELINE" & DTYPE == "AVERAGE" ) # OCCURDS Examples example_ae <- tribble( ~USUBJID, ~AEBODSYS, ~AEDECOD, ~AESEV, ~AESTDY, ~AESEQ, "1015", "GENERAL DISORDERS", "ERYTHEMA", "MILD", 2, 1, "1015", "GENERAL DISORDERS", "PRURITUS", "MILD", 2, 2, "1015", "GI DISORDERS", "DIARRHOEA", "MILD", 8, 3, "1023", "CARDIAC DISORDERS", "AV BLOCK", "MILD", 22, 4, "1023", "SKIN DISORDERS", "ERYTHEMA", "MILD", 3, 1, "1023", "SKIN DISORDERS", "ERYTHEMA", "SEVERE", 5, 2, "1023", "SKIN DISORDERS", "ERYTHEMA", "MILD", 8, 3 ) # Most severe AE first occurrence per patient example_ae %>% mutate( TEMP_AESEVN = as.integer(factor(AESEV, levels = c("SEVERE", "MODERATE", "MILD"))) ) %>% derive_var_extreme_flag( new_var = AOCCIFL, by_vars = exprs(USUBJID), order = exprs(TEMP_AESEVN, AESTDY, AESEQ), mode = "first" ) %>% arrange(USUBJID, AESTDY, AESEQ) %>% select(USUBJID, AEDECOD, AESEV, AESTDY, AESEQ, AOCCIFL) # Most severe AE first occurrence per patient (flag all cases) example_ae %>% mutate( TEMP_AESEVN = as.integer(factor(AESEV, levels = c("SEVERE", "MODERATE", "MILD"))) ) %>% derive_var_extreme_flag( new_var = AOCCIFL, by_vars = exprs(USUBJID), order = exprs(TEMP_AESEVN, AESTDY), mode = "first", flag_all = TRUE ) %>% arrange(USUBJID, AESTDY) %>% select(USUBJID, AEDECOD, AESEV, AESTDY, AOCCIFL) # Most severe AE first occurrence per patient per body system example_ae %>% mutate( TEMP_AESEVN = as.integer(factor(AESEV, levels = c("SEVERE", "MODERATE", "MILD"))) ) %>% derive_var_extreme_flag( new_var = AOCCSIFL, by_vars = exprs(USUBJID, AEBODSYS), order = exprs(TEMP_AESEVN, AESTDY, AESEQ), mode = "first" ) %>% arrange(USUBJID, AESTDY, AESEQ) %>% select(USUBJID, AEBODSYS, AESEV, AESTDY, AOCCSIFL)
Derive a flag which depends on other observations of the dataset. For example, flagging events which need to be confirmed by a second event.
derive_var_joined_exist_flag( dataset, dataset_add, by_vars, order, new_var, tmp_obs_nr_var = NULL, join_vars, join_type, first_cond_lower = NULL, first_cond_upper = NULL, filter_add = NULL, filter_join, true_value = "Y", false_value = NA_character_, check_type = "warning" )
derive_var_joined_exist_flag( dataset, dataset_add, by_vars, order, new_var, tmp_obs_nr_var = NULL, join_vars, join_type, first_cond_lower = NULL, first_cond_upper = NULL, filter_add = NULL, filter_join, true_value = "Y", false_value = NA_character_, check_type = "warning" )
dataset |
Input dataset The variables specified by the |
dataset_add |
Additional dataset The variables specified for |
by_vars |
Grouping variables The specified variables are used for joining the input
dataset ( Permitted Values: list of variables created by |
order |
Order The observations are ordered by the specified order. For handling of |
new_var |
New variable The specified variable is added to the input dataset. |
tmp_obs_nr_var |
Temporary observation number The specified variable is added to the input dataset ( |
join_vars |
Variables to keep from joined dataset The variables needed from the other observations should be specified
for this parameter. The specified variables are added to the joined dataset
with suffix ".join". For example to flag all observations with The |
join_type |
Observations to keep after joining The argument determines which of the joined observations are kept with
respect to the original observation. For example, if For example for confirmed response or BOR in the oncology setting or
confirmed deterioration in questionnaires the confirmatory assessment must
be after the assessment. Thus Whereas, sometimes you might allow for confirmatory observations to occur
prior to the observation. For example, to identify AEs occurring on or
after seven days before a COVID AE. Thus Permitted Values: |
first_cond_lower |
Condition for selecting range of data (before) If this argument is specified, the other observations are restricted from the first observation before the current observation where the specified condition is fulfilled up to the current observation. If the condition is not fulfilled for any of the other observations, no observations are considered, i.e., the observation is not flagged. This parameter should be specified if |
first_cond_upper |
Condition for selecting range of data (after) If this argument is specified, the other observations are restricted up to the first observation where the specified condition is fulfilled. If the condition is not fulfilled for any of the other observations, no observations are considered, i.e., the observation is not flagged. This parameter should be specified if |
filter_add |
Filter for additional dataset ( Only observations from Variables created by The condition can include summary functions like Permitted Values: a condition |
filter_join |
Condition for selecting observations The filter is applied to the joined dataset for flagging the confirmed
observations. The condition can include summary functions like |
true_value |
Value of |
false_value |
Value of |
check_type |
Check uniqueness? If Permitted Values: |
An example usage might be flagging if a patient received two required medications within a certain timeframe of each other.
In the oncology setting, for example, the function could be used to flag if a response value can be confirmed by an other assessment. This is commonly used in endpoints such as best overall response.
The following steps are performed to produce the output dataset.
The variables specified by order
are added to the additional dataset
(dataset_add
).
The variables specified by join_vars
are added to the additional dataset
(dataset_add
).
The records from the additional dataset (dataset_add
) are restricted to
those matching the filter_add
condition.
The input dataset (dataset
) is joined with the restricted additional
dataset by the variables specified for by_vars
. From the additional
dataset only the variables specified for join_vars
are kept. The suffix
".join" is added to those variables which also exist in the input dataset.
For example, for by_vars = USUBJID
, join_vars = exprs(AVISITN, AVALC)
and input dataset and additional dataset
# A tibble: 2 x 4 USUBJID AVISITN AVALC AVAL <chr> <dbl> <chr> <dbl> 1 1 Y 1 1 2 N 0
the joined dataset is
A tibble: 4 x 6 USUBJID AVISITN AVALC AVAL AVISITN.join AVALC.join <chr> <dbl> <chr> <dbl> <dbl> <chr> 1 1 Y 1 1 Y 1 1 Y 1 2 N 1 2 N 0 1 Y 1 2 N 0 2 N
The joined dataset is restricted to observations with respect to
join_type
and order
.
The dataset from the example in the previous step with join_type = "after"
and order = exprs(AVISITN)
is restricted to
A tibble: 4 x 6 USUBJID AVISITN AVALC AVAL AVISITN.join AVALC.join <chr> <dbl> <chr> <dbl> <dbl> <chr> 1 1 Y 1 2 N
If first_cond_lower
is specified, for each observation of the input
dataset the joined dataset is restricted to observations from the first
observation where first_cond_lower
is fulfilled (the observation
fulfilling the condition is included) up to the observation of the input
dataset. If for an observation of the input dataset the condition is not
fulfilled, the observation is removed.
If first_cond_upper
is specified, for each observation of the input
dataset the joined dataset is restricted to observations up to the first
observation where first_cond_upper
is fulfilled (the observation
fulfilling the condition is included). If for an observation of the input
dataset the condition is not fulfilled, the observation is removed.
For an example see the last example in the "Examples" section.
The joined dataset is grouped by the observations from the input dataset
and restricted to the observations fulfilling the condition specified by
filter_join
.
The first observation of each group is selected
The variable specified by new_var
is added to the input dataset. It is
set to true_value
for all observations which were selected in the
previous step. For the other observations it is set to false_value
.
The input dataset with the variable specified by new_var
added.
filter_joined()
, derive_vars_joined()
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_extreme_flag()
,
derive_var_merged_ef_msrc()
,
derive_var_merged_exist_flag()
,
derive_var_merged_summary()
,
derive_var_obs_number()
,
derive_var_relative_flag()
,
derive_vars_cat()
,
derive_vars_computed()
,
derive_vars_joined()
,
derive_vars_merged()
,
derive_vars_merged_lookup()
,
derive_vars_transposed()
library(tibble) # flag observations with a duration longer than 30 and # at, after, or up to 7 days before a COVID AE (ACOVFL == "Y") adae <- tribble( ~USUBJID, ~ADY, ~ACOVFL, ~ADURN, "1", 10, "N", 1, "1", 21, "N", 50, "1", 23, "Y", 14, "1", 32, "N", 31, "1", 42, "N", 20, "2", 11, "Y", 13, "2", 23, "N", 2, "3", 13, "Y", 12, "4", 14, "N", 32, "4", 21, "N", 41 ) derive_var_joined_exist_flag( adae, dataset_add = adae, new_var = ALCOVFL, by_vars = exprs(USUBJID), join_vars = exprs(ACOVFL, ADY), join_type = "all", order = exprs(ADY), filter_join = ADURN > 30 & ACOVFL.join == "Y" & ADY >= ADY.join - 7 ) # flag observations with AVALC == "Y" and AVALC == "Y" at one subsequent visit data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "Y", "1", 2, "N", "1", 3, "Y", "1", 4, "N", "2", 1, "Y", "2", 2, "N", "3", 1, "Y", "4", 1, "N", "4", 2, "N", ) derive_var_joined_exist_flag( data, dataset_add = data, by_vars = exprs(USUBJID), new_var = CONFFL, join_vars = exprs(AVALC, AVISITN), join_type = "after", order = exprs(AVISITN), filter_join = AVALC == "Y" & AVALC.join == "Y" & AVISITN < AVISITN.join ) # select observations with AVALC == "CR", AVALC == "CR" at a subsequent visit, # only "CR" or "NE" in between, and at most one "NE" in between data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "PR", "1", 2, "CR", "1", 3, "NE", "1", 4, "CR", "1", 5, "NE", "2", 1, "CR", "2", 2, "PR", "2", 3, "CR", "3", 1, "CR", "4", 1, "CR", "4", 2, "NE", "4", 3, "NE", "4", 4, "CR", "4", 5, "PR" ) derive_var_joined_exist_flag( data, dataset_add = data, by_vars = exprs(USUBJID), join_vars = exprs(AVALC), join_type = "after", order = exprs(AVISITN), new_var = CONFFL, first_cond_upper = AVALC.join == "CR", filter_join = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1 ) # flag observations with AVALC == "PR", AVALC == "CR" or AVALC == "PR" # at a subsequent visit at least 20 days later, only "CR", "PR", or "NE" # in between, at most one "NE" in between, and "CR" is not followed by "PR" data <- tribble( ~USUBJID, ~ADY, ~AVALC, "1", 6, "PR", "1", 12, "CR", "1", 24, "NE", "1", 32, "CR", "1", 48, "PR", "2", 3, "PR", "2", 21, "CR", "2", 33, "PR", "3", 11, "PR", "4", 7, "PR", "4", 12, "NE", "4", 24, "NE", "4", 32, "PR", "4", 55, "PR" ) derive_var_joined_exist_flag( data, dataset_add = data, by_vars = exprs(USUBJID), join_vars = exprs(AVALC, ADY), join_type = "after", order = exprs(ADY), new_var = CONFFL, first_cond_upper = AVALC.join %in% c("CR", "PR") & ADY.join - ADY >= 20, filter_join = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1 & ( min_cond(var = ADY.join, cond = AVALC.join == "CR") > max_cond(var = ADY.join, cond = AVALC.join == "PR") | count_vals(var = AVALC.join, val = "CR") == 0 ) ) # flag observations with CRIT1FL == "Y" at two consecutive visits or at the last visit data <- tribble( ~USUBJID, ~AVISITN, ~CRIT1FL, "1", 1, "Y", "1", 2, "N", "1", 3, "Y", "1", 5, "N", "2", 1, "Y", "2", 3, "Y", "2", 5, "N", "3", 1, "Y", "4", 1, "Y", "4", 2, "N", ) derive_var_joined_exist_flag( data, dataset_add = data, by_vars = exprs(USUBJID), new_var = CONFFL, tmp_obs_nr_var = tmp_obs_nr, join_vars = exprs(CRIT1FL), join_type = "all", order = exprs(AVISITN), filter_join = CRIT1FL == "Y" & CRIT1FL.join == "Y" & (tmp_obs_nr + 1 == tmp_obs_nr.join | tmp_obs_nr == max(tmp_obs_nr.join)) ) # first_cond_lower and first_cond_upper argument myd <- tribble( ~subj, ~day, ~val, "1", 1, "++", "1", 2, "-", "1", 3, "0", "1", 4, "+", "1", 5, "++", "1", 6, "-", "2", 1, "-", "2", 2, "++", "2", 3, "+", "2", 4, "0", "2", 5, "-", "2", 6, "++" ) # flag "0" where all results from the first "++" before the "0" up to the "0" # (excluding the "0") are "+" or "++" derive_var_joined_exist_flag( myd, dataset_add = myd, by_vars = exprs(subj), order = exprs(day), new_var = flag, join_vars = exprs(val), join_type = "before", first_cond_lower = val.join == "++", filter_join = val == "0" & all(val.join %in% c("+", "++")) ) # flag "0" where all results from the "0" (excluding the "0") up to the first # "++" after the "0" are "+" or "++" derive_var_joined_exist_flag( myd, dataset_add = myd, by_vars = exprs(subj), order = exprs(day), new_var = flag, join_vars = exprs(val), join_type = "after", first_cond_upper = val.join == "++", filter_join = val == "0" & all(val.join %in% c("+", "++")) )
library(tibble) # flag observations with a duration longer than 30 and # at, after, or up to 7 days before a COVID AE (ACOVFL == "Y") adae <- tribble( ~USUBJID, ~ADY, ~ACOVFL, ~ADURN, "1", 10, "N", 1, "1", 21, "N", 50, "1", 23, "Y", 14, "1", 32, "N", 31, "1", 42, "N", 20, "2", 11, "Y", 13, "2", 23, "N", 2, "3", 13, "Y", 12, "4", 14, "N", 32, "4", 21, "N", 41 ) derive_var_joined_exist_flag( adae, dataset_add = adae, new_var = ALCOVFL, by_vars = exprs(USUBJID), join_vars = exprs(ACOVFL, ADY), join_type = "all", order = exprs(ADY), filter_join = ADURN > 30 & ACOVFL.join == "Y" & ADY >= ADY.join - 7 ) # flag observations with AVALC == "Y" and AVALC == "Y" at one subsequent visit data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "Y", "1", 2, "N", "1", 3, "Y", "1", 4, "N", "2", 1, "Y", "2", 2, "N", "3", 1, "Y", "4", 1, "N", "4", 2, "N", ) derive_var_joined_exist_flag( data, dataset_add = data, by_vars = exprs(USUBJID), new_var = CONFFL, join_vars = exprs(AVALC, AVISITN), join_type = "after", order = exprs(AVISITN), filter_join = AVALC == "Y" & AVALC.join == "Y" & AVISITN < AVISITN.join ) # select observations with AVALC == "CR", AVALC == "CR" at a subsequent visit, # only "CR" or "NE" in between, and at most one "NE" in between data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "PR", "1", 2, "CR", "1", 3, "NE", "1", 4, "CR", "1", 5, "NE", "2", 1, "CR", "2", 2, "PR", "2", 3, "CR", "3", 1, "CR", "4", 1, "CR", "4", 2, "NE", "4", 3, "NE", "4", 4, "CR", "4", 5, "PR" ) derive_var_joined_exist_flag( data, dataset_add = data, by_vars = exprs(USUBJID), join_vars = exprs(AVALC), join_type = "after", order = exprs(AVISITN), new_var = CONFFL, first_cond_upper = AVALC.join == "CR", filter_join = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1 ) # flag observations with AVALC == "PR", AVALC == "CR" or AVALC == "PR" # at a subsequent visit at least 20 days later, only "CR", "PR", or "NE" # in between, at most one "NE" in between, and "CR" is not followed by "PR" data <- tribble( ~USUBJID, ~ADY, ~AVALC, "1", 6, "PR", "1", 12, "CR", "1", 24, "NE", "1", 32, "CR", "1", 48, "PR", "2", 3, "PR", "2", 21, "CR", "2", 33, "PR", "3", 11, "PR", "4", 7, "PR", "4", 12, "NE", "4", 24, "NE", "4", 32, "PR", "4", 55, "PR" ) derive_var_joined_exist_flag( data, dataset_add = data, by_vars = exprs(USUBJID), join_vars = exprs(AVALC, ADY), join_type = "after", order = exprs(ADY), new_var = CONFFL, first_cond_upper = AVALC.join %in% c("CR", "PR") & ADY.join - ADY >= 20, filter_join = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1 & ( min_cond(var = ADY.join, cond = AVALC.join == "CR") > max_cond(var = ADY.join, cond = AVALC.join == "PR") | count_vals(var = AVALC.join, val = "CR") == 0 ) ) # flag observations with CRIT1FL == "Y" at two consecutive visits or at the last visit data <- tribble( ~USUBJID, ~AVISITN, ~CRIT1FL, "1", 1, "Y", "1", 2, "N", "1", 3, "Y", "1", 5, "N", "2", 1, "Y", "2", 3, "Y", "2", 5, "N", "3", 1, "Y", "4", 1, "Y", "4", 2, "N", ) derive_var_joined_exist_flag( data, dataset_add = data, by_vars = exprs(USUBJID), new_var = CONFFL, tmp_obs_nr_var = tmp_obs_nr, join_vars = exprs(CRIT1FL), join_type = "all", order = exprs(AVISITN), filter_join = CRIT1FL == "Y" & CRIT1FL.join == "Y" & (tmp_obs_nr + 1 == tmp_obs_nr.join | tmp_obs_nr == max(tmp_obs_nr.join)) ) # first_cond_lower and first_cond_upper argument myd <- tribble( ~subj, ~day, ~val, "1", 1, "++", "1", 2, "-", "1", 3, "0", "1", 4, "+", "1", 5, "++", "1", 6, "-", "2", 1, "-", "2", 2, "++", "2", 3, "+", "2", 4, "0", "2", 5, "-", "2", 6, "++" ) # flag "0" where all results from the first "++" before the "0" up to the "0" # (excluding the "0") are "+" or "++" derive_var_joined_exist_flag( myd, dataset_add = myd, by_vars = exprs(subj), order = exprs(day), new_var = flag, join_vars = exprs(val), join_type = "before", first_cond_lower = val.join == "++", filter_join = val == "0" & all(val.join %in% c("+", "++")) ) # flag "0" where all results from the "0" (excluding the "0") up to the first # "++" after the "0" are "+" or "++" derive_var_joined_exist_flag( myd, dataset_add = myd, by_vars = exprs(subj), order = exprs(day), new_var = flag, join_vars = exprs(val), join_type = "after", first_cond_upper = val.join == "++", filter_join = val == "0" & all(val.join %in% c("+", "++")) )
Adds a flag variable to the input dataset which indicates if
there exists at least one observation in one of the source datasets
fulfilling a certain condition. For example, if a dose adjustment flag
should be added to ADEX
but the dose adjustment information is collected
in different datasets, e.g., EX
, EC
, and FA
.
derive_var_merged_ef_msrc( dataset, by_vars, flag_events, source_datasets, new_var, true_value = "Y", false_value = NA_character_, missing_value = NA_character_ )
derive_var_merged_ef_msrc( dataset, by_vars, flag_events, source_datasets, new_var, true_value = "Y", false_value = NA_character_, missing_value = NA_character_ )
dataset |
Input dataset The variables specified by the |
by_vars |
Grouping variables Permitted Values: list of variables created by |
flag_events |
Flag events A list of |
source_datasets |
Source datasets A named list of datasets is expected. The |
new_var |
New variable The specified variable is added to the input dataset. |
true_value |
True value The new variable ( The values of |
false_value |
False value The new variable ( The values of |
missing_value |
Values used for missing information The new variable is set to the specified value for all by groups without
observations in any of the sources ( The values of |
For each flag_event()
object specified for flag_events
: The
condition (condition
) is evaluated in the dataset referenced by
dataset_name
. If the by_vars
field is specified the dataset is grouped
by the specified variables for evaluating the condition. If named elements
are used in by_vars
like by_vars = exprs(USUBJID, EXLNKID = ECLNKID)
,
the variables are renamed after the evaluation. If the by_vars
element is
not specified, the observations are grouped by the variables specified for
the by_vars
argument.
The new variable (new_var
) is added to the input dataset and set to
the true value (true_value
) if for the by group at least one condition
evaluates to TRUE
in one of the sources. It is set to the false value
(false_value
) if for the by group at least one observation exists and for
all observations the condition evaluates to FALSE
or NA
. Otherwise, it
is set to the missing value (missing_value
).
The output dataset contains all observations and variables of the
input dataset and additionally the variable specified for new_var
.
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_extreme_flag()
,
derive_var_joined_exist_flag()
,
derive_var_merged_exist_flag()
,
derive_var_merged_summary()
,
derive_var_obs_number()
,
derive_var_relative_flag()
,
derive_vars_cat()
,
derive_vars_computed()
,
derive_vars_joined()
,
derive_vars_merged()
,
derive_vars_merged_lookup()
,
derive_vars_transposed()
library(dplyr) # Derive a flag indicating anti-cancer treatment based on CM and PR adsl <- tribble( ~USUBJID, "1", "2", "3", "4" ) cm <- tribble( ~USUBJID, ~CMCAT, ~CMSEQ, "1", "ANTI-CANCER", 1, "1", "GENERAL", 2, "2", "GENERAL", 1, "3", "ANTI-CANCER", 1 ) # Assuming all records in PR indicate cancer treatment pr <- tibble::tribble( ~USUBJID, ~PRSEQ, "2", 1, "3", 1 ) derive_var_merged_ef_msrc( adsl, by_vars = exprs(USUBJID), flag_events = list( flag_event( dataset_name = "cm", condition = CMCAT == "ANTI-CANCER" ), flag_event( dataset_name = "pr" ) ), source_datasets = list(cm = cm, pr = pr), new_var = CANCTRFL ) # Using different by variables depending on the source # Add a dose adjustment flag to ADEX based on ADEX, EC, and FA adex <- tribble( ~USUBJID, ~EXLNKID, ~EXADJ, "1", "1", "AE", "1", "2", NA_character_, "1", "3", NA_character_, "2", "1", NA_character_, "3", "1", NA_character_ ) ec <- tribble( ~USUBJID, ~ECLNKID, ~ECADJ, "1", "3", "AE", "3", "1", NA_character_ ) fa <- tribble( ~USUBJID, ~FALNKID, ~FATESTCD, ~FAOBJ, ~FASTRESC, "3", "1", "OCCUR", "DOSE ADJUSTMENT", "Y" ) derive_var_merged_ef_msrc( adex, by_vars = exprs(USUBJID, EXLNKID), flag_events = list( flag_event( dataset_name = "ex", condition = !is.na(EXADJ) ), flag_event( dataset_name = "ec", condition = !is.na(ECADJ), by_vars = exprs(USUBJID, EXLNKID = ECLNKID) ), flag_event( dataset_name = "fa", condition = FATESTCD == "OCCUR" & FAOBJ == "DOSE ADJUSTMENT" & FASTRESC == "Y", by_vars = exprs(USUBJID, EXLNKID = FALNKID) ) ), source_datasets = list(ex = adex, ec = ec, fa = fa), new_var = DOSADJFL )
library(dplyr) # Derive a flag indicating anti-cancer treatment based on CM and PR adsl <- tribble( ~USUBJID, "1", "2", "3", "4" ) cm <- tribble( ~USUBJID, ~CMCAT, ~CMSEQ, "1", "ANTI-CANCER", 1, "1", "GENERAL", 2, "2", "GENERAL", 1, "3", "ANTI-CANCER", 1 ) # Assuming all records in PR indicate cancer treatment pr <- tibble::tribble( ~USUBJID, ~PRSEQ, "2", 1, "3", 1 ) derive_var_merged_ef_msrc( adsl, by_vars = exprs(USUBJID), flag_events = list( flag_event( dataset_name = "cm", condition = CMCAT == "ANTI-CANCER" ), flag_event( dataset_name = "pr" ) ), source_datasets = list(cm = cm, pr = pr), new_var = CANCTRFL ) # Using different by variables depending on the source # Add a dose adjustment flag to ADEX based on ADEX, EC, and FA adex <- tribble( ~USUBJID, ~EXLNKID, ~EXADJ, "1", "1", "AE", "1", "2", NA_character_, "1", "3", NA_character_, "2", "1", NA_character_, "3", "1", NA_character_ ) ec <- tribble( ~USUBJID, ~ECLNKID, ~ECADJ, "1", "3", "AE", "3", "1", NA_character_ ) fa <- tribble( ~USUBJID, ~FALNKID, ~FATESTCD, ~FAOBJ, ~FASTRESC, "3", "1", "OCCUR", "DOSE ADJUSTMENT", "Y" ) derive_var_merged_ef_msrc( adex, by_vars = exprs(USUBJID, EXLNKID), flag_events = list( flag_event( dataset_name = "ex", condition = !is.na(EXADJ) ), flag_event( dataset_name = "ec", condition = !is.na(ECADJ), by_vars = exprs(USUBJID, EXLNKID = ECLNKID) ), flag_event( dataset_name = "fa", condition = FATESTCD == "OCCUR" & FAOBJ == "DOSE ADJUSTMENT" & FASTRESC == "Y", by_vars = exprs(USUBJID, EXLNKID = FALNKID) ) ), source_datasets = list(ex = adex, ec = ec, fa = fa), new_var = DOSADJFL )
Adds a flag variable to the input dataset which indicates if there exists at least one observation in another dataset fulfilling a certain condition.
Note: This is a wrapper function for the more generic derive_vars_merged()
.
derive_var_merged_exist_flag( dataset, dataset_add, by_vars, new_var, condition, true_value = "Y", false_value = NA_character_, missing_value = NA_character_, filter_add = NULL )
derive_var_merged_exist_flag( dataset, dataset_add, by_vars, new_var, condition, true_value = "Y", false_value = NA_character_, missing_value = NA_character_, filter_add = NULL )
dataset |
Input dataset The variables specified by the |
dataset_add |
Additional dataset The variables specified by the |
by_vars |
Grouping variables Permitted Values: list of variables created by |
new_var |
New variable The specified variable is added to the input dataset. |
condition |
Condition The condition is evaluated at the additional dataset ( |
true_value |
True value |
false_value |
False value |
missing_value |
Values used for missing information The new variable is set to the specified value for all by groups without observations in the additional dataset. Permitted Value: A character scalar |
filter_add |
Filter for additional data Only observations fulfilling the specified condition are taken into account for flagging. If the argument is not specified, all observations are considered. Permitted Values: a condition |
The additional dataset is restricted to the observations matching the
filter_add
condition.
The new variable is added to the input dataset and set to the true value
(true_value
) if for the by group at least one observation exists in the
(restricted) additional dataset where the condition evaluates to TRUE
. It
is set to the false value (false_value
) if for the by group at least one
observation exists and for all observations the condition evaluates to
FALSE
or NA
. Otherwise, it is set to the missing value
(missing_value
).
The output dataset contains all observations and variables of the
input dataset and additionally the variable specified for new_var
derived
from the additional dataset (dataset_add
).
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_extreme_flag()
,
derive_var_joined_exist_flag()
,
derive_var_merged_ef_msrc()
,
derive_var_merged_summary()
,
derive_var_obs_number()
,
derive_var_relative_flag()
,
derive_vars_cat()
,
derive_vars_computed()
,
derive_vars_joined()
,
derive_vars_merged()
,
derive_vars_merged_lookup()
,
derive_vars_transposed()
library(dplyr, warn.conflicts = FALSE) dm <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "DM", "01-1028", 71, "YEARS", "PILOT01", "DM", "04-1127", 84, "YEARS", "PILOT01", "DM", "06-1049", 60, "YEARS" ) ae <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AETERM, ~AEREL, "PILOT01", "AE", "01-1028", "ERYTHEMA", "POSSIBLE", "PILOT01", "AE", "01-1028", "PRURITUS", "PROBABLE", "PILOT01", "AE", "06-1049", "SYNCOPE", "POSSIBLE", "PILOT01", "AE", "06-1049", "SYNCOPE", "PROBABLE" ) derive_var_merged_exist_flag( dm, dataset_add = ae, by_vars = exprs(STUDYID, USUBJID), new_var = AERELFL, condition = AEREL == "PROBABLE" ) %>% select(STUDYID, USUBJID, AGE, AGEU, AERELFL) vs <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~VISIT, ~VSTESTCD, ~VSSTRESN, ~VSBLFL, "PILOT01", "VS", "01-1028", "SCREENING", "HEIGHT", 177.8, NA, "PILOT01", "VS", "01-1028", "SCREENING", "WEIGHT", 98.88, NA, "PILOT01", "VS", "01-1028", "BASELINE", "WEIGHT", 99.34, "Y", "PILOT01", "VS", "01-1028", "WEEK 4", "WEIGHT", 98.88, NA, "PILOT01", "VS", "04-1127", "SCREENING", "HEIGHT", 165.1, NA, "PILOT01", "VS", "04-1127", "SCREENING", "WEIGHT", 42.87, NA, "PILOT01", "VS", "04-1127", "BASELINE", "WEIGHT", 41.05, "Y", "PILOT01", "VS", "04-1127", "WEEK 4", "WEIGHT", 41.73, NA, "PILOT01", "VS", "06-1049", "SCREENING", "HEIGHT", 167.64, NA, "PILOT01", "VS", "06-1049", "SCREENING", "WEIGHT", 57.61, NA, "PILOT01", "VS", "06-1049", "BASELINE", "WEIGHT", 57.83, "Y", "PILOT01", "VS", "06-1049", "WEEK 4", "WEIGHT", 58.97, NA ) derive_var_merged_exist_flag( dm, dataset_add = vs, by_vars = exprs(STUDYID, USUBJID), filter_add = VSTESTCD == "WEIGHT" & VSBLFL == "Y", new_var = WTBLHIFL, condition = VSSTRESN > 90, false_value = "N", missing_value = "M" ) %>% select(STUDYID, USUBJID, AGE, AGEU, WTBLHIFL)
library(dplyr, warn.conflicts = FALSE) dm <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "DM", "01-1028", 71, "YEARS", "PILOT01", "DM", "04-1127", 84, "YEARS", "PILOT01", "DM", "06-1049", 60, "YEARS" ) ae <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AETERM, ~AEREL, "PILOT01", "AE", "01-1028", "ERYTHEMA", "POSSIBLE", "PILOT01", "AE", "01-1028", "PRURITUS", "PROBABLE", "PILOT01", "AE", "06-1049", "SYNCOPE", "POSSIBLE", "PILOT01", "AE", "06-1049", "SYNCOPE", "PROBABLE" ) derive_var_merged_exist_flag( dm, dataset_add = ae, by_vars = exprs(STUDYID, USUBJID), new_var = AERELFL, condition = AEREL == "PROBABLE" ) %>% select(STUDYID, USUBJID, AGE, AGEU, AERELFL) vs <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~VISIT, ~VSTESTCD, ~VSSTRESN, ~VSBLFL, "PILOT01", "VS", "01-1028", "SCREENING", "HEIGHT", 177.8, NA, "PILOT01", "VS", "01-1028", "SCREENING", "WEIGHT", 98.88, NA, "PILOT01", "VS", "01-1028", "BASELINE", "WEIGHT", 99.34, "Y", "PILOT01", "VS", "01-1028", "WEEK 4", "WEIGHT", 98.88, NA, "PILOT01", "VS", "04-1127", "SCREENING", "HEIGHT", 165.1, NA, "PILOT01", "VS", "04-1127", "SCREENING", "WEIGHT", 42.87, NA, "PILOT01", "VS", "04-1127", "BASELINE", "WEIGHT", 41.05, "Y", "PILOT01", "VS", "04-1127", "WEEK 4", "WEIGHT", 41.73, NA, "PILOT01", "VS", "06-1049", "SCREENING", "HEIGHT", 167.64, NA, "PILOT01", "VS", "06-1049", "SCREENING", "WEIGHT", 57.61, NA, "PILOT01", "VS", "06-1049", "BASELINE", "WEIGHT", 57.83, "Y", "PILOT01", "VS", "06-1049", "WEEK 4", "WEIGHT", 58.97, NA ) derive_var_merged_exist_flag( dm, dataset_add = vs, by_vars = exprs(STUDYID, USUBJID), filter_add = VSTESTCD == "WEIGHT" & VSBLFL == "Y", new_var = WTBLHIFL, condition = VSSTRESN > 90, false_value = "N", missing_value = "M" ) %>% select(STUDYID, USUBJID, AGE, AGEU, WTBLHIFL)
Merge a summary variable from a dataset to the input dataset.
derive_var_merged_summary( dataset, dataset_add, by_vars, new_vars = NULL, filter_add = NULL, missing_values = NULL )
derive_var_merged_summary( dataset, dataset_add, by_vars, new_vars = NULL, filter_add = NULL, missing_values = NULL )
dataset |
Input dataset The variables specified by the |
dataset_add |
Additional dataset The variables specified by the |
by_vars |
Grouping variables The expressions on the left hand sides of Permitted Values: list of variables created by |
new_vars |
New variables to add The specified variables are added to the input dataset. A named list of expressions is expected:
For example: new_vars = exprs( DOSESUM = sum(AVAL), DOSEMEAN = mean(AVAL) ) |
filter_add |
Filter for additional dataset ( Only observations fulfilling the specified condition are taken into account for summarizing. If the argument is not specified, all observations are considered. Permitted Values: a condition |
missing_values |
Values for non-matching observations For observations of the input dataset ( Permitted Values: named list of expressions, e.g.,
|
The records from the additional dataset (dataset_add
) are restricted
to those matching the filter_add
condition.
The new variables (new_vars
) are created for each by group (by_vars
)
in the additional dataset (dataset_add
) by calling summarize()
. I.e.,
all observations of a by group are summarized to a single observation.
The new variables are merged to the input dataset. For observations
without a matching observation in the additional dataset the new variables
are set to NA
. Observations in the additional dataset which have no
matching observation in the input dataset are ignored.
The output dataset contains all observations and variables of the
input dataset and additionally the variables specified for new_vars
.
derive_summary_records()
, get_summary_records()
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_extreme_flag()
,
derive_var_joined_exist_flag()
,
derive_var_merged_ef_msrc()
,
derive_var_merged_exist_flag()
,
derive_var_obs_number()
,
derive_var_relative_flag()
,
derive_vars_cat()
,
derive_vars_computed()
,
derive_vars_joined()
,
derive_vars_merged()
,
derive_vars_merged_lookup()
,
derive_vars_transposed()
library(tibble) # Add a variable for the mean of AVAL within each visit adbds <- tribble( ~USUBJID, ~AVISIT, ~ASEQ, ~AVAL, "1", "WEEK 1", 1, 10, "1", "WEEK 1", 2, NA, "1", "WEEK 2", 3, NA, "1", "WEEK 3", 4, 42, "1", "WEEK 4", 5, 12, "1", "WEEK 4", 6, 12, "1", "WEEK 4", 7, 15, "2", "WEEK 1", 1, 21, "2", "WEEK 4", 2, 22 ) derive_var_merged_summary( adbds, dataset_add = adbds, by_vars = exprs(USUBJID, AVISIT), new_vars = exprs( MEANVIS = mean(AVAL, na.rm = TRUE), MAXVIS = max(AVAL, na.rm = TRUE) ) ) # Add a variable listing the lesion ids at baseline adsl <- tribble( ~USUBJID, "1", "2", "3" ) adtr <- tribble( ~USUBJID, ~AVISIT, ~LESIONID, "1", "BASELINE", "INV-T1", "1", "BASELINE", "INV-T2", "1", "BASELINE", "INV-T3", "1", "BASELINE", "INV-T4", "1", "WEEK 1", "INV-T1", "1", "WEEK 1", "INV-T2", "1", "WEEK 1", "INV-T4", "2", "BASELINE", "INV-T1", "2", "BASELINE", "INV-T2", "2", "BASELINE", "INV-T3", "2", "WEEK 1", "INV-T1", "2", "WEEK 1", "INV-N1" ) derive_var_merged_summary( adsl, dataset_add = adtr, by_vars = exprs(USUBJID), filter_add = AVISIT == "BASELINE", new_vars = exprs(LESIONSBL = paste(LESIONID, collapse = ", ")) )
library(tibble) # Add a variable for the mean of AVAL within each visit adbds <- tribble( ~USUBJID, ~AVISIT, ~ASEQ, ~AVAL, "1", "WEEK 1", 1, 10, "1", "WEEK 1", 2, NA, "1", "WEEK 2", 3, NA, "1", "WEEK 3", 4, 42, "1", "WEEK 4", 5, 12, "1", "WEEK 4", 6, 12, "1", "WEEK 4", 7, 15, "2", "WEEK 1", 1, 21, "2", "WEEK 4", 2, 22 ) derive_var_merged_summary( adbds, dataset_add = adbds, by_vars = exprs(USUBJID, AVISIT), new_vars = exprs( MEANVIS = mean(AVAL, na.rm = TRUE), MAXVIS = max(AVAL, na.rm = TRUE) ) ) # Add a variable listing the lesion ids at baseline adsl <- tribble( ~USUBJID, "1", "2", "3" ) adtr <- tribble( ~USUBJID, ~AVISIT, ~LESIONID, "1", "BASELINE", "INV-T1", "1", "BASELINE", "INV-T2", "1", "BASELINE", "INV-T3", "1", "BASELINE", "INV-T4", "1", "WEEK 1", "INV-T1", "1", "WEEK 1", "INV-T2", "1", "WEEK 1", "INV-T4", "2", "BASELINE", "INV-T1", "2", "BASELINE", "INV-T2", "2", "BASELINE", "INV-T3", "2", "WEEK 1", "INV-T1", "2", "WEEK 1", "INV-N1" ) derive_var_merged_summary( adsl, dataset_add = adtr, by_vars = exprs(USUBJID), filter_add = AVISIT == "BASELINE", new_vars = exprs(LESIONSBL = paste(LESIONID, collapse = ", ")) )
Adds a variable numbering the observations within each by group
derive_var_obs_number( dataset, by_vars = NULL, order = NULL, new_var = ASEQ, check_type = "none" )
derive_var_obs_number( dataset, by_vars = NULL, order = NULL, new_var = ASEQ, check_type = "none" )
dataset |
Input dataset The variables specified by the |
by_vars |
Grouping variables Permitted Values: list of variables created by |
order |
Sort order Within each by group the observations are ordered by the specified order. For handling of Permitted Values: list of variables or functions of variables |
new_var |
Name of variable to create The new variable is set to the observation number for each by group. The numbering starts with 1. Default: |
check_type |
Check uniqueness? If Default: Permitted Values: |
For each group (with respect to the variables specified for the
by_vars
parameter) the first or last observation (with respect to the
order specified for the order
parameter and the mode specified for the
mode
parameter) is included in the output dataset.
A dataset containing all observations and variables of the input
dataset and additionally the variable specified by the new_var
parameter.
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_extreme_flag()
,
derive_var_joined_exist_flag()
,
derive_var_merged_ef_msrc()
,
derive_var_merged_exist_flag()
,
derive_var_merged_summary()
,
derive_var_relative_flag()
,
derive_vars_cat()
,
derive_vars_computed()
,
derive_vars_joined()
,
derive_vars_merged()
,
derive_vars_merged_lookup()
,
derive_vars_transposed()
library(dplyr, warn.conflicts = FALSE) vs <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~VSTESTCD, ~VISITNUM, ~VSTPTNUM, "PILOT01", "VS", "01-703-1182", "DIABP", 3, 815, "PILOT01", "VS", "01-703-1182", "DIABP", 3, 816, "PILOT01", "VS", "01-703-1182", "DIABP", 4, 815, "PILOT01", "VS", "01-703-1182", "DIABP", 4, 816, "PILOT01", "VS", "01-703-1182", "PULSE", 3, 815, "PILOT01", "VS", "01-703-1182", "PULSE", 3, 816, "PILOT01", "VS", "01-703-1182", "PULSE", 4, 815, "PILOT01", "VS", "01-703-1182", "PULSE", 4, 816, "PILOT01", "VS", "01-703-1182", "SYSBP", 3, 815, "PILOT01", "VS", "01-703-1182", "SYSBP", 3, 816, "PILOT01", "VS", "01-703-1182", "SYSBP", 4, 815, "PILOT01", "VS", "01-703-1182", "SYSBP", 4, 816, "PILOT01", "VS", "01-716-1229", "DIABP", 3, 815, "PILOT01", "VS", "01-716-1229", "DIABP", 3, 816, "PILOT01", "VS", "01-716-1229", "DIABP", 4, 815, "PILOT01", "VS", "01-716-1229", "DIABP", 4, 816, "PILOT01", "VS", "01-716-1229", "PULSE", 3, 815, "PILOT01", "VS", "01-716-1229", "PULSE", 3, 816, "PILOT01", "VS", "01-716-1229", "PULSE", 4, 815, "PILOT01", "VS", "01-716-1229", "PULSE", 4, 816, "PILOT01", "VS", "01-716-1229", "SYSBP", 3, 815, "PILOT01", "VS", "01-716-1229", "SYSBP", 3, 816, "PILOT01", "VS", "01-716-1229", "SYSBP", 4, 815, "PILOT01", "VS", "01-716-1229", "SYSBP", 4, 816 ) vs %>% derive_var_obs_number( by_vars = exprs(USUBJID, VSTESTCD), order = exprs(VISITNUM, desc(VSTPTNUM)) )
library(dplyr, warn.conflicts = FALSE) vs <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~VSTESTCD, ~VISITNUM, ~VSTPTNUM, "PILOT01", "VS", "01-703-1182", "DIABP", 3, 815, "PILOT01", "VS", "01-703-1182", "DIABP", 3, 816, "PILOT01", "VS", "01-703-1182", "DIABP", 4, 815, "PILOT01", "VS", "01-703-1182", "DIABP", 4, 816, "PILOT01", "VS", "01-703-1182", "PULSE", 3, 815, "PILOT01", "VS", "01-703-1182", "PULSE", 3, 816, "PILOT01", "VS", "01-703-1182", "PULSE", 4, 815, "PILOT01", "VS", "01-703-1182", "PULSE", 4, 816, "PILOT01", "VS", "01-703-1182", "SYSBP", 3, 815, "PILOT01", "VS", "01-703-1182", "SYSBP", 3, 816, "PILOT01", "VS", "01-703-1182", "SYSBP", 4, 815, "PILOT01", "VS", "01-703-1182", "SYSBP", 4, 816, "PILOT01", "VS", "01-716-1229", "DIABP", 3, 815, "PILOT01", "VS", "01-716-1229", "DIABP", 3, 816, "PILOT01", "VS", "01-716-1229", "DIABP", 4, 815, "PILOT01", "VS", "01-716-1229", "DIABP", 4, 816, "PILOT01", "VS", "01-716-1229", "PULSE", 3, 815, "PILOT01", "VS", "01-716-1229", "PULSE", 3, 816, "PILOT01", "VS", "01-716-1229", "PULSE", 4, 815, "PILOT01", "VS", "01-716-1229", "PULSE", 4, 816, "PILOT01", "VS", "01-716-1229", "SYSBP", 3, 815, "PILOT01", "VS", "01-716-1229", "SYSBP", 3, 816, "PILOT01", "VS", "01-716-1229", "SYSBP", 4, 815, "PILOT01", "VS", "01-716-1229", "SYSBP", 4, 816 ) vs %>% derive_var_obs_number( by_vars = exprs(USUBJID, VSTESTCD), order = exprs(VISITNUM, desc(VSTPTNUM)) )
Derive on-treatment flag (ONTRTFL
) in an ADaM dataset with a single
assessment date (e.g ADT
) or event start and end dates (e.g.
ASTDT
/AENDT
).
derive_var_ontrtfl( dataset, new_var = ONTRTFL, start_date, end_date = NULL, ref_start_date, ref_end_date = NULL, ref_end_window = 0, ignore_time_for_ref_end_date = TRUE, filter_pre_timepoint = NULL, span_period = FALSE )
derive_var_ontrtfl( dataset, new_var = ONTRTFL, start_date, end_date = NULL, ref_start_date, ref_end_date = NULL, ref_end_window = 0, ignore_time_for_ref_end_date = TRUE, filter_pre_timepoint = NULL, span_period = FALSE )
dataset |
Input dataset Required columns are |
new_var |
On-treatment flag variable name to be created. Default is |
start_date |
The start date (e.g. Refer to |
end_date |
The end date of assessment/event (e.g. Refer to Optional; Default is null. If the used and date value is missing on an
observation, it is assumed the medication is ongoing and |
ref_start_date |
The lower bound of the on-treatment period Required; A date or date-time object column is expected. Refer to |
ref_end_date |
The upper bound of the on-treatment period A date or date-time object column is expected. Refer to Optional; This can be null and everything after |
ref_end_window |
A window to add to the upper bound |
ignore_time_for_ref_end_date |
If the argument is set to Permitted Values: |
filter_pre_timepoint |
An expression to filter observations as not
on-treatment when |
span_period |
A logical scalar. If |
On-Treatment is calculated by determining whether the assessment
date or start/stop dates fall between 2 dates. The following logic is used
to assign on-treatment = "Y"
:
start_date
is missing and ref_start_date
is non-missing
No timepoint filter is provided (filter_pre_timepoint
) and both
start_date
and ref_start_date
are non-missing and start_date
=
ref_start_date
A timepoint is provided (filter_pre_timepoint
) and both start_date
and ref_start_date
are non-missing and start_date = ref_start_date
and
the filter provided in filter_pre_timepoint
is not true.
ref_end_date
is not provided and ref_start_date < start_date
ref_end_date
is provided and ref_start_date < start_date
<=
ref_end_date + ref_end_window
.
If the end_date
is provided and the end_date
< ref_start_date then the
ONTRTFL
is set to NULL
.This would be applicable to cases where the
start_date
is missing and ONTRTFL
has been assigned as "Y"
above.
If the span_period
is TRUE
, this allows the user to assign
ONTRTFL
as "Y"
to cases where the record started prior to the
ref_start_date
and was ongoing or ended after the ref_start_date
.
Any date imputations needed should be done prior to calling this function.
The input dataset with an additional column named ONTRTFL
with a
value of "Y"
or NA
BDS-Findings Functions that returns variable appended to dataset:
derive_basetype_records()
,
derive_var_analysis_ratio()
,
derive_var_anrind()
,
derive_var_atoxgr()
,
derive_var_atoxgr_dir()
,
derive_var_base()
,
derive_var_chg()
,
derive_var_pchg()
,
derive_var_shift()
,
derive_vars_crit_flag()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate, warn.conflicts = FALSE) advs <- tribble( ~USUBJID, ~ADT, ~TRTSDT, ~TRTEDT, "P01", ymd("2020-02-24"), ymd("2020-01-01"), ymd("2020-03-01"), "P02", ymd("2020-01-01"), ymd("2020-01-01"), ymd("2020-03-01"), "P03", ymd("2019-12-31"), ymd("2020-01-01"), ymd("2020-03-01") ) derive_var_ontrtfl( advs, start_date = ADT, ref_start_date = TRTSDT, ref_end_date = TRTEDT ) advs <- tribble( ~USUBJID, ~ADT, ~TRTSDT, ~TRTEDT, "P01", ymd("2020-07-01"), ymd("2020-01-01"), ymd("2020-03-01"), "P02", ymd("2020-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), "P03", ymd("2020-03-15"), ymd("2020-01-01"), ymd("2020-03-01") ) derive_var_ontrtfl( advs, start_date = ADT, ref_start_date = TRTSDT, ref_end_date = TRTEDT, ref_end_window = 60 ) advs <- tribble( ~USUBJID, ~ADTM, ~TRTSDTM, ~TRTEDTM, "P01", ymd_hm("2020-01-02T12:00"), ymd_hm("2020-01-01T12:00"), ymd_hm("2020-03-01T12:00"), "P02", ymd("2020-01-01"), ymd_hm("2020-01-01T12:00"), ymd_hm("2020-03-01T12:00"), "P03", ymd("2019-12-31"), ymd_hm("2020-01-01T12:00"), ymd_hm("2020-03-01T12:00"), ) %>% mutate(TPT = c(NA, "PRE", NA)) derive_var_ontrtfl( advs, start_date = ADTM, ref_start_date = TRTSDTM, ref_end_date = TRTEDTM, filter_pre_timepoint = TPT == "PRE" ) advs <- tribble( ~USUBJID, ~ASTDT, ~TRTSDT, ~TRTEDT, ~AENDT, "P01", ymd("2020-03-15"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-12-01"), "P02", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-03-15"), "P03", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), NA, ) derive_var_ontrtfl( advs, start_date = ASTDT, end_date = AENDT, ref_start_date = TRTSDT, ref_end_date = TRTEDT, ref_end_window = 60, span_period = TRUE ) advs <- tribble( ~USUBJID, ~ASTDT, ~AP01SDT, ~AP01EDT, ~AENDT, "P01", ymd("2020-03-15"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-12-01"), "P02", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-03-15"), "P03", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), NA, ) derive_var_ontrtfl( advs, new_var = ONTR01FL, start_date = ASTDT, end_date = AENDT, ref_start_date = AP01SDT, ref_end_date = AP01EDT, span_period = TRUE )
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate, warn.conflicts = FALSE) advs <- tribble( ~USUBJID, ~ADT, ~TRTSDT, ~TRTEDT, "P01", ymd("2020-02-24"), ymd("2020-01-01"), ymd("2020-03-01"), "P02", ymd("2020-01-01"), ymd("2020-01-01"), ymd("2020-03-01"), "P03", ymd("2019-12-31"), ymd("2020-01-01"), ymd("2020-03-01") ) derive_var_ontrtfl( advs, start_date = ADT, ref_start_date = TRTSDT, ref_end_date = TRTEDT ) advs <- tribble( ~USUBJID, ~ADT, ~TRTSDT, ~TRTEDT, "P01", ymd("2020-07-01"), ymd("2020-01-01"), ymd("2020-03-01"), "P02", ymd("2020-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), "P03", ymd("2020-03-15"), ymd("2020-01-01"), ymd("2020-03-01") ) derive_var_ontrtfl( advs, start_date = ADT, ref_start_date = TRTSDT, ref_end_date = TRTEDT, ref_end_window = 60 ) advs <- tribble( ~USUBJID, ~ADTM, ~TRTSDTM, ~TRTEDTM, "P01", ymd_hm("2020-01-02T12:00"), ymd_hm("2020-01-01T12:00"), ymd_hm("2020-03-01T12:00"), "P02", ymd("2020-01-01"), ymd_hm("2020-01-01T12:00"), ymd_hm("2020-03-01T12:00"), "P03", ymd("2019-12-31"), ymd_hm("2020-01-01T12:00"), ymd_hm("2020-03-01T12:00"), ) %>% mutate(TPT = c(NA, "PRE", NA)) derive_var_ontrtfl( advs, start_date = ADTM, ref_start_date = TRTSDTM, ref_end_date = TRTEDTM, filter_pre_timepoint = TPT == "PRE" ) advs <- tribble( ~USUBJID, ~ASTDT, ~TRTSDT, ~TRTEDT, ~AENDT, "P01", ymd("2020-03-15"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-12-01"), "P02", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-03-15"), "P03", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), NA, ) derive_var_ontrtfl( advs, start_date = ASTDT, end_date = AENDT, ref_start_date = TRTSDT, ref_end_date = TRTEDT, ref_end_window = 60, span_period = TRUE ) advs <- tribble( ~USUBJID, ~ASTDT, ~AP01SDT, ~AP01EDT, ~AENDT, "P01", ymd("2020-03-15"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-12-01"), "P02", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-03-15"), "P03", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), NA, ) derive_var_ontrtfl( advs, new_var = ONTR01FL, start_date = ASTDT, end_date = AENDT, ref_start_date = AP01SDT, ref_end_date = AP01EDT, span_period = TRUE )
Derive percent change from baseline (PCHG
) in a BDS dataset
derive_var_pchg(dataset)
derive_var_pchg(dataset)
dataset |
Input dataset
|
Percent change from baseline is calculated by dividing change from
baseline by the absolute value of the baseline value and
multiplying the result by 100
.
The input dataset with an additional column named PCHG
BDS-Findings Functions that returns variable appended to dataset:
derive_basetype_records()
,
derive_var_analysis_ratio()
,
derive_var_anrind()
,
derive_var_atoxgr()
,
derive_var_atoxgr_dir()
,
derive_var_base()
,
derive_var_chg()
,
derive_var_ontrtfl()
,
derive_var_shift()
,
derive_vars_crit_flag()
library(tibble) advs <- tribble( ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BASE, "P01", "WEIGHT", 80, "Y", 80, "P01", "WEIGHT", 80.8, "", 80, "P01", "WEIGHT", 81.4, "", 80, "P02", "WEIGHT", 75.3, "Y", 75.3, "P02", "WEIGHT", 76, "", 75.3 ) derive_var_pchg(advs)
library(tibble) advs <- tribble( ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BASE, "P01", "WEIGHT", 80, "Y", 80, "P01", "WEIGHT", 80.8, "", 80, "P01", "WEIGHT", 81.4, "", 80, "P02", "WEIGHT", 75.3, "Y", 75.3, "P02", "WEIGHT", 76, "", 75.3 ) derive_var_pchg(advs)
Flag all observations before or after the observation where a specified condition is fulfilled for each by group. For example, the function could be called to flag for each subject all observations before the first disease progression or to flag all AEs after a specific AE.
derive_var_relative_flag( dataset, by_vars, order, new_var, condition, mode, selection, inclusive, flag_no_ref_groups = TRUE, check_type = "warning" )
derive_var_relative_flag( dataset, by_vars, order, new_var, condition, mode, selection, inclusive, flag_no_ref_groups = TRUE, check_type = "warning" )
dataset |
Input dataset The variables specified by the |
by_vars |
Grouping variables Permitted Values: list of variables created by |
order |
Sort order Within each by group the observations are ordered by the specified order. For handling of Permitted Values: list of expressions created by |
new_var |
New variable The variable is added to the input dataset and set to |
condition |
Condition for Reference Observation The specified condition determines the reference observation. In the output
dataset all observations before or after ( |
mode |
Selection mode (first or last) If Permitted Values: |
selection |
Flag observations before or after the reference observation? Permitted Values: |
inclusive |
Flag the reference observation? Permitted Values: |
flag_no_ref_groups |
Should by groups without reference observation be flagged? Permitted Values: |
check_type |
Check uniqueness? If Permitted Values: |
For each by group (by_vars
argument) the observations before or
after (selection
argument) the observations where the condition
(condition
argument) is fulfilled the first or last time (order
argument and mode
argument) is flagged in the output dataset.
The input dataset with the new variable (new_var
) added
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_extreme_flag()
,
derive_var_joined_exist_flag()
,
derive_var_merged_ef_msrc()
,
derive_var_merged_exist_flag()
,
derive_var_merged_summary()
,
derive_var_obs_number()
,
derive_vars_cat()
,
derive_vars_computed()
,
derive_vars_joined()
,
derive_vars_merged()
,
derive_vars_merged_lookup()
,
derive_vars_transposed()
library(tibble) library(dplyr, warn.conflicts = FALSE) # Flag all AEs after the first COVID AE adae <- tribble( ~USUBJID, ~ASTDY, ~ACOVFL, ~AESEQ, "1", 2, NA, 1, "1", 5, "Y", 2, "1", 5, NA, 3, "1", 17, NA, 4, "1", 27, "Y", 5, "1", 32, NA, 6, "2", 8, NA, 1, "2", 11, NA, 2, ) derive_var_relative_flag( adae, by_vars = exprs(USUBJID), order = exprs(ASTDY, AESEQ), new_var = PSTCOVFL, condition = ACOVFL == "Y", mode = "first", selection = "after", inclusive = FALSE, flag_no_ref_groups = FALSE ) response <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 0, "PR", "1", 1, "CR", "1", 2, "CR", "1", 3, "SD", "1", 4, "NE", "2", 0, "SD", "2", 1, "PD", "2", 2, "PD", "3", 0, "SD", "4", 0, "SD", "4", 1, "PR", "4", 2, "PD", "4", 3, "SD", "4", 4, "PR" ) # Flag observations up to first PD for each patient response %>% derive_var_relative_flag( by_vars = exprs(USUBJID), order = exprs(AVISITN), new_var = ANL02FL, condition = AVALC == "PD", mode = "first", selection = "before", inclusive = TRUE ) # Flag observations up to first PD excluding baseline (AVISITN = 0) for each patient response %>% restrict_derivation( derivation = derive_var_relative_flag, args = params( by_vars = exprs(USUBJID), order = exprs(AVISITN), new_var = ANL02FL, condition = AVALC == "PD", mode = "first", selection = "before", inclusive = TRUE ), filter = AVISITN > 0 ) %>% arrange(USUBJID, AVISITN)
library(tibble) library(dplyr, warn.conflicts = FALSE) # Flag all AEs after the first COVID AE adae <- tribble( ~USUBJID, ~ASTDY, ~ACOVFL, ~AESEQ, "1", 2, NA, 1, "1", 5, "Y", 2, "1", 5, NA, 3, "1", 17, NA, 4, "1", 27, "Y", 5, "1", 32, NA, 6, "2", 8, NA, 1, "2", 11, NA, 2, ) derive_var_relative_flag( adae, by_vars = exprs(USUBJID), order = exprs(ASTDY, AESEQ), new_var = PSTCOVFL, condition = ACOVFL == "Y", mode = "first", selection = "after", inclusive = FALSE, flag_no_ref_groups = FALSE ) response <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 0, "PR", "1", 1, "CR", "1", 2, "CR", "1", 3, "SD", "1", 4, "NE", "2", 0, "SD", "2", 1, "PD", "2", 2, "PD", "3", 0, "SD", "4", 0, "SD", "4", 1, "PR", "4", 2, "PD", "4", 3, "SD", "4", 4, "PR" ) # Flag observations up to first PD for each patient response %>% derive_var_relative_flag( by_vars = exprs(USUBJID), order = exprs(AVISITN), new_var = ANL02FL, condition = AVALC == "PD", mode = "first", selection = "before", inclusive = TRUE ) # Flag observations up to first PD excluding baseline (AVISITN = 0) for each patient response %>% restrict_derivation( derivation = derive_var_relative_flag, args = params( by_vars = exprs(USUBJID), order = exprs(AVISITN), new_var = ANL02FL, condition = AVALC == "PD", mode = "first", selection = "before", inclusive = TRUE ), filter = AVISITN > 0 ) %>% arrange(USUBJID, AVISITN)
Derives a character shift variable containing concatenated shift in values based on user-defined pairing, e.g., shift from baseline to analysis value, shift from baseline grade to analysis grade, ...
derive_var_shift( dataset, new_var, from_var, to_var, missing_value = "NULL", sep_val = " to " )
derive_var_shift( dataset, new_var, from_var, to_var, missing_value = "NULL", sep_val = " to " )
dataset |
Input dataset The variables specified by the |
new_var |
Name of the character shift variable to create. |
from_var |
Variable containing value to shift from. |
to_var |
Variable containing value to shift to. |
missing_value |
Character string to replace missing values in Default: "NULL" |
sep_val |
Character string to concatenate values of Default: " to " |
new_var
is derived by concatenating the values of from_var
to values of to_var
(e.g. "NORMAL to HIGH"). When from_var
or to_var
has missing value, the
missing value is replaced by missing_value
(e.g. "NORMAL to NULL").
The input dataset with the character shift variable added
BDS-Findings Functions that returns variable appended to dataset:
derive_basetype_records()
,
derive_var_analysis_ratio()
,
derive_var_anrind()
,
derive_var_atoxgr()
,
derive_var_atoxgr_dir()
,
derive_var_base()
,
derive_var_chg()
,
derive_var_ontrtfl()
,
derive_var_pchg()
,
derive_vars_crit_flag()
library(tibble) data <- tribble( ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND, "P01", "ALB", 33, "Y", "LOW", "LOW", "P01", "ALB", 38, NA, "LOW", "NORMAL", "P01", "ALB", NA, NA, "LOW", NA, "P02", "ALB", 37, "Y", "NORMAL", "NORMAL", "P02", "ALB", 49, NA, "NORMAL", "HIGH", "P02", "SODIUM", 147, "Y", "HIGH", "HIGH" ) data %>% convert_blanks_to_na() %>% derive_var_shift( new_var = SHIFT1, from_var = BNRIND, to_var = ANRIND ) # or only populate post-baseline records data %>% convert_blanks_to_na() %>% restrict_derivation( derivation = derive_var_shift, args = params( new_var = SHIFT1, from_var = BNRIND, to_var = ANRIND ), filter = is.na(ABLFL) )
library(tibble) data <- tribble( ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND, "P01", "ALB", 33, "Y", "LOW", "LOW", "P01", "ALB", 38, NA, "LOW", "NORMAL", "P01", "ALB", NA, NA, "LOW", NA, "P02", "ALB", 37, "Y", "NORMAL", "NORMAL", "P02", "ALB", 49, NA, "NORMAL", "HIGH", "P02", "SODIUM", 147, "Y", "HIGH", "HIGH" ) data %>% convert_blanks_to_na() %>% derive_var_shift( new_var = SHIFT1, from_var = BNRIND, to_var = ANRIND ) # or only populate post-baseline records data %>% convert_blanks_to_na() %>% restrict_derivation( derivation = derive_var_shift, args = params( new_var = SHIFT1, from_var = BNRIND, to_var = ANRIND ), filter = is.na(ABLFL) )
Derives total treatment duration (days) (TRTDURD
).
Note: This is a wrapper function for the more generic derive_vars_duration()
.
derive_var_trtdurd(dataset, start_date = TRTSDT, end_date = TRTEDT)
derive_var_trtdurd(dataset, start_date = TRTSDT, end_date = TRTEDT)
dataset |
Input dataset The variables specified by the |
start_date |
The start date A date or date-time object is expected. Refer to Default: |
end_date |
The end date A date or date-time object is expected. Refer to Default: |
The total treatment duration is derived as the number of days from start to end date plus one.
The input dataset with TRTDURD
added
Date/Time Derivation Functions that returns variable appended to dataset:
derive_vars_dt()
,
derive_vars_dtm()
,
derive_vars_dtm_to_dt()
,
derive_vars_dtm_to_tm()
,
derive_vars_duration()
,
derive_vars_dy()
library(tibble) library(lubridate) data <- tribble( ~TRTSDT, ~TRTEDT, ymd("2020-01-01"), ymd("2020-02-24") ) derive_var_trtdurd(data)
library(tibble) library(lubridate) data <- tribble( ~TRTSDT, ~TRTEDT, ymd("2020-01-01"), ymd("2020-02-24") ) derive_var_trtdurd(data)
Derive treatment emergent analysis flag (e.g., TRTEMFL
).
derive_var_trtemfl( dataset, new_var = TRTEMFL, start_date = ASTDTM, end_date = AENDTM, trt_start_date = TRTSDTM, trt_end_date = NULL, end_window = NULL, ignore_time_for_trt_end = TRUE, initial_intensity = NULL, intensity = NULL, group_var = NULL, subject_keys = get_admiral_option("subject_keys") )
derive_var_trtemfl( dataset, new_var = TRTEMFL, start_date = ASTDTM, end_date = AENDTM, trt_start_date = TRTSDTM, trt_end_date = NULL, end_window = NULL, ignore_time_for_trt_end = TRUE, initial_intensity = NULL, intensity = NULL, group_var = NULL, subject_keys = get_admiral_option("subject_keys") )
dataset |
Input dataset The variables specified by |
new_var |
New variable |
start_date |
Event start date Permitted Values: A symbol referring to a date or datetime variable of the input dataset |
end_date |
Event end date Permitted Values: A symbol referring to a date or datetime variable of the input dataset |
trt_start_date |
Treatment start date Permitted Values: A symbol referring to a date or datetime variable of the input dataset |
trt_end_date |
Treatment end date Permitted Values: A symbol referring to a date or datetime variable of
the input dataset or |
end_window |
If the argument is specified (in 'days'), events starting more than the specified number of days after end of treatment, are not flagged. Permitted Values: A non-negative integer or |
ignore_time_for_trt_end |
If the argument is set to Permitted Values: |
initial_intensity |
Initial severity/intensity or toxicity
If this argument is specified and The values of the specified variable must be comparable with the usual
comparison operators. I.e., if the intensity is greater than the initial
intensity Permitted Values: A symbol referring to a variable of the input dataset
or |
intensity |
Severity/intensity or toxicity If the argument is specified, events which start before treatment start and end after treatment start (or are ongoing) and worsened (i.e., the intensity is greater than the initial intensity), are flagged. The values of the specified variable must be comparable with the usual
comparison operators. I.e., if the intensity is greater than the initial
intensity Permitted Values: A symbol referring to a variable of the input dataset
or |
group_var |
Grouping variable If the argument is specified, it assumes that AEs are recorded as one episode of AE with multiple lines using a grouping variable. Events starting during treatment or before treatment and worsening afterward are flagged. Once an AE record in a group is flagged, all subsequent records in the treatment window are flagged regardless of severity. Permitted Values: A symbol referring to a variable of the input dataset
or |
subject_keys |
Variables to uniquely identify a subject. A list of symbols created using |
For the derivation of the new variable the following cases are considered in this order. The first case which applies, defines the value of the variable.
not treated: If trt_start_date
is NA
, it is set to NA_character_
.
event before treatment: If end_date
is before trt_start_date
(and
end_date
is not NA
), it is set to NA_character_
.
no event date: If start_date
is NA
, it is set to "Y"
as in such
cases it is usually considered more conservative to assume the event was
treatment-emergent.
event started during treatment:
if end_window
is not specified:
if start_date
is on or after trt_start_date
, it is set to "Y"
,
if end_window
is specified:
if start_date
is on or after trt_start_date
and start_date
is on
or before trt_end_date
+ end_window
days, it is set to "Y"
,
event started before treatment and (possibly) worsened on treatment:
if initial_intensity
, intensity
is specified and group_var
is not specified:
if initial_intensity < intensity
and start_date
is before trt_start_date
and end_date
is on or after trt_start_date
or end_date
is NA
, it
is set to "Y"
;
if group_var
is specified:
if previous intensity
< intensity
and start_date
is after trt_start_date
and end_date
is on or after trt_start_date
or end_date
is NA
, it
is set to "Y"
;
Otherwise it is set to NA_character_
.
The input dataset with the variable specified by new_var
added
OCCDS Functions:
derive_vars_atc()
,
derive_vars_query()
,
get_terms_from_db()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) adae <- tribble( ~USUBJID, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR, # before treatment "1", "2021-12-13T20:15", "2021-12-15T12:45", "1", "1", "1", "2021-12-14T20:15", "2021-12-14T22:00", "1", "3", # starting before treatment and ending during treatment "1", "2021-12-30T20:00", "2022-01-14T11:00", "1", "3", "1", "2021-12-31T20:15", "2022-01-01T01:23", "1", "1", # starting during treatment "1", "2022-01-01T12:00", "2022-01-02T23:25", "3", "4", # after treatment "1", "2022-05-10T11:00", "2022-05-10T13:05", "2", "2", "1", "2022-05-11T11:00", "2022-05-11T13:05", "2", "2", # missing dates "1", "", "", "3", "4", "1", "2021-12-30T09:00", "", "3", "4", "1", "2021-12-30T11:00", "", "3", "3", "1", "", "2022-01-04T09:00", "3", "4", "1", "", "2021-12-24T19:00", "3", "4", "1", "", "2022-06-04T09:00", "3", "4", # without treatment "2", "", "2021-12-03T12:00", "1", "2", "2", "2021-12-01T12:00", "2021-12-03T12:00", "1", "2", "2", "2021-12-06T18:00", "", "1", "2" ) %>% mutate( ASTDTM = ymd_hm(ASTDTM), AENDTM = ymd_hm(AENDTM), TRTSDTM = if_else(USUBJID == "1", ymd_hm("2022-01-01T01:01"), ymd_hms("")), TRTEDTM = if_else(USUBJID == "1", ymd_hm("2022-04-30T23:59"), ymd_hms("")) ) # derive TRTEMFL without considering treatment end and worsening derive_var_trtemfl(adae) %>% select(ASTDTM, AENDTM, TRTSDTM, TRTEMFL) # derive TRTEM2FL taking treatment end and worsening into account derive_var_trtemfl( adae, new_var = TRTEM2FL, trt_end_date = TRTEDTM, end_window = 10, initial_intensity = AEITOXGR, intensity = AETOXGR ) %>% select(ASTDTM, AENDTM, AEITOXGR, AETOXGR, TRTEM2FL) adae2 <- tribble( ~USUBJID, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR, ~AEGRPID, # before treatment "1", "2021-12-13T20:15", "2021-12-15T12:45", "1", "1", "1", "1", "2021-12-14T20:15", "2021-12-14T22:00", "1", "3", "1", # starting before treatment and ending during treatment "1", "2021-12-30T20:15", "2022-01-14T01:23", "3", "3", "2", "1", "2022-01-05T20:00", "2022-06-01T11:00", "3", "1", "2", "1", "2022-01-10T20:15", "2022-01-11T01:23", "3", "2", "2", "1", "2022-01-13T20:15", "2022-03-01T01:23", "3", "1", "2", # starting during treatment "1", "2022-01-01T12:00", "2022-01-02T23:25", "4", "4", "3", # after treatment "1", "2022-05-10T11:00", "2022-05-10T13:05", "2", "2", "4", "1", "2022-05-10T12:00", "2022-05-10T13:05", "2", "2", "4", "1", "2022-05-11T11:00", "2022-05-11T13:05", "2", "2", "4", # missing dates "1", "", "", "3", "4", "5", "1", "2021-12-30T09:00", "", "3", "4", "5", "1", "2021-12-30T11:00", "", "3", "3", "5", "1", "", "2022-01-04T09:00", "3", "4", "5", "1", "", "2021-12-24T19:00", "3", "4", "5", "1", "", "2022-06-04T09:00", "3", "4", "5", # without treatment "2", "", "2021-12-03T12:00", "1", "2", "1", "2", "2021-12-01T12:00", "2021-12-03T12:00", "1", "2", "2", "2", "2021-12-06T18:00", "", "1", "2", "3" ) %>% mutate( STUDYID = "ABC12345", ASTDTM = ymd_hm(ASTDTM), AENDTM = ymd_hm(AENDTM), TRTSDTM = if_else(USUBJID == "1", ymd_hm("2022-01-01T01:01"), ymd_hms("")), TRTEDTM = if_else(USUBJID == "1", ymd_hm("2022-04-30T23:59"), ymd_hms("")) ) # derive TRTEMFL taking treatment end and worsening into account within a grouping variable derive_var_trtemfl( adae2, new_var = TRTEMFL, trt_end_date = TRTEDTM, end_window = 10, intensity = AETOXGR, group_var = AEGRPID ) %>% select(ASTDTM, AENDTM, AEITOXGR, AETOXGR, AEGRPID, TRTEMFL)
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) adae <- tribble( ~USUBJID, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR, # before treatment "1", "2021-12-13T20:15", "2021-12-15T12:45", "1", "1", "1", "2021-12-14T20:15", "2021-12-14T22:00", "1", "3", # starting before treatment and ending during treatment "1", "2021-12-30T20:00", "2022-01-14T11:00", "1", "3", "1", "2021-12-31T20:15", "2022-01-01T01:23", "1", "1", # starting during treatment "1", "2022-01-01T12:00", "2022-01-02T23:25", "3", "4", # after treatment "1", "2022-05-10T11:00", "2022-05-10T13:05", "2", "2", "1", "2022-05-11T11:00", "2022-05-11T13:05", "2", "2", # missing dates "1", "", "", "3", "4", "1", "2021-12-30T09:00", "", "3", "4", "1", "2021-12-30T11:00", "", "3", "3", "1", "", "2022-01-04T09:00", "3", "4", "1", "", "2021-12-24T19:00", "3", "4", "1", "", "2022-06-04T09:00", "3", "4", # without treatment "2", "", "2021-12-03T12:00", "1", "2", "2", "2021-12-01T12:00", "2021-12-03T12:00", "1", "2", "2", "2021-12-06T18:00", "", "1", "2" ) %>% mutate( ASTDTM = ymd_hm(ASTDTM), AENDTM = ymd_hm(AENDTM), TRTSDTM = if_else(USUBJID == "1", ymd_hm("2022-01-01T01:01"), ymd_hms("")), TRTEDTM = if_else(USUBJID == "1", ymd_hm("2022-04-30T23:59"), ymd_hms("")) ) # derive TRTEMFL without considering treatment end and worsening derive_var_trtemfl(adae) %>% select(ASTDTM, AENDTM, TRTSDTM, TRTEMFL) # derive TRTEM2FL taking treatment end and worsening into account derive_var_trtemfl( adae, new_var = TRTEM2FL, trt_end_date = TRTEDTM, end_window = 10, initial_intensity = AEITOXGR, intensity = AETOXGR ) %>% select(ASTDTM, AENDTM, AEITOXGR, AETOXGR, TRTEM2FL) adae2 <- tribble( ~USUBJID, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR, ~AEGRPID, # before treatment "1", "2021-12-13T20:15", "2021-12-15T12:45", "1", "1", "1", "1", "2021-12-14T20:15", "2021-12-14T22:00", "1", "3", "1", # starting before treatment and ending during treatment "1", "2021-12-30T20:15", "2022-01-14T01:23", "3", "3", "2", "1", "2022-01-05T20:00", "2022-06-01T11:00", "3", "1", "2", "1", "2022-01-10T20:15", "2022-01-11T01:23", "3", "2", "2", "1", "2022-01-13T20:15", "2022-03-01T01:23", "3", "1", "2", # starting during treatment "1", "2022-01-01T12:00", "2022-01-02T23:25", "4", "4", "3", # after treatment "1", "2022-05-10T11:00", "2022-05-10T13:05", "2", "2", "4", "1", "2022-05-10T12:00", "2022-05-10T13:05", "2", "2", "4", "1", "2022-05-11T11:00", "2022-05-11T13:05", "2", "2", "4", # missing dates "1", "", "", "3", "4", "5", "1", "2021-12-30T09:00", "", "3", "4", "5", "1", "2021-12-30T11:00", "", "3", "3", "5", "1", "", "2022-01-04T09:00", "3", "4", "5", "1", "", "2021-12-24T19:00", "3", "4", "5", "1", "", "2022-06-04T09:00", "3", "4", "5", # without treatment "2", "", "2021-12-03T12:00", "1", "2", "1", "2", "2021-12-01T12:00", "2021-12-03T12:00", "1", "2", "2", "2", "2021-12-06T18:00", "", "1", "2", "3" ) %>% mutate( STUDYID = "ABC12345", ASTDTM = ymd_hm(ASTDTM), AENDTM = ymd_hm(AENDTM), TRTSDTM = if_else(USUBJID == "1", ymd_hm("2022-01-01T01:01"), ymd_hms("")), TRTEDTM = if_else(USUBJID == "1", ymd_hm("2022-04-30T23:59"), ymd_hms("")) ) # derive TRTEMFL taking treatment end and worsening into account within a grouping variable derive_var_trtemfl( adae2, new_var = TRTEMFL, trt_end_date = TRTEDTM, end_window = 10, intensity = AETOXGR, group_var = AEGRPID ) %>% select(ASTDTM, AENDTM, AEITOXGR, AETOXGR, AEGRPID, TRTEMFL)
Derives analysis age (AAGE
) and analysis age unit (AAGEU
).
Note: This is a wrapper function for the more generic derive_vars_duration()
.
derive_vars_aage( dataset, start_date = BRTHDT, end_date = RANDDT, age_unit = "YEARS", type = "interval" )
derive_vars_aage( dataset, start_date = BRTHDT, end_date = RANDDT, age_unit = "YEARS", type = "interval" )
dataset |
Input dataset The variables specified by the |
start_date |
The start date A date or date-time object is expected. Refer to Default: |
end_date |
The end date A date or date-time object is expected. Refer to Default: |
age_unit |
Age unit The age is derived in the specified unit Permitted Values (case-insensitive): For years: For months: For weeks: For days: For hours: For minutes: For seconds: |
type |
lubridate duration type. See below for details. Default: Permitted Values: |
The duration is derived as time from start to end date in the specified output unit. If the end date is before the start date, the duration is negative. The start and end date variable must be present in the specified input dataset.
The lubridate package calculates two types of spans between two dates: duration and interval. While these calculations are largely the same, when the unit of the time period is month or year the result can be slightly different.
The difference arises from the ambiguity in the length of "1 month"
or
"1 year"
.
Months may have 31, 30, 28, or 29 days, and years are 365 days and 366 during leap years.
Durations and intervals help solve the ambiguity in these measures.
The interval between 2000-02-01
and 2000-03-01
is 1
(i.e. one month).
The duration between these two dates is 0.95
, which accounts for the fact
that the year 2000 is a leap year, February has 29 days, and the average month
length is 30.4375
, i.e. 29 / 30.4375 = 0.95
.
For additional details, review the lubridate time span reference page.
The input dataset with AAGE
and AAGEU
added
ADSL Functions that returns variable appended to dataset:
derive_var_age_years()
,
derive_vars_extreme_event()
,
derive_vars_period()
library(tibble) library(lubridate) data <- tribble( ~BRTHDT, ~RANDDT, ymd("1984-09-06"), ymd("2020-02-24") ) derive_vars_aage(data)
library(tibble) library(lubridate) data <- tribble( ~BRTHDT, ~RANDDT, ymd("1984-09-06"), ymd("2020-02-24") ) derive_vars_aage(data)
Add Anatomical Therapeutic Chemical class variables from FACM
to ADCM
.
Note: This is a wrapper function for the more generic derive_vars_transposed()
.
derive_vars_atc( dataset, dataset_facm, by_vars = exprs(USUBJID, CMREFID = FAREFID), id_vars = NULL, value_var = FASTRESC )
derive_vars_atc( dataset, dataset_facm, by_vars = exprs(USUBJID, CMREFID = FAREFID), id_vars = NULL, value_var = FASTRESC )
dataset |
Input dataset The variables specified by the |
dataset_facm |
FACM dataset The variables specified by the |
by_vars |
Grouping variables Keys used to merge |
id_vars |
ID variables Variables (excluding by_vars) that uniquely identify each observation in Permitted Values: list of variables created by |
value_var |
The variable of Default: |
The input dataset with ATC variables added
OCCDS Functions:
derive_var_trtemfl()
,
derive_vars_query()
,
get_terms_from_db()
library(tibble) cm <- tribble( ~USUBJID, ~CMGRPID, ~CMREFID, ~CMDECOD, "BP40257-1001", "14", "1192056", "PARACETAMOL", "BP40257-1001", "18", "2007001", "SOLUMEDROL", "BP40257-1002", "19", "2791596", "SPIRONOLACTONE" ) facm <- tribble( ~USUBJID, ~FAGRPID, ~FAREFID, ~FATESTCD, ~FASTRESC, "BP40257-1001", "1", "1192056", "CMATC1CD", "N", "BP40257-1001", "1", "1192056", "CMATC2CD", "N02", "BP40257-1001", "1", "1192056", "CMATC3CD", "N02B", "BP40257-1001", "1", "1192056", "CMATC4CD", "N02BE", "BP40257-1001", "1", "2007001", "CMATC1CD", "D", "BP40257-1001", "1", "2007001", "CMATC2CD", "D10", "BP40257-1001", "1", "2007001", "CMATC3CD", "D10A", "BP40257-1001", "1", "2007001", "CMATC4CD", "D10AA", "BP40257-1001", "2", "2007001", "CMATC1CD", "D", "BP40257-1001", "2", "2007001", "CMATC2CD", "D07", "BP40257-1001", "2", "2007001", "CMATC3CD", "D07A", "BP40257-1001", "2", "2007001", "CMATC4CD", "D07AA", "BP40257-1001", "3", "2007001", "CMATC1CD", "H", "BP40257-1001", "3", "2007001", "CMATC2CD", "H02", "BP40257-1001", "3", "2007001", "CMATC3CD", "H02A", "BP40257-1001", "3", "2007001", "CMATC4CD", "H02AB", "BP40257-1002", "1", "2791596", "CMATC1CD", "C", "BP40257-1002", "1", "2791596", "CMATC2CD", "C03", "BP40257-1002", "1", "2791596", "CMATC3CD", "C03D", "BP40257-1002", "1", "2791596", "CMATC4CD", "C03DA" ) derive_vars_atc(cm, facm)
library(tibble) cm <- tribble( ~USUBJID, ~CMGRPID, ~CMREFID, ~CMDECOD, "BP40257-1001", "14", "1192056", "PARACETAMOL", "BP40257-1001", "18", "2007001", "SOLUMEDROL", "BP40257-1002", "19", "2791596", "SPIRONOLACTONE" ) facm <- tribble( ~USUBJID, ~FAGRPID, ~FAREFID, ~FATESTCD, ~FASTRESC, "BP40257-1001", "1", "1192056", "CMATC1CD", "N", "BP40257-1001", "1", "1192056", "CMATC2CD", "N02", "BP40257-1001", "1", "1192056", "CMATC3CD", "N02B", "BP40257-1001", "1", "1192056", "CMATC4CD", "N02BE", "BP40257-1001", "1", "2007001", "CMATC1CD", "D", "BP40257-1001", "1", "2007001", "CMATC2CD", "D10", "BP40257-1001", "1", "2007001", "CMATC3CD", "D10A", "BP40257-1001", "1", "2007001", "CMATC4CD", "D10AA", "BP40257-1001", "2", "2007001", "CMATC1CD", "D", "BP40257-1001", "2", "2007001", "CMATC2CD", "D07", "BP40257-1001", "2", "2007001", "CMATC3CD", "D07A", "BP40257-1001", "2", "2007001", "CMATC4CD", "D07AA", "BP40257-1001", "3", "2007001", "CMATC1CD", "H", "BP40257-1001", "3", "2007001", "CMATC2CD", "H02", "BP40257-1001", "3", "2007001", "CMATC3CD", "H02A", "BP40257-1001", "3", "2007001", "CMATC4CD", "H02AB", "BP40257-1002", "1", "2791596", "CMATC1CD", "C", "BP40257-1002", "1", "2791596", "CMATC2CD", "C03", "BP40257-1002", "1", "2791596", "CMATC3CD", "C03D", "BP40257-1002", "1", "2791596", "CMATC4CD", "C03DA" ) derive_vars_atc(cm, facm)
AVALCATy
and AVALCAyN
Derive Categorization Variables Like AVALCATy
and AVALCAyN
derive_vars_cat(dataset, definition, by_vars = NULL)
derive_vars_cat(dataset, definition, by_vars = NULL)
dataset |
Input dataset The variables specified by the |
definition |
List of expressions created by Must contain:
e.g. if exprs(~condition, ~AVALCAT1, ~AVALCA1N, AVAL >= 140, ">=140 cm", 1, AVAL < 140, "<140 cm", 2) e.g. if exprs(~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, "Height", AVAL >= 140, ">=140 cm", 1, "Height", AVAL < 140, "<140 cm", 2) |
by_vars |
list of expressions with one element. |
If conditions are overlapping, the row order of definitions
must be carefully considered.
The first match will determine the category.
i.e. if
AVAL = 155
and the definition
is:
definition <- exprs( ~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, "Height", AVAL > 170, ">170 cm", 1, "Height", AVAL <= 170, "<=170 cm", 2, "Height", AVAL <= 160, "<=160 cm", 3 )
then AVALCAT1
will be "<=170 cm"
, as this is the first match for AVAL
.
If you specify:
definition <- exprs( ~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, "Height", AVAL <= 160, "<=160 cm", 3, "Height", AVAL <= 170, "<=170 cm", 2, "Height", AVAL > 170, ">170 cm", 1 )
Then AVAL <= 160
will lead to AVALCAT1 == "<=160 cm"
,
AVAL
in-between 160
and 170
will lead to AVALCAT1 == "<=170 cm"
,
and AVAL <= 170
will lead to AVALCAT1 == ">170 cm"
.
However, we suggest to be more explicit when defining the condition
, to avoid overlap.
In this case, the middle condition should be:
AVAL <= 170 & AVAL > 160
The input dataset with the new variables defined in definition
added
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_extreme_flag()
,
derive_var_joined_exist_flag()
,
derive_var_merged_ef_msrc()
,
derive_var_merged_exist_flag()
,
derive_var_merged_summary()
,
derive_var_obs_number()
,
derive_var_relative_flag()
,
derive_vars_computed()
,
derive_vars_joined()
,
derive_vars_merged()
,
derive_vars_merged_lookup()
,
derive_vars_transposed()
library(dplyr) library(tibble) advs <- tibble::tribble( ~USUBJID, ~VSTEST, ~AVAL, "01-701-1015", "Height", 147.32, "01-701-1015", "Weight", 53.98, "01-701-1023", "Height", 162.56, "01-701-1023", "Weight", NA, "01-701-1028", "Height", NA, "01-701-1028", "Weight", NA, "01-701-1033", "Height", 175.26, "01-701-1033", "Weight", 88.45 ) definition <- exprs( ~condition, ~AVALCAT1, ~AVALCA1N, ~NEWCOL, VSTEST == "Height" & AVAL > 160, ">160 cm", 1, "extra1", VSTEST == "Height" & AVAL <= 160, "<=160 cm", 2, "extra2" ) derive_vars_cat( dataset = advs, definition = definition ) # Using by_vars: definition2 <- exprs( ~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, "Height", AVAL > 160, ">160 cm", 1, "Height", AVAL <= 160, "<=160 cm", 2, "Weight", AVAL > 70, ">70 kg", 1, "Weight", AVAL <= 70, "<=70 kg", 2 ) derive_vars_cat( dataset = advs, definition = definition2, by_vars = exprs(VSTEST) ) # With three conditions: definition3 <- exprs( ~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, "Height", AVAL > 170, ">170 cm", 1, "Height", AVAL <= 170 & AVAL > 160, "<=170 cm", 2, "Height", AVAL <= 160, "<=160 cm", 3 ) derive_vars_cat( dataset = advs, definition = definition3, by_vars = exprs(VSTEST) ) # Let's derive both the MCRITyML and the MCRITyMN variables adlb <- tibble::tribble( ~USUBJID, ~PARAM, ~AVAL, ~AVALU, ~ANRHI, "01-701-1015", "ALT", 150, "U/L", 40, "01-701-1023", "ALT", 70, "U/L", 40, "01-701-1036", "ALT", 130, "U/L", 40, "01-701-1048", "ALT", 30, "U/L", 40, "01-701-1015", "AST", 50, "U/L", 35 ) definition_mcrit <- exprs( ~PARAM, ~condition, ~MCRIT1ML, ~MCRIT1MN, "ALT", AVAL <= ANRHI, "<=ANRHI", 1, "ALT", ANRHI < AVAL & AVAL <= 3 * ANRHI, ">1-3*ANRHI", 2, "ALT", 3 * ANRHI < AVAL, ">3*ANRHI", 3 ) adlb %>% derive_vars_cat( definition = definition_mcrit, by_vars = exprs(PARAM) )
library(dplyr) library(tibble) advs <- tibble::tribble( ~USUBJID, ~VSTEST, ~AVAL, "01-701-1015", "Height", 147.32, "01-701-1015", "Weight", 53.98, "01-701-1023", "Height", 162.56, "01-701-1023", "Weight", NA, "01-701-1028", "Height", NA, "01-701-1028", "Weight", NA, "01-701-1033", "Height", 175.26, "01-701-1033", "Weight", 88.45 ) definition <- exprs( ~condition, ~AVALCAT1, ~AVALCA1N, ~NEWCOL, VSTEST == "Height" & AVAL > 160, ">160 cm", 1, "extra1", VSTEST == "Height" & AVAL <= 160, "<=160 cm", 2, "extra2" ) derive_vars_cat( dataset = advs, definition = definition ) # Using by_vars: definition2 <- exprs( ~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, "Height", AVAL > 160, ">160 cm", 1, "Height", AVAL <= 160, "<=160 cm", 2, "Weight", AVAL > 70, ">70 kg", 1, "Weight", AVAL <= 70, "<=70 kg", 2 ) derive_vars_cat( dataset = advs, definition = definition2, by_vars = exprs(VSTEST) ) # With three conditions: definition3 <- exprs( ~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, "Height", AVAL > 170, ">170 cm", 1, "Height", AVAL <= 170 & AVAL > 160, "<=170 cm", 2, "Height", AVAL <= 160, "<=160 cm", 3 ) derive_vars_cat( dataset = advs, definition = definition3, by_vars = exprs(VSTEST) ) # Let's derive both the MCRITyML and the MCRITyMN variables adlb <- tibble::tribble( ~USUBJID, ~PARAM, ~AVAL, ~AVALU, ~ANRHI, "01-701-1015", "ALT", 150, "U/L", 40, "01-701-1023", "ALT", 70, "U/L", 40, "01-701-1036", "ALT", 130, "U/L", 40, "01-701-1048", "ALT", 30, "U/L", 40, "01-701-1015", "AST", 50, "U/L", 35 ) definition_mcrit <- exprs( ~PARAM, ~condition, ~MCRIT1ML, ~MCRIT1MN, "ALT", AVAL <= ANRHI, "<=ANRHI", 1, "ALT", ANRHI < AVAL & AVAL <= 3 * ANRHI, ">1-3*ANRHI", 2, "ALT", 3 * ANRHI < AVAL, ">3*ANRHI", 3 ) adlb %>% derive_vars_cat( definition = definition_mcrit, by_vars = exprs(PARAM) )
Adds Variable(s) computed from the analysis value of one or more parameters.
It is expected that the value of the new variable is defined by an expression
using the analysis values of other parameters. For example Body Mass Index at
Baseline (BMIBL
) in ADSL
can be derived from of HEIGHT and WEIGHT
parameters in ADVS
.
derive_vars_computed( dataset, dataset_add, by_vars, parameters, new_vars, filter_add = NULL, constant_by_vars = NULL, constant_parameters = NULL )
derive_vars_computed( dataset, dataset_add, by_vars, parameters, new_vars, filter_add = NULL, constant_by_vars = NULL, constant_parameters = NULL )
dataset |
The variables specified by the |
dataset_add |
Additional dataset The variables specified by the The variable specified by |
by_vars |
Grouping variables Grouping variables uniquely identifying a set of records for which
Permitted Values: list of variables created by exprs() |
parameters |
Required parameter codes It is expected that all parameter codes ( If observations should be considered which do not have a parameter code,
e.g., if an SDTM dataset is used, temporary parameter codes can be derived
by specifying a list of expressions. The name of the element defines the
temporary parameter code and the expression defines the condition for
selecting the records. For example,
Unnamed elements in the list of expressions are considered as parameter
codes. For example, Permitted Values: A character vector of |
new_vars |
Name of the newly created variables The specified variables are set to the specified values. The values of
variables of the parameters specified by exprs( BMIBL = (AVAL.WEIGHT / (AVAL.HEIGHT/100)^2) ) defines the value for the new variable. Variable names in the expression must not contain more than one dot. Permitted Values: List of variable-value pairs |
filter_add |
Filter condition of additional dataset The specified condition is applied to the additional dataset before deriving the new variable, i.e., only observations fulfilling the condition are taken into account. Permitted Values: a condition |
constant_by_vars |
By variables for constant parameters The constant parameters (parameters that are measured only once) are merged to the other parameters using the specified variables. (Refer to the Example) Permitted Values: list of variables |
constant_parameters |
Required constant parameter codes It is expected that all the parameter codes ( If observations should be considered which do not have a parameter code,
e.g., if an SDTM dataset is used, temporary parameter codes can be derived
by specifying a list of expressions. The name of the element defines the
temporary parameter code and the expression defines the condition for
selecting the records. For example Unnamed elements in the list of expressions are considered as parameter
codes. For example, Permitted Values: A character vector of |
For each group (with respect to the variables specified for the
by_vars
argument), the values of the new variables (new_vars
) are
computed based on the parameters in the additional dataset
(dataset_add
) and then the new variables are merged to the input
dataset (dataset
).
The input dataset with the new variables added.
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_extreme_flag()
,
derive_var_joined_exist_flag()
,
derive_var_merged_ef_msrc()
,
derive_var_merged_exist_flag()
,
derive_var_merged_summary()
,
derive_var_obs_number()
,
derive_var_relative_flag()
,
derive_vars_cat()
,
derive_vars_joined()
,
derive_vars_merged()
,
derive_vars_merged_lookup()
,
derive_vars_transposed()
library(tibble) library(dplyr) # Example 1: Derive BMIBL adsl <- tribble( ~STUDYID, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "01-1302", 61, "YEARS", "PILOT01", "17-1344", 64, "YEARS" ) advs <- tribble( ~STUDYID, ~USUBJID, ~PARAMCD, ~PARAM, ~VISIT, ~AVAL, ~AVALU, ~ABLFL, "PILOT01", "01-1302", "HEIGHT", "Height (cm)", "SCREENING", 177.8, "cm", "Y", "PILOT01", "01-1302", "WEIGHT", "Weight (kg)", "SCREENING", 81.19, "kg", "N", "PILOT01", "01-1302", "WEIGHT", "Weight (kg)", "BASELINE", 82.1, "kg", "Y", "PILOT01", "01-1302", "WEIGHT", "Weight (kg)", "WEEK 2", 81.19, "kg", "N", "PILOT01", "01-1302", "WEIGHT", "Weight (kg)", "WEEK 4", 82.56, "kg", "N", "PILOT01", "01-1302", "WEIGHT", "Weight (kg)", "WEEK 6", 80.74, "kg", "N", "PILOT01", "17-1344", "HEIGHT", "Height (cm)", "SCREENING", 163.5, "cm", "Y", "PILOT01", "17-1344", "WEIGHT", "Weight (kg)", "SCREENING", 58.06, "kg", "N", "PILOT01", "17-1344", "WEIGHT", "Weight (kg)", "BASELINE", 58.06, "kg", "Y", "PILOT01", "17-1344", "WEIGHT", "Weight (kg)", "WEEK 2", 58.97, "kg", "N", "PILOT01", "17-1344", "WEIGHT", "Weight (kg)", "WEEK 4", 57.97, "kg", "N", "PILOT01", "17-1344", "WEIGHT", "Weight (kg)", "WEEK 6", 58.97, "kg", "N" ) derive_vars_computed( dataset = adsl, dataset_add = advs, by_vars = exprs(STUDYID, USUBJID), parameters = c("WEIGHT", "HEIGHT"), new_vars = exprs(BMIBL = compute_bmi(height = AVAL.HEIGHT, weight = AVAL.WEIGHT)), filter_add = ABLFL == "Y" )
library(tibble) library(dplyr) # Example 1: Derive BMIBL adsl <- tribble( ~STUDYID, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "01-1302", 61, "YEARS", "PILOT01", "17-1344", 64, "YEARS" ) advs <- tribble( ~STUDYID, ~USUBJID, ~PARAMCD, ~PARAM, ~VISIT, ~AVAL, ~AVALU, ~ABLFL, "PILOT01", "01-1302", "HEIGHT", "Height (cm)", "SCREENING", 177.8, "cm", "Y", "PILOT01", "01-1302", "WEIGHT", "Weight (kg)", "SCREENING", 81.19, "kg", "N", "PILOT01", "01-1302", "WEIGHT", "Weight (kg)", "BASELINE", 82.1, "kg", "Y", "PILOT01", "01-1302", "WEIGHT", "Weight (kg)", "WEEK 2", 81.19, "kg", "N", "PILOT01", "01-1302", "WEIGHT", "Weight (kg)", "WEEK 4", 82.56, "kg", "N", "PILOT01", "01-1302", "WEIGHT", "Weight (kg)", "WEEK 6", 80.74, "kg", "N", "PILOT01", "17-1344", "HEIGHT", "Height (cm)", "SCREENING", 163.5, "cm", "Y", "PILOT01", "17-1344", "WEIGHT", "Weight (kg)", "SCREENING", 58.06, "kg", "N", "PILOT01", "17-1344", "WEIGHT", "Weight (kg)", "BASELINE", 58.06, "kg", "Y", "PILOT01", "17-1344", "WEIGHT", "Weight (kg)", "WEEK 2", 58.97, "kg", "N", "PILOT01", "17-1344", "WEIGHT", "Weight (kg)", "WEEK 4", 57.97, "kg", "N", "PILOT01", "17-1344", "WEIGHT", "Weight (kg)", "WEEK 6", 58.97, "kg", "N" ) derive_vars_computed( dataset = adsl, dataset_add = advs, by_vars = exprs(STUDYID, USUBJID), parameters = c("WEIGHT", "HEIGHT"), new_vars = exprs(BMIBL = compute_bmi(height = AVAL.HEIGHT, weight = AVAL.WEIGHT)), filter_add = ABLFL == "Y" )
CRITy
, CRITyFL
, and CRITyFLN
The function derives ADaM compliant criterion flags, e.g., to facilitate subgroup analyses.
If a criterion flag can't be derived with this function, the derivation is not ADaM compliant. It helps to ensure that
the condition of the criterion depends only on variables of the same row,
the CRITyFL
is populated with valid values, i.e, either "Y"
and NA
or
"Y"
, "N"
, and NA
,
the CRITy
variable is populated correctly, i.e.,
set to a constant value within a parameter if CRITyFL
is populated with
"Y"
, "N"
, and NA
and
set to a constant value within a parameter if the criterion condition is
fulfilled and to NA
otherwise if CRITyFL
is populated with "Y"
, and
NA
derive_vars_crit_flag( dataset, crit_nr = 1, condition, description, values_yn = FALSE, create_numeric_flag = FALSE )
derive_vars_crit_flag( dataset, crit_nr = 1, condition, description, values_yn = FALSE, create_numeric_flag = FALSE )
dataset |
Input dataset |
crit_nr |
The criterion number, i.e., the Permitted Values: a positive integer |
condition |
Condition for flagging records See description of the Permitted Values: an unquoted expression which evaluates to a logical (in
|
description |
The description of the criterion The An expression can be specified to set the value depending on the parameter. Please note that the value must be constant within a parameter. Permitted Values: an unquoted expression which evaluates to a character
(in |
values_yn |
Should If set to Otherwise, the Permitted Values: |
create_numeric_flag |
Create a numeric flag? If set to Permitted Values: |
The input dataset with the variables CRITy
, CRITyFL
, and
optionally CRITyFLN
added.
BDS-Findings Functions that returns variable appended to dataset:
derive_basetype_records()
,
derive_var_analysis_ratio()
,
derive_var_anrind()
,
derive_var_atoxgr()
,
derive_var_atoxgr_dir()
,
derive_var_base()
,
derive_var_chg()
,
derive_var_ontrtfl()
,
derive_var_pchg()
,
derive_var_shift()
library(tibble) adbds <- tribble( ~PARAMCD, ~AVAL, "AST", 42, "AST", 52, "AST", NA_real_, "ALT", 33, "ALT", 51 ) # Create a criterion flag with values "Y" and NA derive_vars_crit_flag( adbds, condition = AVAL > 50, description = "Absolute value > 50" ) # Create criterion flag with values "Y", "N", and NA and parameter dependent # criterion description derive_vars_crit_flag( adbds, crit_nr = 2, condition = AVAL > 50, description = paste(PARAMCD, "> 50"), values_yn = TRUE, create_numeric_flag = TRUE )
library(tibble) adbds <- tribble( ~PARAMCD, ~AVAL, "AST", 42, "AST", 52, "AST", NA_real_, "ALT", 33, "ALT", 51 ) # Create a criterion flag with values "Y" and NA derive_vars_crit_flag( adbds, condition = AVAL > 50, description = "Absolute value > 50" ) # Create criterion flag with values "Y", "N", and NA and parameter dependent # criterion description derive_vars_crit_flag( adbds, crit_nr = 2, condition = AVAL > 50, description = paste(PARAMCD, "> 50"), values_yn = TRUE, create_numeric_flag = TRUE )
Derive a date ('--DT'
) from a date character vector ('--DTC
').
The date can be imputed (see date_imputation
argument)
and the date imputation flag ('--DTF'
) can be added.
derive_vars_dt( dataset, new_vars_prefix, dtc, highest_imputation = "n", date_imputation = "first", flag_imputation = "auto", min_dates = NULL, max_dates = NULL, preserve = FALSE )
derive_vars_dt( dataset, new_vars_prefix, dtc, highest_imputation = "n", date_imputation = "first", flag_imputation = "auto", min_dates = NULL, max_dates = NULL, preserve = FALSE )
dataset |
Input dataset The variables specified by the |
new_vars_prefix |
Prefix used for the output variable(s). A character scalar is expected. For the date variable "DT" is appended to
the specified prefix and for the date imputation flag "DTF". I.e., for
|
dtc |
The A character date is expected in a format like |
highest_imputation |
Highest imputation level The If a component at a higher level than the highest imputation level is
missing, If If Permitted Values: |
date_imputation |
The value to impute the day/month when a datepart is missing. A character value is expected, either as a
The argument is ignored if |
flag_imputation |
Whether the date imputation flag must also be derived. If If If Permitted Values: |
min_dates |
Minimum dates A list of dates is expected. It is ensured that the imputed date is not
before any of the specified dates, e.g., that the imputed adverse event start
date is not before the first treatment date. Only dates which are in the
range of possible dates of the impute_dtc_dtm( "2020-11", min_dates = list( ymd_hms("2020-12-06T12:12:12"), ymd_hms("2020-11-11T11:11:11") ), highest_imputation = "M" ) returns |
max_dates |
Maximum dates A list of dates is expected. It is ensured that the imputed date is not after any of the specified dates, e.g., that the imputed date is not after the data cut off date. Only dates which are in the range of possible dates are considered. A date or date-time object is expected. |
preserve |
Preserve day if month is missing and day is present For example Permitted Values: |
In {admiral}
we don't allow users to pick any single part of the date/time to
impute, we only enable to impute up to a highest level, i.e. you couldn't
choose to say impute months, but not days.
The presence of a '--DTF'
variable is checked and if it already exists in the input dataset,
a warning is issued and '--DTF'
will be overwritten.
The input dataset with the date '--DT'
(and the date imputation flag '--DTF'
if requested) added.
Date/Time Derivation Functions that returns variable appended to dataset:
derive_var_trtdurd()
,
derive_vars_dtm()
,
derive_vars_dtm_to_dt()
,
derive_vars_dtm_to_tm()
,
derive_vars_duration()
,
derive_vars_dy()
library(tibble) library(lubridate) mhdt <- tribble( ~MHSTDTC, "2019-07-18T15:25:40", "2019-07-18T15:25", "2019-07-18", "2019-02", "2019", "2019---07", "" ) # Create ASTDT and ASTDTF # No imputation for partial date derive_vars_dt( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC ) # Create ASTDT and ASTDTF # Impute partial dates to first day/month derive_vars_dt( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC, highest_imputation = "M" ) # Impute partial dates to 6th of April derive_vars_dt( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC, highest_imputation = "M", date_imputation = "04-06" ) # Create AENDT and AENDTF # Impute partial dates to last day/month derive_vars_dt( mhdt, new_vars_prefix = "AEN", dtc = MHSTDTC, highest_imputation = "M", date_imputation = "last" ) # Create BIRTHDT # Impute partial dates to 15th of June. No Date Imputation Flag derive_vars_dt( mhdt, new_vars_prefix = "BIRTH", dtc = MHSTDTC, highest_imputation = "M", date_imputation = "mid", flag_imputation = "none" ) # Impute AE start date to the first date and ensure that the imputed date # is not before the treatment start date adae <- tribble( ~AESTDTC, ~TRTSDTM, "2020-12", ymd_hms("2020-12-06T12:12:12"), "2020-11", ymd_hms("2020-12-06T12:12:12") ) derive_vars_dt( adae, dtc = AESTDTC, new_vars_prefix = "AST", highest_imputation = "M", min_dates = exprs(TRTSDTM) ) # A user imputing dates as middle month/day, i.e. date_imputation = "mid" can # use preserve argument to "preserve" partial dates. For example, "2019---07", # will be displayed as "2019-06-07" rather than 2019-06-15 with preserve = TRUE derive_vars_dt( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC, highest_imputation = "M", date_imputation = "mid", preserve = TRUE )
library(tibble) library(lubridate) mhdt <- tribble( ~MHSTDTC, "2019-07-18T15:25:40", "2019-07-18T15:25", "2019-07-18", "2019-02", "2019", "2019---07", "" ) # Create ASTDT and ASTDTF # No imputation for partial date derive_vars_dt( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC ) # Create ASTDT and ASTDTF # Impute partial dates to first day/month derive_vars_dt( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC, highest_imputation = "M" ) # Impute partial dates to 6th of April derive_vars_dt( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC, highest_imputation = "M", date_imputation = "04-06" ) # Create AENDT and AENDTF # Impute partial dates to last day/month derive_vars_dt( mhdt, new_vars_prefix = "AEN", dtc = MHSTDTC, highest_imputation = "M", date_imputation = "last" ) # Create BIRTHDT # Impute partial dates to 15th of June. No Date Imputation Flag derive_vars_dt( mhdt, new_vars_prefix = "BIRTH", dtc = MHSTDTC, highest_imputation = "M", date_imputation = "mid", flag_imputation = "none" ) # Impute AE start date to the first date and ensure that the imputed date # is not before the treatment start date adae <- tribble( ~AESTDTC, ~TRTSDTM, "2020-12", ymd_hms("2020-12-06T12:12:12"), "2020-11", ymd_hms("2020-12-06T12:12:12") ) derive_vars_dt( adae, dtc = AESTDTC, new_vars_prefix = "AST", highest_imputation = "M", min_dates = exprs(TRTSDTM) ) # A user imputing dates as middle month/day, i.e. date_imputation = "mid" can # use preserve argument to "preserve" partial dates. For example, "2019---07", # will be displayed as "2019-06-07" rather than 2019-06-15 with preserve = TRUE derive_vars_dt( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC, highest_imputation = "M", date_imputation = "mid", preserve = TRUE )
Derive a datetime object ('--DTM'
) from a date character vector ('--DTC'
).
The date and time can be imputed (see date_imputation
/time_imputation
arguments)
and the date/time imputation flag ('--DTF'
, '--TMF'
) can be added.
derive_vars_dtm( dataset, new_vars_prefix, dtc, highest_imputation = "h", date_imputation = "first", time_imputation = "first", flag_imputation = "auto", min_dates = NULL, max_dates = NULL, preserve = FALSE, ignore_seconds_flag = FALSE )
derive_vars_dtm( dataset, new_vars_prefix, dtc, highest_imputation = "h", date_imputation = "first", time_imputation = "first", flag_imputation = "auto", min_dates = NULL, max_dates = NULL, preserve = FALSE, ignore_seconds_flag = FALSE )
dataset |
Input dataset The variables specified by the |
new_vars_prefix |
Prefix used for the output variable(s). A character scalar is expected. For the date variable "DT" is appended to
the specified prefix, for the date imputation flag "DTF", and for the time
imputation flag "TMF". I.e., for |
dtc |
The A character date is expected in a format like |
highest_imputation |
Highest imputation level The If a component at a higher level than the highest imputation level is
missing, If If Permitted Values: |
date_imputation |
The value to impute the day/month when a datepart is missing. A character value is expected, either as a
The argument is ignored if |
time_imputation |
The value to impute the time when a timepart is missing. A character value is expected, either as a
The argument is ignored if |
flag_imputation |
Whether the date/time imputation flag(s) must also be derived. If If If Permitted Values: |
min_dates |
Minimum dates A list of dates is expected. It is ensured that the imputed date is not
before any of the specified dates, e.g., that the imputed adverse event start
date is not before the first treatment date. Only dates which are in the
range of possible dates of the impute_dtc_dtm( "2020-11", min_dates = list( ymd_hms("2020-12-06T12:12:12"), ymd_hms("2020-11-11T11:11:11") ), highest_imputation = "M" ) returns For date variables (not datetime) in the list the time is imputed to
|
max_dates |
Maximum dates A list of dates is expected. It is ensured that the imputed date is not after any of the specified dates, e.g., that the imputed date is not after the data cut off date. Only dates which are in the range of possible dates are considered. A date or date-time object is expected. For date variables (not datetime) in the list the time is imputed to
|
preserve |
Preserve lower level date/time part when higher order part is missing, e.g. preserve day if month is missing or preserve minute when hour is missing. For example Permitted Values: |
ignore_seconds_flag |
ADaM IG states that given SDTM ( Permitted Values: A logical value |
In {admiral}
we don't allow users to pick any single part of the date/time to
impute, we only enable to impute up to a highest level, i.e. you couldn't
choose to say impute months, but not days.
The presence of a '--DTF'
variable is checked and the variable is not derived
if it already exists in the input dataset. However, if '--TMF'
already exists
in the input dataset, a warning is issued and '--TMF'
will be overwritten.
The input dataset with the datetime '--DTM'
(and the date/time imputation
flag '--DTF'
, '--TMF'
) added.
Date/Time Derivation Functions that returns variable appended to dataset:
derive_var_trtdurd()
,
derive_vars_dt()
,
derive_vars_dtm_to_dt()
,
derive_vars_dtm_to_tm()
,
derive_vars_duration()
,
derive_vars_dy()
library(tibble) library(lubridate) mhdt <- tribble( ~MHSTDTC, "2019-07-18T15:25:40", "2019-07-18T15:25", "2019-07-18", "2019-02", "2019", "2019---07", "" ) derive_vars_dtm( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC, highest_imputation = "M" ) # Impute AE end date to the last date and ensure that the imputed date is not # after the death or data cut off date adae <- tribble( ~AEENDTC, ~DTHDT, ~DCUTDT, "2020-12", ymd("2020-12-06"), ymd("2020-12-24"), "2020-11", ymd("2020-12-06"), ymd("2020-12-24") ) derive_vars_dtm( adae, dtc = AEENDTC, new_vars_prefix = "AEN", highest_imputation = "M", date_imputation = "last", time_imputation = "last", max_dates = exprs(DTHDT, DCUTDT) ) # Seconds has been removed from the input dataset. Function now uses # ignore_seconds_flag to remove the 'S' from the --TMF variable. mhdt <- tribble( ~MHSTDTC, "2019-07-18T15:25", "2019-07-18T15:25", "2019-07-18", "2019-02", "2019", "2019---07", "" ) derive_vars_dtm( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC, highest_imputation = "M", ignore_seconds_flag = TRUE ) # A user imputing dates as middle month/day, i.e. date_imputation = "MID" can # use preserve argument to "preserve" partial dates. For example, "2019---07", # will be displayed as "2019-06-07" rather than 2019-06-15 with preserve = TRUE derive_vars_dtm( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC, highest_imputation = "M", date_imputation = "mid", preserve = TRUE )
library(tibble) library(lubridate) mhdt <- tribble( ~MHSTDTC, "2019-07-18T15:25:40", "2019-07-18T15:25", "2019-07-18", "2019-02", "2019", "2019---07", "" ) derive_vars_dtm( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC, highest_imputation = "M" ) # Impute AE end date to the last date and ensure that the imputed date is not # after the death or data cut off date adae <- tribble( ~AEENDTC, ~DTHDT, ~DCUTDT, "2020-12", ymd("2020-12-06"), ymd("2020-12-24"), "2020-11", ymd("2020-12-06"), ymd("2020-12-24") ) derive_vars_dtm( adae, dtc = AEENDTC, new_vars_prefix = "AEN", highest_imputation = "M", date_imputation = "last", time_imputation = "last", max_dates = exprs(DTHDT, DCUTDT) ) # Seconds has been removed from the input dataset. Function now uses # ignore_seconds_flag to remove the 'S' from the --TMF variable. mhdt <- tribble( ~MHSTDTC, "2019-07-18T15:25", "2019-07-18T15:25", "2019-07-18", "2019-02", "2019", "2019---07", "" ) derive_vars_dtm( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC, highest_imputation = "M", ignore_seconds_flag = TRUE ) # A user imputing dates as middle month/day, i.e. date_imputation = "MID" can # use preserve argument to "preserve" partial dates. For example, "2019---07", # will be displayed as "2019-06-07" rather than 2019-06-15 with preserve = TRUE derive_vars_dtm( mhdt, new_vars_prefix = "AST", dtc = MHSTDTC, highest_imputation = "M", date_imputation = "mid", preserve = TRUE )
This function creates date(s) as output from datetime variable(s)
derive_vars_dtm_to_dt(dataset, source_vars)
derive_vars_dtm_to_dt(dataset, source_vars)
dataset |
Input dataset The variables specified by the |
source_vars |
A list of datetime variables created using |
A data frame containing the input dataset with the corresponding date (--DT
)
variable(s) of all datetime variables (--DTM
) specified in source_vars.
Date/Time Derivation Functions that returns variable appended to dataset:
derive_var_trtdurd()
,
derive_vars_dt()
,
derive_vars_dtm()
,
derive_vars_dtm_to_tm()
,
derive_vars_duration()
,
derive_vars_dy()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) adcm <- tribble( ~USUBJID, ~TRTSDTM, ~ASTDTM, ~AENDTM, "PAT01", "2012-02-25 23:00:00", "2012-02-28 19:00:00", "2012-02-25 23:00:00", "PAT01", NA, "2012-02-28 19:00:00", NA, "PAT01", "2017-02-25 23:00:00", "2013-02-25 19:00:00", "2014-02-25 19:00:00", "PAT01", "2017-02-25 16:00:00", "2017-02-25 14:00:00", "2017-03-25 23:00:00", "PAT01", "2017-02-25 16:00:00", "2017-02-25 14:00:00", "2017-04-29 14:00:00", ) %>% mutate( TRTSDTM = as_datetime(TRTSDTM), ASTDTM = as_datetime(ASTDTM), AENDTM = as_datetime(AENDTM) ) adcm %>% derive_vars_dtm_to_dt(exprs(TRTSDTM, ASTDTM, AENDTM)) %>% select(USUBJID, starts_with("TRT"), starts_with("AST"), starts_with("AEN"))
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) adcm <- tribble( ~USUBJID, ~TRTSDTM, ~ASTDTM, ~AENDTM, "PAT01", "2012-02-25 23:00:00", "2012-02-28 19:00:00", "2012-02-25 23:00:00", "PAT01", NA, "2012-02-28 19:00:00", NA, "PAT01", "2017-02-25 23:00:00", "2013-02-25 19:00:00", "2014-02-25 19:00:00", "PAT01", "2017-02-25 16:00:00", "2017-02-25 14:00:00", "2017-03-25 23:00:00", "PAT01", "2017-02-25 16:00:00", "2017-02-25 14:00:00", "2017-04-29 14:00:00", ) %>% mutate( TRTSDTM = as_datetime(TRTSDTM), ASTDTM = as_datetime(ASTDTM), AENDTM = as_datetime(AENDTM) ) adcm %>% derive_vars_dtm_to_dt(exprs(TRTSDTM, ASTDTM, AENDTM)) %>% select(USUBJID, starts_with("TRT"), starts_with("AST"), starts_with("AEN"))
This function creates time variable(s) as output from datetime variable(s)
derive_vars_dtm_to_tm(dataset, source_vars)
derive_vars_dtm_to_tm(dataset, source_vars)
dataset |
Input dataset The variables specified by the |
source_vars |
A list of datetime variables created using |
The names of the newly added variables are automatically set by replacing the
--DTM
suffix of the source_vars
with --TM
. The --TM
variables are created
using the {hms}
package.
A data frame containing the input dataset with the corresponding time
(--TM
) variable(s) of all datetime variables (--DTM
) specified in
source_vars
with the correct name.
Date/Time Derivation Functions that returns variable appended to dataset:
derive_var_trtdurd()
,
derive_vars_dt()
,
derive_vars_dtm()
,
derive_vars_dtm_to_dt()
,
derive_vars_duration()
,
derive_vars_dy()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) adcm <- tribble( ~USUBJID, ~TRTSDTM, ~ASTDTM, ~AENDTM, "PAT01", "2012-02-25 23:41:10", "2012-02-28 19:03:00", "2013-02-25 23:32:16", "PAT01", "", "2012-02-28 19:00:00", "", "PAT01", "2017-02-25 23:00:02", "2013-02-25 19:00:15", "2014-02-25 19:00:56", "PAT01", "2017-02-25 16:00:00", "2017-02-25 14:25:00", "2017-03-25 23:00:00", "PAT01", "2017-02-25 16:05:17", "2017-02-25 14:20:00", "2018-04-29 14:06:45", ) %>% mutate( TRTSDTM = as_datetime(TRTSDTM), ASTDTM = as_datetime(ASTDTM), AENDTM = as_datetime(AENDTM) ) adcm %>% derive_vars_dtm_to_tm(exprs(TRTSDTM)) %>% select(USUBJID, starts_with("TRT"), everything()) adcm %>% derive_vars_dtm_to_tm(exprs(TRTSDTM, ASTDTM, AENDTM)) %>% select(USUBJID, starts_with("TRT"), starts_with("AS"), starts_with("AE"))
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) adcm <- tribble( ~USUBJID, ~TRTSDTM, ~ASTDTM, ~AENDTM, "PAT01", "2012-02-25 23:41:10", "2012-02-28 19:03:00", "2013-02-25 23:32:16", "PAT01", "", "2012-02-28 19:00:00", "", "PAT01", "2017-02-25 23:00:02", "2013-02-25 19:00:15", "2014-02-25 19:00:56", "PAT01", "2017-02-25 16:00:00", "2017-02-25 14:25:00", "2017-03-25 23:00:00", "PAT01", "2017-02-25 16:05:17", "2017-02-25 14:20:00", "2018-04-29 14:06:45", ) %>% mutate( TRTSDTM = as_datetime(TRTSDTM), ASTDTM = as_datetime(ASTDTM), AENDTM = as_datetime(AENDTM) ) adcm %>% derive_vars_dtm_to_tm(exprs(TRTSDTM)) %>% select(USUBJID, starts_with("TRT"), everything()) adcm %>% derive_vars_dtm_to_tm(exprs(TRTSDTM, ASTDTM, AENDTM)) %>% select(USUBJID, starts_with("TRT"), starts_with("AS"), starts_with("AE"))
Derives duration between two dates, specified by the variables present in input dataset e.g., duration of adverse events, relative day, age, ...
derive_vars_duration( dataset, new_var, new_var_unit = NULL, start_date, end_date, in_unit = "days", out_unit = "DAYS", floor_in = TRUE, add_one = TRUE, trunc_out = FALSE, type = "duration" )
derive_vars_duration( dataset, new_var, new_var_unit = NULL, start_date, end_date, in_unit = "days", out_unit = "DAYS", floor_in = TRUE, add_one = TRUE, trunc_out = FALSE, type = "duration" )
dataset |
Input dataset The variables specified by the |
new_var |
Name of variable to create |
new_var_unit |
Name of the unit variable If the parameter is not specified, no variable for the unit is created. |
start_date |
The start date A date or date-time object is expected. Refer to Refer to |
end_date |
The end date A date or date-time object is expected. Refer to Refer to |
in_unit |
Input unit See floor_in and add_one parameter for details. Permitted Values (case-insensitive): For years: For months: For days: For hours: For minutes: For seconds: |
out_unit |
Output unit The duration is derived in the specified unit Permitted Values (case-insensitive): For years: For months: For weeks: For days: For hours: For minutes: For seconds: |
floor_in |
Round down input dates? The input dates are round down with respect to the input unit, e.g., if the input unit is 'days', the time of the input dates is ignored. Default: Permitted Values: |
add_one |
Add one input unit? If the duration is non-negative, one input unit is added. i.e., the duration can not be zero. Default: Permitted Values: |
trunc_out |
Return integer part The fractional part of the duration (in output unit) is removed, i.e., the integer part is returned. Default: Permitted Values: |
type |
lubridate duration type. See below for details. Default: Permitted Values: |
The duration is derived as time from start to end date in the specified output unit. If the end date is before the start date, the duration is negative. The start and end date variable must be present in the specified input dataset.
The lubridate package calculates two types of spans between two dates: duration and interval. While these calculations are largely the same, when the unit of the time period is month or year the result can be slightly different.
The difference arises from the ambiguity in the length of "1 month"
or
"1 year"
.
Months may have 31, 30, 28, or 29 days, and years are 365 days and 366 during leap years.
Durations and intervals help solve the ambiguity in these measures.
The interval between 2000-02-01
and 2000-03-01
is 1
(i.e. one month).
The duration between these two dates is 0.95
, which accounts for the fact
that the year 2000 is a leap year, February has 29 days, and the average month
length is 30.4375
, i.e. 29 / 30.4375 = 0.95
.
For additional details, review the lubridate time span reference page.
The input dataset with the duration and unit variable added
Date/Time Derivation Functions that returns variable appended to dataset:
derive_var_trtdurd()
,
derive_vars_dt()
,
derive_vars_dtm()
,
derive_vars_dtm_to_dt()
,
derive_vars_dtm_to_tm()
,
derive_vars_dy()
library(lubridate) library(tibble) # Derive age in years data <- tribble( ~USUBJID, ~BRTHDT, ~RANDDT, "P01", ymd("1984-09-06"), ymd("2020-02-24"), "P02", ymd("1985-01-01"), NA, "P03", NA, ymd("2021-03-10"), "P04", NA, NA ) derive_vars_duration(data, new_var = AAGE, new_var_unit = AAGEU, start_date = BRTHDT, end_date = RANDDT, out_unit = "years", add_one = FALSE, trunc_out = TRUE ) # Derive adverse event duration in days data <- tribble( ~USUBJID, ~ASTDT, ~AENDT, "P01", ymd("2021-03-05"), ymd("2021-03-02"), "P02", ymd("2019-09-18"), ymd("2019-09-18"), "P03", ymd("1985-01-01"), NA, "P04", NA, NA ) derive_vars_duration(data, new_var = ADURN, new_var_unit = ADURU, start_date = ASTDT, end_date = AENDT, out_unit = "days" ) # Derive adverse event duration in minutes data <- tribble( ~USUBJID, ~ADTM, ~TRTSDTM, "P01", ymd_hms("2019-08-09T04:30:56"), ymd_hms("2019-08-09T05:00:00"), "P02", ymd_hms("2019-11-11T10:30:00"), ymd_hms("2019-11-11T11:30:00"), "P03", ymd_hms("2019-11-11T00:00:00"), ymd_hms("2019-11-11T04:00:00"), "P04", NA, ymd_hms("2019-11-11T12:34:56"), ) derive_vars_duration(data, new_var = ADURN, new_var_unit = ADURU, start_date = ADTM, end_date = TRTSDTM, in_unit = "minutes", out_unit = "minutes", add_one = FALSE ) # Derive adverse event start time since last dose in hours data <- tribble( ~USUBJID, ~ASTDTM, ~LDOSEDTM, "P01", ymd_hms("2019-08-09T04:30:56"), ymd_hms("2019-08-08T10:05:00"), "P02", ymd_hms("2019-11-11T23:59:59"), ymd_hms("2019-10-11T11:37:00"), "P03", ymd_hms("2019-11-11T00:00:00"), ymd_hms("2019-11-10T23:59:59"), "P04", ymd_hms("2019-11-11T12:34:56"), NA, "P05", NA, ymd_hms("2019-09-28T12:34:56") ) derive_vars_duration( data, new_var = LDRELTM, new_var_unit = LDRELTMU, start_date = LDOSEDTM, end_date = ASTDTM, in_unit = "hours", out_unit = "hours", add_one = FALSE )
library(lubridate) library(tibble) # Derive age in years data <- tribble( ~USUBJID, ~BRTHDT, ~RANDDT, "P01", ymd("1984-09-06"), ymd("2020-02-24"), "P02", ymd("1985-01-01"), NA, "P03", NA, ymd("2021-03-10"), "P04", NA, NA ) derive_vars_duration(data, new_var = AAGE, new_var_unit = AAGEU, start_date = BRTHDT, end_date = RANDDT, out_unit = "years", add_one = FALSE, trunc_out = TRUE ) # Derive adverse event duration in days data <- tribble( ~USUBJID, ~ASTDT, ~AENDT, "P01", ymd("2021-03-05"), ymd("2021-03-02"), "P02", ymd("2019-09-18"), ymd("2019-09-18"), "P03", ymd("1985-01-01"), NA, "P04", NA, NA ) derive_vars_duration(data, new_var = ADURN, new_var_unit = ADURU, start_date = ASTDT, end_date = AENDT, out_unit = "days" ) # Derive adverse event duration in minutes data <- tribble( ~USUBJID, ~ADTM, ~TRTSDTM, "P01", ymd_hms("2019-08-09T04:30:56"), ymd_hms("2019-08-09T05:00:00"), "P02", ymd_hms("2019-11-11T10:30:00"), ymd_hms("2019-11-11T11:30:00"), "P03", ymd_hms("2019-11-11T00:00:00"), ymd_hms("2019-11-11T04:00:00"), "P04", NA, ymd_hms("2019-11-11T12:34:56"), ) derive_vars_duration(data, new_var = ADURN, new_var_unit = ADURU, start_date = ADTM, end_date = TRTSDTM, in_unit = "minutes", out_unit = "minutes", add_one = FALSE ) # Derive adverse event start time since last dose in hours data <- tribble( ~USUBJID, ~ASTDTM, ~LDOSEDTM, "P01", ymd_hms("2019-08-09T04:30:56"), ymd_hms("2019-08-08T10:05:00"), "P02", ymd_hms("2019-11-11T23:59:59"), ymd_hms("2019-10-11T11:37:00"), "P03", ymd_hms("2019-11-11T00:00:00"), ymd_hms("2019-11-10T23:59:59"), "P04", ymd_hms("2019-11-11T12:34:56"), NA, "P05", NA, ymd_hms("2019-09-28T12:34:56") ) derive_vars_duration( data, new_var = LDRELTM, new_var_unit = LDRELTMU, start_date = LDOSEDTM, end_date = ASTDTM, in_unit = "hours", out_unit = "hours", add_one = FALSE )
Adds relative day variables (--DY
) to the dataset, e.g., ASTDY
and
AENDY
.
derive_vars_dy(dataset, reference_date, source_vars)
derive_vars_dy(dataset, reference_date, source_vars)
dataset |
Input dataset The variables specified by the |
reference_date |
A date or date-time column, e.g., date of first treatment or date-time of last exposure to treatment. Refer to |
source_vars |
A list of datetime or date variables created using
|
The relative day is derived as number of days from the reference date to the end date. If it is nonnegative, one is added. I.e., the relative day of the reference date is 1. Unless a name is explicitly specified, the name of the resulting relative day variable is generated from the source variable name by replacing DT (or DTM as appropriate) with DY.
The input dataset with --DY
corresponding to the --DTM
or --DT
source variable(s) added
Date/Time Derivation Functions that returns variable appended to dataset:
derive_var_trtdurd()
,
derive_vars_dt()
,
derive_vars_dtm()
,
derive_vars_dtm_to_dt()
,
derive_vars_dtm_to_tm()
,
derive_vars_duration()
library(tibble) library(lubridate) library(dplyr, warn.conflicts = FALSE) datain <- tribble( ~TRTSDTM, ~ASTDTM, ~AENDT, "2014-01-17T23:59:59", "2014-01-18T13:09:O9", "2014-01-20" ) %>% mutate( TRTSDTM = as_datetime(TRTSDTM), ASTDTM = as_datetime(ASTDTM), AENDT = ymd(AENDT) ) derive_vars_dy( datain, reference_date = TRTSDTM, source_vars = exprs(TRTSDTM, ASTDTM, AENDT) ) # specifying name of new variables datain <- tribble( ~TRTSDT, ~DTHDT, "2014-01-17", "2014-02-01" ) %>% mutate( TRTSDT = ymd(TRTSDT), DTHDT = ymd(DTHDT) ) derive_vars_dy( datain, reference_date = TRTSDT, source_vars = exprs(TRTSDT, DEATHDY = DTHDT) )
library(tibble) library(lubridate) library(dplyr, warn.conflicts = FALSE) datain <- tribble( ~TRTSDTM, ~ASTDTM, ~AENDT, "2014-01-17T23:59:59", "2014-01-18T13:09:O9", "2014-01-20" ) %>% mutate( TRTSDTM = as_datetime(TRTSDTM), ASTDTM = as_datetime(ASTDTM), AENDT = ymd(AENDT) ) derive_vars_dy( datain, reference_date = TRTSDTM, source_vars = exprs(TRTSDTM, ASTDTM, AENDT) ) # specifying name of new variables datain <- tribble( ~TRTSDT, ~DTHDT, "2014-01-17", "2014-02-01" ) %>% mutate( TRTSDT = ymd(TRTSDT), DTHDT = ymd(DTHDT) ) derive_vars_dy( datain, reference_date = TRTSDT, source_vars = exprs(TRTSDT, DEATHDY = DTHDT) )
Add the first available record from events
for each by group as new
variables, all variables of the selected observation are kept. It can be used
for selecting the extreme observation from a series of user-defined events.
derive_vars_extreme_event( dataset, by_vars, events, tmp_event_nr_var = NULL, order, mode, source_datasets = NULL, check_type = "warning", new_vars )
derive_vars_extreme_event( dataset, by_vars, events, tmp_event_nr_var = NULL, order, mode, source_datasets = NULL, check_type = "warning", new_vars )
dataset |
Input dataset The variables specified by the |
by_vars |
Grouping variables Default: Permitted Values: list of variables created by |
events |
Conditions and new values defining events A list of For |
tmp_event_nr_var |
Temporary event number variable The specified variable is added to all source datasets and is set to the number of the event before selecting the records of the event. It can be used in The variable is not included in the output dataset. |
order |
Sort order If a particular event from For handling of Permitted Values: list of expressions created by |
mode |
Selection mode (first or last) If a particular event from Permitted Values: |
source_datasets |
Source datasets A named list of datasets is expected. The |
check_type |
Check uniqueness? If Default: Permitted Values: |
new_vars |
Variables to add The specified variables from the events are added to the output
dataset. Variables can be renamed by naming the element, i.e., |
For each event select the observations to consider:
If the event is of class event
, the observations of the source dataset
are restricted by condition
and then the first or last (mode
)
observation per by group (by_vars
) is selected.
If the event is of class event_joined
, filter_joined()
is called to
select the observations.
The variables specified by the set_values_to
field of the event
are added to the selected observations.
The variable specified for tmp_event_nr_var
is added and set to
the number of the event.
All selected observations are bound together.
For each group (with respect to the variables specified for the
by_vars
parameter) the first or last observation (with respect to the
order specified for the order
parameter and the mode specified for the
mode
parameter) is selected.
The variables specified by the new_vars
parameter are added to
the selected observations.
The variables are added to input dataset.
The input dataset with the best or worst observation of each by group added as new variables.
event()
, event_joined()
, derive_extreme_event()
ADSL Functions that returns variable appended to dataset:
derive_var_age_years()
,
derive_vars_aage()
,
derive_vars_period()
library(tibble) library(dplyr) library(lubridate) adsl <- tribble( ~STUDYID, ~USUBJID, ~TRTEDT, ~DTHDT, "PILOT01", "01-1130", ymd("2014-08-16"), ymd("2014-09-13"), "PILOT01", "01-1133", ymd("2013-04-28"), ymd(""), "PILOT01", "01-1211", ymd("2013-01-12"), ymd(""), "PILOT01", "09-1081", ymd("2014-04-27"), ymd(""), "PILOT01", "09-1088", ymd("2014-10-09"), ymd("2014-11-01"), ) lb <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~LBSEQ, ~LBDTC, "PILOT01", "LB", "01-1130", 219, "2014-06-07T13:20", "PILOT01", "LB", "01-1130", 322, "2014-08-16T13:10", "PILOT01", "LB", "01-1133", 268, "2013-04-18T15:30", "PILOT01", "LB", "01-1133", 304, "2013-05-01T10:13", "PILOT01", "LB", "01-1211", 8, "2012-10-30T14:26", "PILOT01", "LB", "01-1211", 162, "2013-01-08T12:13", "PILOT01", "LB", "09-1081", 47, "2014-02-01T10:55", "PILOT01", "LB", "09-1081", 219, "2014-05-10T11:15", "PILOT01", "LB", "09-1088", 283, "2014-09-27T12:13", "PILOT01", "LB", "09-1088", 322, "2014-10-09T13:25" ) %>% mutate( ADT = convert_dtc_to_dt(LBDTC) ) derive_vars_extreme_event( adsl, by_vars = exprs(STUDYID, USUBJID), events = list( event( dataset_name = "adsl", condition = !is.na(DTHDT), set_values_to = exprs(LSTALVDT = DTHDT, DTHFL = "Y") ), event( dataset_name = "lb", condition = !is.na(ADT), order = exprs(ADT), mode = "last", set_values_to = exprs(LSTALVDT = ADT, DTHFL = "N") ), event( dataset_name = "adsl", condition = !is.na(TRTEDT), order = exprs(TRTEDT), mode = "last", set_values_to = exprs(LSTALVDT = TRTEDT, DTHFL = "N") ) ), source_datasets = list(adsl = adsl, lb = lb), tmp_event_nr_var = event_nr, order = exprs(LSTALVDT, event_nr), mode = "last", new_vars = exprs(LSTALVDT, DTHFL) ) # Derive DTHCAUS from AE and DS domain data adsl <- tribble( ~STUDYID, ~USUBJID, "STUDY01", "PAT01", "STUDY01", "PAT02", "STUDY01", "PAT03" ) ae <- tribble( ~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC, "STUDY01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-04-04", "STUDY01", "PAT01", 13, "CARDIAC ARREST", "FATAL", "2021-04-03", ) ds <- tribble( ~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC, "STUDY01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03", "STUDY01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11", "STUDY01", "PAT02", 3, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-01", "STUDY01", "PAT03", 1, "DEATH", "POST STUDY REPORTING OF DEATH", "2022-03-03" ) derive_vars_extreme_event( adsl, by_vars = exprs(STUDYID, USUBJID), events = list( event( dataset_name = "ae", condition = AEOUT == "FATAL", set_values_to = exprs(DTHCAUS = AEDECOD, DTHDT = convert_dtc_to_dt(AEDTHDTC)), order = exprs(DTHDT) ), event( dataset_name = "ds", condition = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM), set_values_to = exprs(DTHCAUS = DSTERM, DTHDT = convert_dtc_to_dt(DSSTDTC)), order = exprs(DTHDT) ) ), source_datasets = list(ae = ae, ds = ds), tmp_event_nr_var = event_nr, order = exprs(DTHDT, event_nr), mode = "first", new_vars = exprs(DTHCAUS, DTHDT) )
library(tibble) library(dplyr) library(lubridate) adsl <- tribble( ~STUDYID, ~USUBJID, ~TRTEDT, ~DTHDT, "PILOT01", "01-1130", ymd("2014-08-16"), ymd("2014-09-13"), "PILOT01", "01-1133", ymd("2013-04-28"), ymd(""), "PILOT01", "01-1211", ymd("2013-01-12"), ymd(""), "PILOT01", "09-1081", ymd("2014-04-27"), ymd(""), "PILOT01", "09-1088", ymd("2014-10-09"), ymd("2014-11-01"), ) lb <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~LBSEQ, ~LBDTC, "PILOT01", "LB", "01-1130", 219, "2014-06-07T13:20", "PILOT01", "LB", "01-1130", 322, "2014-08-16T13:10", "PILOT01", "LB", "01-1133", 268, "2013-04-18T15:30", "PILOT01", "LB", "01-1133", 304, "2013-05-01T10:13", "PILOT01", "LB", "01-1211", 8, "2012-10-30T14:26", "PILOT01", "LB", "01-1211", 162, "2013-01-08T12:13", "PILOT01", "LB", "09-1081", 47, "2014-02-01T10:55", "PILOT01", "LB", "09-1081", 219, "2014-05-10T11:15", "PILOT01", "LB", "09-1088", 283, "2014-09-27T12:13", "PILOT01", "LB", "09-1088", 322, "2014-10-09T13:25" ) %>% mutate( ADT = convert_dtc_to_dt(LBDTC) ) derive_vars_extreme_event( adsl, by_vars = exprs(STUDYID, USUBJID), events = list( event( dataset_name = "adsl", condition = !is.na(DTHDT), set_values_to = exprs(LSTALVDT = DTHDT, DTHFL = "Y") ), event( dataset_name = "lb", condition = !is.na(ADT), order = exprs(ADT), mode = "last", set_values_to = exprs(LSTALVDT = ADT, DTHFL = "N") ), event( dataset_name = "adsl", condition = !is.na(TRTEDT), order = exprs(TRTEDT), mode = "last", set_values_to = exprs(LSTALVDT = TRTEDT, DTHFL = "N") ) ), source_datasets = list(adsl = adsl, lb = lb), tmp_event_nr_var = event_nr, order = exprs(LSTALVDT, event_nr), mode = "last", new_vars = exprs(LSTALVDT, DTHFL) ) # Derive DTHCAUS from AE and DS domain data adsl <- tribble( ~STUDYID, ~USUBJID, "STUDY01", "PAT01", "STUDY01", "PAT02", "STUDY01", "PAT03" ) ae <- tribble( ~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC, "STUDY01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-04-04", "STUDY01", "PAT01", 13, "CARDIAC ARREST", "FATAL", "2021-04-03", ) ds <- tribble( ~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC, "STUDY01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03", "STUDY01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11", "STUDY01", "PAT02", 3, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-01", "STUDY01", "PAT03", 1, "DEATH", "POST STUDY REPORTING OF DEATH", "2022-03-03" ) derive_vars_extreme_event( adsl, by_vars = exprs(STUDYID, USUBJID), events = list( event( dataset_name = "ae", condition = AEOUT == "FATAL", set_values_to = exprs(DTHCAUS = AEDECOD, DTHDT = convert_dtc_to_dt(AEDTHDTC)), order = exprs(DTHDT) ), event( dataset_name = "ds", condition = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM), set_values_to = exprs(DTHCAUS = DSTERM, DTHDT = convert_dtc_to_dt(DSSTDTC)), order = exprs(DTHDT) ) ), source_datasets = list(ae = ae, ds = ds), tmp_event_nr_var = event_nr, order = exprs(DTHDT, event_nr), mode = "first", new_vars = exprs(DTHCAUS, DTHDT) )
The function adds variables from an additional dataset to the input dataset. The selection of the observations from the additional dataset can depend on variables from both datasets. For example, add the lowest value (nadir) before the current observation.
derive_vars_joined( dataset, dataset_add, by_vars = NULL, order = NULL, new_vars = NULL, tmp_obs_nr_var = NULL, join_vars = NULL, join_type, filter_add = NULL, first_cond_lower = NULL, first_cond_upper = NULL, filter_join = NULL, mode = NULL, exist_flag = NULL, true_value = "Y", false_value = NA_character_, missing_values = NULL, check_type = "warning" )
derive_vars_joined( dataset, dataset_add, by_vars = NULL, order = NULL, new_vars = NULL, tmp_obs_nr_var = NULL, join_vars = NULL, join_type, filter_add = NULL, first_cond_lower = NULL, first_cond_upper = NULL, filter_join = NULL, mode = NULL, exist_flag = NULL, true_value = "Y", false_value = NA_character_, missing_values = NULL, check_type = "warning" )
dataset |
Input dataset The variables specified by the |
dataset_add |
Additional dataset The variables specified by the |
by_vars |
Grouping variables The two datasets are joined by the specified variables. Variables can be renamed by naming the element, i.e.
Permitted Values: list of variables created by |
order |
Sort order If the argument is set to a non-null value, for each observation of the
input dataset the first or last observation from the joined dataset is
selected with respect to the specified order. The specified variables are
expected in the additional dataset ( If an expression is named, e.g., For handling of Permitted Values: list of expressions created by |
new_vars |
Variables to add The specified variables from the additional dataset are added to the output
dataset. Variables can be renamed by naming the element, i.e., For example And Values of the added variables can be modified by specifying an expression.
For example, If the argument is not specified or set to Permitted Values: list of variables or named expressions created by |
tmp_obs_nr_var |
Temporary observation number The specified variable is added to the input dataset ( The variable is not included in the output dataset. To include it specify
it for |
join_vars |
Variables to use from additional dataset Any extra variables required from the additional dataset for If an expression is named, e.g., The variables are not included in the output dataset. Permitted Values: list of variables or named expressions created by |
join_type |
Observations to keep after joining The argument determines which of the joined observations are kept with
respect to the original observation. For example, if For example for confirmed response or BOR in the oncology setting or
confirmed deterioration in questionnaires the confirmatory assessment must
be after the assessment. Thus Whereas, sometimes you might allow for confirmatory observations to occur
prior to the observation. For example, to identify AEs occurring on or
after seven days before a COVID AE. Thus Permitted Values: |
filter_add |
Filter for additional dataset ( Only observations from Variables created by The condition can include summary functions like Permitted Values: a condition |
first_cond_lower |
Condition for selecting range of data (before) If this argument is specified, the other observations are restricted from the first observation before the current observation where the specified condition is fulfilled up to the current observation. If the condition is not fulfilled for any of the other observations, no observations are considered. This argument should be specified if |
first_cond_upper |
Condition for selecting range of data (after) If this argument is specified, the other observations are restricted up to the first observation where the specified condition is fulfilled. If the condition is not fulfilled for any of the other observations, no observations are considered. This argument should be specified if |
filter_join |
Filter for the joined dataset The specified condition is applied to the joined dataset. Therefore
variables from both datasets Variables created by The condition can include summary functions like Permitted Values: a condition |
mode |
Selection mode Determines if the first or last observation is selected. If the If the Permitted Values: |
exist_flag |
Exist flag If the argument is specified (e.g., Permitted Values: Variable name |
true_value |
True value The value for the specified variable Permitted Values: An atomic scalar |
false_value |
False value The value for the specified variable Permitted Values: An atomic scalar |
missing_values |
Values for non-matching observations For observations of the input dataset ( Permitted Values: named list of expressions, e.g.,
|
check_type |
Check uniqueness? If This argument is ignored if Permitted Values: |
The variables specified by order
are added to the additional dataset
(dataset_add
).
The variables specified by join_vars
are added to the additional dataset
(dataset_add
).
The records from the additional dataset (dataset_add
) are restricted to
those matching the filter_add
condition.
The input dataset and the (restricted) additional dataset are left joined
by the grouping variables (by_vars
). If no grouping variables are
specified, a full join is performed.
If first_cond_lower
is specified, for each observation of the input
dataset the joined dataset is restricted to observations from the first
observation where first_cond_lower
is fulfilled (the observation fulfilling
the condition is included) up to the observation of the input dataset. If for
an observation of the input dataset the condition is not fulfilled, the
observation is removed.
If first_cond_upper
is specified, for each observation of the input
dataset the joined dataset is restricted to observations up to the first
observation where first_cond_upper
is fulfilled (the observation
fulfilling the condition is included). If for an observation of the input
dataset the condition is not fulfilled, the observation is removed.
For an example see the last example in the "Examples" section.
The joined dataset is restricted by the filter_join
condition.
If order
is specified, for each observation of the input dataset the
first or last observation (depending on mode
) is selected.
The variables specified for new_vars
are created (if requested) and
merged to the input dataset. I.e., the output dataset contains all
observations from the input dataset. For observations without a matching
observation in the joined dataset the new variables are set as specified by
missing_values
(or to NA
for variables not in missing_values
).
Observations in the additional dataset which have no matching observation in
the input dataset are ignored.
The output dataset contains all observations and variables of the
input dataset and additionally the variables specified for new_vars
from
the additional dataset (dataset_add
).
derive_var_joined_exist_flag()
, filter_joined()
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_extreme_flag()
,
derive_var_joined_exist_flag()
,
derive_var_merged_ef_msrc()
,
derive_var_merged_exist_flag()
,
derive_var_merged_summary()
,
derive_var_obs_number()
,
derive_var_relative_flag()
,
derive_vars_cat()
,
derive_vars_computed()
,
derive_vars_merged()
,
derive_vars_merged_lookup()
,
derive_vars_transposed()
library(tibble) library(lubridate) library(dplyr, warn.conflicts = FALSE) library(tidyr) # Add AVISIT (based on time windows), AWLO, and AWHI adbds <- tribble( ~USUBJID, ~ADY, "1", -33, "1", -2, "1", 3, "1", 24, "2", NA, ) windows <- tribble( ~AVISIT, ~AWLO, ~AWHI, "BASELINE", -30, 1, "WEEK 1", 2, 7, "WEEK 2", 8, 15, "WEEK 3", 16, 22, "WEEK 4", 23, 30 ) derive_vars_joined( adbds, dataset_add = windows, join_type = "all", filter_join = AWLO <= ADY & ADY <= AWHI ) # derive the nadir after baseline and before the current observation adbds <- tribble( ~USUBJID, ~ADY, ~AVAL, "1", -7, 10, "1", 1, 12, "1", 8, 11, "1", 15, 9, "1", 20, 14, "1", 24, 12, "2", 13, 8 ) derive_vars_joined( adbds, dataset_add = adbds, by_vars = exprs(USUBJID), order = exprs(AVAL), new_vars = exprs(NADIR = AVAL), join_vars = exprs(ADY), join_type = "all", filter_add = ADY > 0, filter_join = ADY.join < ADY, mode = "first", check_type = "none" ) # add highest hemoglobin value within two weeks before AE, # take earliest if more than one adae <- tribble( ~USUBJID, ~ASTDY, "1", 3, "1", 22, "2", 2 ) adlb <- tribble( ~USUBJID, ~PARAMCD, ~ADY, ~AVAL, "1", "HGB", 1, 8.5, "1", "HGB", 3, 7.9, "1", "HGB", 5, 8.9, "1", "HGB", 8, 8.0, "1", "HGB", 9, 8.0, "1", "HGB", 16, 7.4, "1", "HGB", 24, 8.1, "1", "ALB", 1, 42, ) derive_vars_joined( adae, dataset_add = adlb, by_vars = exprs(USUBJID), order = exprs(AVAL, desc(ADY)), new_vars = exprs(HGB_MAX = AVAL, HGB_DY = ADY), join_type = "all", filter_add = PARAMCD == "HGB", filter_join = ASTDY - 14 <= ADY & ADY <= ASTDY, mode = "last" ) # Add APERIOD, APERIODC based on ADSL adsl <- tribble( ~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT, "1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01" ) %>% mutate(across(ends_with("DT"), ymd)) %>% mutate(STUDYID = "xyz") period_ref <- create_period_dataset( adsl, new_vars = exprs(APERSDT = APxxSDT, APEREDT = APxxEDT) ) period_ref adae <- tribble( ~USUBJID, ~ASTDT, "1", "2021-01-01", "1", "2021-01-05", "1", "2021-02-05", "1", "2021-03-05", "1", "2021-04-05", "2", "2021-02-15", ) %>% mutate( ASTDT = ymd(ASTDT), STUDYID = "xyz" ) derive_vars_joined( adae, dataset_add = period_ref, by_vars = exprs(STUDYID, USUBJID), join_vars = exprs(APERSDT, APEREDT), join_type = "all", filter_join = APERSDT <= ASTDT & ASTDT <= APEREDT ) # Add day since last dose (LDRELD) adae <- tribble( ~USUBJID, ~ASTDT, ~AESEQ, "1", "2020-02-02", 1, "1", "2020-02-04", 2 ) %>% mutate(ASTDT = ymd(ASTDT)) ex <- tribble( ~USUBJID, ~EXSDTC, "1", "2020-01-10", "1", "2020-01", "1", "2020-01-20", "1", "2020-02-03" ) ## Please note that EXSDT is created via the order argument and then used ## for new_vars, filter_add, and filter_join derive_vars_joined( adae, dataset_add = ex, by_vars = exprs(USUBJID), order = exprs(EXSDT = convert_dtc_to_dt(EXSDTC)), join_type = "all", new_vars = exprs(LDRELD = compute_duration( start_date = EXSDT, end_date = ASTDT )), filter_add = !is.na(EXSDT), filter_join = EXSDT <= ASTDT, mode = "last" ) # first_cond_lower and first_cond_upper argument myd <- tribble( ~subj, ~day, ~val, "1", 1, "++", "1", 2, "-", "1", 3, "0", "1", 4, "+", "1", 5, "++", "1", 6, "-", "2", 1, "-", "2", 2, "++", "2", 3, "+", "2", 4, "0", "2", 5, "-", "2", 6, "++" ) # derive last "++" day before "0" where all results in between are "+" or "++" derive_vars_joined( myd, dataset_add = myd, by_vars = exprs(subj), order = exprs(day), mode = "first", new_vars = exprs(prev_plus_day = day), join_vars = exprs(val), join_type = "before", first_cond_lower = val.join == "++", filter_join = val == "0" & all(val.join %in% c("+", "++")) ) # derive first "++" day after "0" where all results in between are "+" or "++" derive_vars_joined( myd, dataset_add = myd, by_vars = exprs(subj), order = exprs(day), mode = "last", new_vars = exprs(next_plus_day = day), join_vars = exprs(val), join_type = "after", first_cond_upper = val.join == "++", filter_join = val == "0" & all(val.join %in% c("+", "++")) )
library(tibble) library(lubridate) library(dplyr, warn.conflicts = FALSE) library(tidyr) # Add AVISIT (based on time windows), AWLO, and AWHI adbds <- tribble( ~USUBJID, ~ADY, "1", -33, "1", -2, "1", 3, "1", 24, "2", NA, ) windows <- tribble( ~AVISIT, ~AWLO, ~AWHI, "BASELINE", -30, 1, "WEEK 1", 2, 7, "WEEK 2", 8, 15, "WEEK 3", 16, 22, "WEEK 4", 23, 30 ) derive_vars_joined( adbds, dataset_add = windows, join_type = "all", filter_join = AWLO <= ADY & ADY <= AWHI ) # derive the nadir after baseline and before the current observation adbds <- tribble( ~USUBJID, ~ADY, ~AVAL, "1", -7, 10, "1", 1, 12, "1", 8, 11, "1", 15, 9, "1", 20, 14, "1", 24, 12, "2", 13, 8 ) derive_vars_joined( adbds, dataset_add = adbds, by_vars = exprs(USUBJID), order = exprs(AVAL), new_vars = exprs(NADIR = AVAL), join_vars = exprs(ADY), join_type = "all", filter_add = ADY > 0, filter_join = ADY.join < ADY, mode = "first", check_type = "none" ) # add highest hemoglobin value within two weeks before AE, # take earliest if more than one adae <- tribble( ~USUBJID, ~ASTDY, "1", 3, "1", 22, "2", 2 ) adlb <- tribble( ~USUBJID, ~PARAMCD, ~ADY, ~AVAL, "1", "HGB", 1, 8.5, "1", "HGB", 3, 7.9, "1", "HGB", 5, 8.9, "1", "HGB", 8, 8.0, "1", "HGB", 9, 8.0, "1", "HGB", 16, 7.4, "1", "HGB", 24, 8.1, "1", "ALB", 1, 42, ) derive_vars_joined( adae, dataset_add = adlb, by_vars = exprs(USUBJID), order = exprs(AVAL, desc(ADY)), new_vars = exprs(HGB_MAX = AVAL, HGB_DY = ADY), join_type = "all", filter_add = PARAMCD == "HGB", filter_join = ASTDY - 14 <= ADY & ADY <= ASTDY, mode = "last" ) # Add APERIOD, APERIODC based on ADSL adsl <- tribble( ~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT, "1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01" ) %>% mutate(across(ends_with("DT"), ymd)) %>% mutate(STUDYID = "xyz") period_ref <- create_period_dataset( adsl, new_vars = exprs(APERSDT = APxxSDT, APEREDT = APxxEDT) ) period_ref adae <- tribble( ~USUBJID, ~ASTDT, "1", "2021-01-01", "1", "2021-01-05", "1", "2021-02-05", "1", "2021-03-05", "1", "2021-04-05", "2", "2021-02-15", ) %>% mutate( ASTDT = ymd(ASTDT), STUDYID = "xyz" ) derive_vars_joined( adae, dataset_add = period_ref, by_vars = exprs(STUDYID, USUBJID), join_vars = exprs(APERSDT, APEREDT), join_type = "all", filter_join = APERSDT <= ASTDT & ASTDT <= APEREDT ) # Add day since last dose (LDRELD) adae <- tribble( ~USUBJID, ~ASTDT, ~AESEQ, "1", "2020-02-02", 1, "1", "2020-02-04", 2 ) %>% mutate(ASTDT = ymd(ASTDT)) ex <- tribble( ~USUBJID, ~EXSDTC, "1", "2020-01-10", "1", "2020-01", "1", "2020-01-20", "1", "2020-02-03" ) ## Please note that EXSDT is created via the order argument and then used ## for new_vars, filter_add, and filter_join derive_vars_joined( adae, dataset_add = ex, by_vars = exprs(USUBJID), order = exprs(EXSDT = convert_dtc_to_dt(EXSDTC)), join_type = "all", new_vars = exprs(LDRELD = compute_duration( start_date = EXSDT, end_date = ASTDT )), filter_add = !is.na(EXSDT), filter_join = EXSDT <= ASTDT, mode = "last" ) # first_cond_lower and first_cond_upper argument myd <- tribble( ~subj, ~day, ~val, "1", 1, "++", "1", 2, "-", "1", 3, "0", "1", 4, "+", "1", 5, "++", "1", 6, "-", "2", 1, "-", "2", 2, "++", "2", 3, "+", "2", 4, "0", "2", 5, "-", "2", 6, "++" ) # derive last "++" day before "0" where all results in between are "+" or "++" derive_vars_joined( myd, dataset_add = myd, by_vars = exprs(subj), order = exprs(day), mode = "first", new_vars = exprs(prev_plus_day = day), join_vars = exprs(val), join_type = "before", first_cond_lower = val.join == "++", filter_join = val == "0" & all(val.join %in% c("+", "++")) ) # derive first "++" day after "0" where all results in between are "+" or "++" derive_vars_joined( myd, dataset_add = myd, by_vars = exprs(subj), order = exprs(day), mode = "last", new_vars = exprs(next_plus_day = day), join_vars = exprs(val), join_type = "after", first_cond_upper = val.join == "++", filter_join = val == "0" & all(val.join %in% c("+", "++")) )
Add new variable(s) to the input dataset based on variables from another
dataset. The observations to merge can be selected by a condition
(filter_add
argument) and/or selecting the first or last observation for
each by group (order
and mode
argument).
derive_vars_merged( dataset, dataset_add, by_vars, order = NULL, new_vars = NULL, filter_add = NULL, mode = NULL, exist_flag = NULL, true_value = "Y", false_value = NA_character_, missing_values = NULL, check_type = "warning", duplicate_msg = NULL, relationship = NULL )
derive_vars_merged( dataset, dataset_add, by_vars, order = NULL, new_vars = NULL, filter_add = NULL, mode = NULL, exist_flag = NULL, true_value = "Y", false_value = NA_character_, missing_values = NULL, check_type = "warning", duplicate_msg = NULL, relationship = NULL )
dataset |
Input dataset The variables specified by the |
dataset_add |
Additional dataset The variables specified by the |
by_vars |
Grouping variables The input dataset and the selected observations from the additional dataset are merged by the specified variables. Variables can be renamed by naming the element, i.e.
Permitted Values: list of variables created by |
order |
Sort order If the argument is set to a non-null value, for each by group the first or last observation from the additional dataset is selected with respect to the specified order. Variables defined by the For handling of Permitted Values: list of expressions created by |
new_vars |
Variables to add The specified variables from the additional dataset are added to the output
dataset. Variables can be renamed by naming the element, i.e., For example And Values of the added variables can be modified by specifying an expression.
For example, If the argument is not specified or set to Permitted Values: list of variables or named expressions created by |
filter_add |
Filter for additional dataset ( Only observations fulfilling the specified condition are taken into account for merging. If the argument is not specified, all observations are considered. Variables defined by the Permitted Values: a condition |
mode |
Selection mode Determines if the first or last observation is selected. If the If the Permitted Values: |
exist_flag |
Exist flag If the argument is specified (e.g., Permitted Values: Variable name |
true_value |
True value The value for the specified variable Permitted Values: An atomic scalar |
false_value |
False value The value for the specified variable Permitted Values: An atomic scalar |
missing_values |
Values for non-matching observations For observations of the input dataset ( Permitted Values: named list of expressions, e.g.,
|
check_type |
Check uniqueness? If If the Permitted Values: |
duplicate_msg |
Message of unique check If the uniqueness check fails, the specified message is displayed. Default: paste( "Dataset {.arg dataset_add} contains duplicate records with respect to", "{.var {vars2chr(by_vars)}}." ) |
relationship |
Expected merge-relationship between the This argument is passed to the Permitted Values: |
The new variables (new_vars
) are added to the additional dataset
(dataset_add
).
The records from the additional dataset (dataset_add
) are restricted
to those matching the filter_add
condition.
If order
is specified, for each by group the first or last observation
(depending on mode
) is selected.
The variables specified for new_vars
are merged to the input dataset
using left_join()
. I.e., the output dataset contains all observations
from the input dataset. For observations without a matching observation in
the additional dataset the new variables are set as specified by
missing_values
(or to NA
for variables not in missing_values
).
Observations in the additional dataset which have no matching observation
in the input dataset are ignored.
The output dataset contains all observations and variables of the
input dataset and additionally the variables specified for new_vars
from
the additional dataset (dataset_add
).
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_extreme_flag()
,
derive_var_joined_exist_flag()
,
derive_var_merged_ef_msrc()
,
derive_var_merged_exist_flag()
,
derive_var_merged_summary()
,
derive_var_obs_number()
,
derive_var_relative_flag()
,
derive_vars_cat()
,
derive_vars_computed()
,
derive_vars_joined()
,
derive_vars_merged_lookup()
,
derive_vars_transposed()
library(dplyr, warn.conflicts = FALSE) vs <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~VSTESTCD, ~VISIT, ~VSSTRESN, ~VSSTRESU, ~VSDTC, "PILOT01", "VS", "01-1302", "HEIGHT", "SCREENING", 177.8, "cm", "2013-08-20", "PILOT01", "VS", "01-1302", "WEIGHT", "SCREENING", 81.19, "kg", "2013-08-20", "PILOT01", "VS", "01-1302", "WEIGHT", "BASELINE", 82.1, "kg", "2013-08-29", "PILOT01", "VS", "01-1302", "WEIGHT", "WEEK 2", 81.19, "kg", "2013-09-15", "PILOT01", "VS", "01-1302", "WEIGHT", "WEEK 4", 82.56, "kg", "2013-09-24", "PILOT01", "VS", "01-1302", "WEIGHT", "WEEK 6", 80.74, "kg", "2013-10-08", "PILOT01", "VS", "01-1302", "WEIGHT", "WEEK 8", 82.1, "kg", "2013-10-22", "PILOT01", "VS", "01-1302", "WEIGHT", "WEEK 12", 82.1, "kg", "2013-11-05", "PILOT01", "VS", "17-1344", "HEIGHT", "SCREENING", 163.5, "cm", "2014-01-01", "PILOT01", "VS", "17-1344", "WEIGHT", "SCREENING", 58.06, "kg", "2014-01-01", "PILOT01", "VS", "17-1344", "WEIGHT", "BASELINE", 58.06, "kg", "2014-01-11", "PILOT01", "VS", "17-1344", "WEIGHT", "WEEK 2", 58.97, "kg", "2014-01-24", "PILOT01", "VS", "17-1344", "WEIGHT", "WEEK 4", 57.97, "kg", "2014-02-07", "PILOT01", "VS", "17-1344", "WEIGHT", "WEEK 6", 58.97, "kg", "2014-02-19", "PILOT01", "VS", "17-1344", "WEIGHT", "WEEK 8", 57.79, "kg", "2014-03-14" ) dm <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "DM", "01-1302", 61, "YEARS", "PILOT01", "DM", "17-1344", 64, "YEARS" ) # Merging all dm variables to vs derive_vars_merged( vs, dataset_add = select(dm, -DOMAIN), by_vars = exprs(STUDYID, USUBJID) ) %>% select(STUDYID, USUBJID, VSTESTCD, VISIT, VSSTRESN, AGE, AGEU) # Merge last weight to adsl adsl <- tribble( ~STUDYID, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "01-1302", 61, "YEARS", "PILOT01", "17-1344", 64, "YEARS" ) derive_vars_merged( adsl, dataset_add = vs, by_vars = exprs(STUDYID, USUBJID), order = exprs(convert_dtc_to_dtm(VSDTC)), mode = "last", new_vars = exprs(LASTWGT = VSSTRESN, LASTWGTU = VSSTRESU), filter_add = VSTESTCD == "WEIGHT", exist_flag = vsdatafl ) %>% select(STUDYID, USUBJID, AGE, AGEU, LASTWGT, LASTWGTU, vsdatafl) # Derive treatment start datetime (TRTSDTM) ex <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~EXSTDY, ~EXENDY, ~EXSTDTC, ~EXENDTC, "PILOT01", "EX", "01-1302", 1, 18, "2013-08-29", "2013-09-15", "PILOT01", "EX", "01-1302", 19, 69, "2013-09-16", "2013-11-05", "PILOT01", "EX", "17-1344", 1, 14, "2014-01-11", "2014-01-24", "PILOT01", "EX", "17-1344", 15, 63, "2014-01-25", "2014-03-14" ) ## Impute exposure start date to first date/time ex_ext <- derive_vars_dtm( ex, dtc = EXSTDTC, new_vars_prefix = "EXST", highest_imputation = "M", ) ## Add first exposure datetime and imputation flags to adsl derive_vars_merged( select(dm, STUDYID, USUBJID), dataset_add = ex_ext, by_vars = exprs(STUDYID, USUBJID), new_vars = exprs(TRTSDTM = EXSTDTM, TRTSDTF = EXSTDTF, TRTSTMF = EXSTTMF), order = exprs(EXSTDTM), mode = "first" ) # Derive treatment end datetime (TRTEDTM) ## Impute exposure end datetime to last time, no date imputation ex_ext <- derive_vars_dtm( ex, dtc = EXENDTC, new_vars_prefix = "EXEN", time_imputation = "last", ) ## Add last exposure datetime and imputation flag to adsl derive_vars_merged( select(adsl, STUDYID, USUBJID), dataset_add = ex_ext, filter_add = !is.na(EXENDTM), by_vars = exprs(STUDYID, USUBJID), new_vars = exprs(TRTEDTM = EXENDTM, TRTETMF = EXENTMF), order = exprs(EXENDTM), mode = "last" ) # Modify merged values and set value for non matching observations adsl <- tribble( ~USUBJID, ~SEX, ~COUNTRY, "ST42-1", "F", "AUT", "ST42-2", "M", "MWI", "ST42-3", "M", "NOR", "ST42-4", "F", "UGA" ) advs <- tribble( ~USUBJID, ~PARAMCD, ~AVISIT, ~AVISITN, ~AVAL, "ST42-1", "WEIGHT", "BASELINE", 0, 66, "ST42-1", "WEIGHT", "WEEK 2", 1, 68, "ST42-2", "WEIGHT", "BASELINE", 0, 88, "ST42-3", "WEIGHT", "WEEK 2", 1, 55, "ST42-3", "WEIGHT", "WEEK 4", 2, 50 ) derive_vars_merged( adsl, dataset_add = advs, by_vars = exprs(USUBJID), new_vars = exprs( LSTVSCAT = if_else(AVISIT == "BASELINE", "BASELINE", "POST-BASELINE") ), order = exprs(AVISITN), mode = "last", missing_values = exprs(LSTVSCAT = "MISSING") )
library(dplyr, warn.conflicts = FALSE) vs <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~VSTESTCD, ~VISIT, ~VSSTRESN, ~VSSTRESU, ~VSDTC, "PILOT01", "VS", "01-1302", "HEIGHT", "SCREENING", 177.8, "cm", "2013-08-20", "PILOT01", "VS", "01-1302", "WEIGHT", "SCREENING", 81.19, "kg", "2013-08-20", "PILOT01", "VS", "01-1302", "WEIGHT", "BASELINE", 82.1, "kg", "2013-08-29", "PILOT01", "VS", "01-1302", "WEIGHT", "WEEK 2", 81.19, "kg", "2013-09-15", "PILOT01", "VS", "01-1302", "WEIGHT", "WEEK 4", 82.56, "kg", "2013-09-24", "PILOT01", "VS", "01-1302", "WEIGHT", "WEEK 6", 80.74, "kg", "2013-10-08", "PILOT01", "VS", "01-1302", "WEIGHT", "WEEK 8", 82.1, "kg", "2013-10-22", "PILOT01", "VS", "01-1302", "WEIGHT", "WEEK 12", 82.1, "kg", "2013-11-05", "PILOT01", "VS", "17-1344", "HEIGHT", "SCREENING", 163.5, "cm", "2014-01-01", "PILOT01", "VS", "17-1344", "WEIGHT", "SCREENING", 58.06, "kg", "2014-01-01", "PILOT01", "VS", "17-1344", "WEIGHT", "BASELINE", 58.06, "kg", "2014-01-11", "PILOT01", "VS", "17-1344", "WEIGHT", "WEEK 2", 58.97, "kg", "2014-01-24", "PILOT01", "VS", "17-1344", "WEIGHT", "WEEK 4", 57.97, "kg", "2014-02-07", "PILOT01", "VS", "17-1344", "WEIGHT", "WEEK 6", 58.97, "kg", "2014-02-19", "PILOT01", "VS", "17-1344", "WEIGHT", "WEEK 8", 57.79, "kg", "2014-03-14" ) dm <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "DM", "01-1302", 61, "YEARS", "PILOT01", "DM", "17-1344", 64, "YEARS" ) # Merging all dm variables to vs derive_vars_merged( vs, dataset_add = select(dm, -DOMAIN), by_vars = exprs(STUDYID, USUBJID) ) %>% select(STUDYID, USUBJID, VSTESTCD, VISIT, VSSTRESN, AGE, AGEU) # Merge last weight to adsl adsl <- tribble( ~STUDYID, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "01-1302", 61, "YEARS", "PILOT01", "17-1344", 64, "YEARS" ) derive_vars_merged( adsl, dataset_add = vs, by_vars = exprs(STUDYID, USUBJID), order = exprs(convert_dtc_to_dtm(VSDTC)), mode = "last", new_vars = exprs(LASTWGT = VSSTRESN, LASTWGTU = VSSTRESU), filter_add = VSTESTCD == "WEIGHT", exist_flag = vsdatafl ) %>% select(STUDYID, USUBJID, AGE, AGEU, LASTWGT, LASTWGTU, vsdatafl) # Derive treatment start datetime (TRTSDTM) ex <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~EXSTDY, ~EXENDY, ~EXSTDTC, ~EXENDTC, "PILOT01", "EX", "01-1302", 1, 18, "2013-08-29", "2013-09-15", "PILOT01", "EX", "01-1302", 19, 69, "2013-09-16", "2013-11-05", "PILOT01", "EX", "17-1344", 1, 14, "2014-01-11", "2014-01-24", "PILOT01", "EX", "17-1344", 15, 63, "2014-01-25", "2014-03-14" ) ## Impute exposure start date to first date/time ex_ext <- derive_vars_dtm( ex, dtc = EXSTDTC, new_vars_prefix = "EXST", highest_imputation = "M", ) ## Add first exposure datetime and imputation flags to adsl derive_vars_merged( select(dm, STUDYID, USUBJID), dataset_add = ex_ext, by_vars = exprs(STUDYID, USUBJID), new_vars = exprs(TRTSDTM = EXSTDTM, TRTSDTF = EXSTDTF, TRTSTMF = EXSTTMF), order = exprs(EXSTDTM), mode = "first" ) # Derive treatment end datetime (TRTEDTM) ## Impute exposure end datetime to last time, no date imputation ex_ext <- derive_vars_dtm( ex, dtc = EXENDTC, new_vars_prefix = "EXEN", time_imputation = "last", ) ## Add last exposure datetime and imputation flag to adsl derive_vars_merged( select(adsl, STUDYID, USUBJID), dataset_add = ex_ext, filter_add = !is.na(EXENDTM), by_vars = exprs(STUDYID, USUBJID), new_vars = exprs(TRTEDTM = EXENDTM, TRTETMF = EXENTMF), order = exprs(EXENDTM), mode = "last" ) # Modify merged values and set value for non matching observations adsl <- tribble( ~USUBJID, ~SEX, ~COUNTRY, "ST42-1", "F", "AUT", "ST42-2", "M", "MWI", "ST42-3", "M", "NOR", "ST42-4", "F", "UGA" ) advs <- tribble( ~USUBJID, ~PARAMCD, ~AVISIT, ~AVISITN, ~AVAL, "ST42-1", "WEIGHT", "BASELINE", 0, 66, "ST42-1", "WEIGHT", "WEEK 2", 1, 68, "ST42-2", "WEIGHT", "BASELINE", 0, 88, "ST42-3", "WEIGHT", "WEEK 2", 1, 55, "ST42-3", "WEIGHT", "WEEK 4", 2, 50 ) derive_vars_merged( adsl, dataset_add = advs, by_vars = exprs(USUBJID), new_vars = exprs( LSTVSCAT = if_else(AVISIT == "BASELINE", "BASELINE", "POST-BASELINE") ), order = exprs(AVISITN), mode = "last", missing_values = exprs(LSTVSCAT = "MISSING") )
Merge user-defined lookup table with the input dataset. Optionally print a list of records from the input dataset that do not have corresponding mapping from the lookup table.
derive_vars_merged_lookup( dataset, dataset_add, by_vars, order = NULL, new_vars = NULL, mode = NULL, filter_add = NULL, check_type = "warning", duplicate_msg = NULL, print_not_mapped = TRUE )
derive_vars_merged_lookup( dataset, dataset_add, by_vars, order = NULL, new_vars = NULL, mode = NULL, filter_add = NULL, check_type = "warning", duplicate_msg = NULL, print_not_mapped = TRUE )
dataset |
Input dataset The variables specified by the |
dataset_add |
Lookup table The variables specified by the |
by_vars |
Grouping variables The input dataset and the selected observations from the additional dataset are merged by the specified variables. Variables can be renamed by naming the element, i.e.
Permitted Values: list of variables created by |
order |
Sort order If the argument is set to a non-null value, for each by group the first or last observation from the additional dataset is selected with respect to the specified order. Variables defined by the For handling of Permitted Values: list of expressions created by |
new_vars |
Variables to add The specified variables from the additional dataset are added to the output
dataset. Variables can be renamed by naming the element, i.e., For example And Values of the added variables can be modified by specifying an expression.
For example, If the argument is not specified or set to Permitted Values: list of variables or named expressions created by |
mode |
Selection mode Determines if the first or last observation is selected. If the If the Permitted Values: |
filter_add |
Filter for additional dataset ( Only observations fulfilling the specified condition are taken into account for merging. If the argument is not specified, all observations are considered. Variables defined by the Permitted Values: a condition |
check_type |
Check uniqueness? If If the Permitted Values: |
duplicate_msg |
Message of unique check If the uniqueness check fails, the specified message is displayed. Default: paste( "Dataset {.arg dataset_add} contains duplicate records with respect to", "{.var {vars2chr(by_vars)}}." ) |
print_not_mapped |
Print a list of unique Default: Permitted Values: |
The output dataset contains all observations and variables of the
input dataset, and add the variables specified in new_vars
from the lookup
table specified in dataset_add
. Optionally prints a list of unique
by_vars
values that do not have corresponding records
from the lookup table (by specifying print_not_mapped = TRUE
).
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_extreme_flag()
,
derive_var_joined_exist_flag()
,
derive_var_merged_ef_msrc()
,
derive_var_merged_exist_flag()
,
derive_var_merged_summary()
,
derive_var_obs_number()
,
derive_var_relative_flag()
,
derive_vars_cat()
,
derive_vars_computed()
,
derive_vars_joined()
,
derive_vars_merged()
,
derive_vars_transposed()
library(dplyr, warn.conflicts = FALSE) vs <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~VISIT, ~VSTESTCD, ~VSTEST, "PILOT01", "VS", "01-1028", "SCREENING", "HEIGHT", "Height", "PILOT01", "VS", "01-1028", "SCREENING", "TEMP", "Temperature", "PILOT01", "VS", "01-1028", "BASELINE", "TEMP", "Temperature", "PILOT01", "VS", "01-1028", "WEEK 4", "TEMP", "Temperature", "PILOT01", "VS", "01-1028", "SCREENING 1", "WEIGHT", "Weight", "PILOT01", "VS", "01-1028", "BASELINE", "WEIGHT", "Weight", "PILOT01", "VS", "01-1028", "WEEK 4", "WEIGHT", "Weight", "PILOT01", "VS", "04-1325", "SCREENING", "HEIGHT", "Height", "PILOT01", "VS", "04-1325", "SCREENING", "TEMP", "Temperature", "PILOT01", "VS", "04-1325", "BASELINE", "TEMP", "Temperature", "PILOT01", "VS", "04-1325", "WEEK 4", "TEMP", "Temperature", "PILOT01", "VS", "04-1325", "SCREENING 1", "WEIGHT", "Weight", "PILOT01", "VS", "04-1325", "BASELINE", "WEIGHT", "Weight", "PILOT01", "VS", "04-1325", "WEEK 4", "WEIGHT", "Weight", "PILOT01", "VS", "10-1027", "SCREENING", "HEIGHT", "Height", "PILOT01", "VS", "10-1027", "SCREENING", "TEMP", "Temperature", "PILOT01", "VS", "10-1027", "BASELINE", "TEMP", "Temperature", "PILOT01", "VS", "10-1027", "WEEK 4", "TEMP", "Temperature", "PILOT01", "VS", "10-1027", "SCREENING 1", "WEIGHT", "Weight", "PILOT01", "VS", "10-1027", "BASELINE", "WEIGHT", "Weight", "PILOT01", "VS", "10-1027", "WEEK 4", "WEIGHT", "Weight" ) param_lookup <- tribble( ~VSTESTCD, ~VSTEST, ~PARAMCD, ~PARAM, "SYSBP", "Systolic Blood Pressure", "SYSBP", "Syst Blood Pressure (mmHg)", "WEIGHT", "Weight", "WEIGHT", "Weight (kg)", "HEIGHT", "Height", "HEIGHT", "Height (cm)", "TEMP", "Temperature", "TEMP", "Temperature (C)", "MAP", "Mean Arterial Pressure", "MAP", "Mean Art Pressure (mmHg)", "BMI", "Body Mass Index", "BMI", "Body Mass Index(kg/m^2)", "BSA", "Body Surface Area", "BSA", "Body Surface Area(m^2)" ) derive_vars_merged_lookup( dataset = vs, dataset_add = param_lookup, by_vars = exprs(VSTESTCD), new_vars = exprs(PARAMCD, PARAM), print_not_mapped = TRUE )
library(dplyr, warn.conflicts = FALSE) vs <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~VISIT, ~VSTESTCD, ~VSTEST, "PILOT01", "VS", "01-1028", "SCREENING", "HEIGHT", "Height", "PILOT01", "VS", "01-1028", "SCREENING", "TEMP", "Temperature", "PILOT01", "VS", "01-1028", "BASELINE", "TEMP", "Temperature", "PILOT01", "VS", "01-1028", "WEEK 4", "TEMP", "Temperature", "PILOT01", "VS", "01-1028", "SCREENING 1", "WEIGHT", "Weight", "PILOT01", "VS", "01-1028", "BASELINE", "WEIGHT", "Weight", "PILOT01", "VS", "01-1028", "WEEK 4", "WEIGHT", "Weight", "PILOT01", "VS", "04-1325", "SCREENING", "HEIGHT", "Height", "PILOT01", "VS", "04-1325", "SCREENING", "TEMP", "Temperature", "PILOT01", "VS", "04-1325", "BASELINE", "TEMP", "Temperature", "PILOT01", "VS", "04-1325", "WEEK 4", "TEMP", "Temperature", "PILOT01", "VS", "04-1325", "SCREENING 1", "WEIGHT", "Weight", "PILOT01", "VS", "04-1325", "BASELINE", "WEIGHT", "Weight", "PILOT01", "VS", "04-1325", "WEEK 4", "WEIGHT", "Weight", "PILOT01", "VS", "10-1027", "SCREENING", "HEIGHT", "Height", "PILOT01", "VS", "10-1027", "SCREENING", "TEMP", "Temperature", "PILOT01", "VS", "10-1027", "BASELINE", "TEMP", "Temperature", "PILOT01", "VS", "10-1027", "WEEK 4", "TEMP", "Temperature", "PILOT01", "VS", "10-1027", "SCREENING 1", "WEIGHT", "Weight", "PILOT01", "VS", "10-1027", "BASELINE", "WEIGHT", "Weight", "PILOT01", "VS", "10-1027", "WEEK 4", "WEIGHT", "Weight" ) param_lookup <- tribble( ~VSTESTCD, ~VSTEST, ~PARAMCD, ~PARAM, "SYSBP", "Systolic Blood Pressure", "SYSBP", "Syst Blood Pressure (mmHg)", "WEIGHT", "Weight", "WEIGHT", "Weight (kg)", "HEIGHT", "Height", "HEIGHT", "Height (cm)", "TEMP", "Temperature", "TEMP", "Temperature (C)", "MAP", "Mean Arterial Pressure", "MAP", "Mean Art Pressure (mmHg)", "BMI", "Body Mass Index", "BMI", "Body Mass Index(kg/m^2)", "BSA", "Body Surface Area", "BSA", "Body Surface Area(m^2)" ) derive_vars_merged_lookup( dataset = vs, dataset_add = param_lookup, by_vars = exprs(VSTESTCD), new_vars = exprs(PARAMCD, PARAM), print_not_mapped = TRUE )
The function adds subperiod, period, or phase variables like P01S1SDT
,
P01S2SDT
, AP01SDTM
, AP02SDTM
, TRT01A
, TRT02A
, PH1SDT
, PH2SDT
,
... to the input dataset. The values of the variables are defined by a period
reference dataset which has one observations per patient and subperiod,
period, or phase.
derive_vars_period( dataset, dataset_ref, new_vars, subject_keys = get_admiral_option("subject_keys") )
derive_vars_period( dataset, dataset_ref, new_vars, subject_keys = get_admiral_option("subject_keys") )
dataset |
Input dataset The variables specified by the |
dataset_ref |
Period reference dataset The variables specified by If subperiod variables are requested, |
new_vars |
New variables A named list of variables like If the lower case letter "w" is used it refers to a phase variable, if the lower case letters "xx" are used it refers to a period variable, and if both "xx" and "w" are used it refers to a subperiod variable. Only one type must be used, e.g., all left hand side values must refer to period variables. It is not allowed to mix for example period and subperiod variables. If period and subperiod variables are required, separate calls must be used. |
subject_keys |
Variables to uniquely identify a subject A list of expressions where the expressions are symbols as returned by
|
For each subperiod/period/phase in the period reference dataset and
each element in new_vars
a variable (LHS value of new_vars
) is added to
the output dataset and set to the value of the source variable (RHS value
of new_vars
.
The input dataset with subperiod/period/phase variables added (see "Details" section)
ADSL Functions that returns variable appended to dataset:
derive_var_age_years()
,
derive_vars_aage()
,
derive_vars_extreme_event()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) adsl <- tibble(STUDYID = "xyz", USUBJID = c("1", "2")) # Add period variables to ADSL period_ref <- tribble( ~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT, "1", 1, "2021-01-04", "2021-02-06", "1", 2, "2021-02-07", "2021-03-07", "2", 1, "2021-02-02", "2021-03-02", "2", 2, "2021-03-03", "2021-04-01" ) %>% mutate( STUDYID = "xyz", APERIOD = as.integer(APERIOD), across(matches("APER[ES]DT"), ymd) ) derive_vars_period( adsl, dataset_ref = period_ref, new_vars = exprs(APxxSDT = APERSDT, APxxEDT = APEREDT) ) %>% select(STUDYID, USUBJID, AP01SDT, AP01EDT, AP02SDT, AP02EDT) # Add phase variables to ADSL phase_ref <- tribble( ~USUBJID, ~APHASEN, ~PHSDT, ~PHEDT, ~APHASE, "1", 1, "2021-01-04", "2021-02-06", "TREATMENT", "1", 2, "2021-02-07", "2021-03-07", "FUP", "2", 1, "2021-02-02", "2021-03-02", "TREATMENT" ) %>% mutate( STUDYID = "xyz", APHASEN = as.integer(APHASEN), across(matches("PH[ES]DT"), ymd) ) derive_vars_period( adsl, dataset_ref = phase_ref, new_vars = exprs(PHwSDT = PHSDT, PHwEDT = PHEDT, APHASEw = APHASE) ) %>% select(STUDYID, USUBJID, PH1SDT, PH1EDT, PH2SDT, PH2EDT, APHASE1, APHASE2) # Add subperiod variables to ADSL subperiod_ref <- tribble( ~USUBJID, ~APERIOD, ~ASPER, ~ASPRSDT, ~ASPREDT, "1", 1, 1, "2021-01-04", "2021-01-19", "1", 1, 2, "2021-01-20", "2021-02-06", "1", 2, 1, "2021-02-07", "2021-03-07", "2", 1, 1, "2021-02-02", "2021-03-02", "2", 2, 1, "2021-03-03", "2021-04-01" ) %>% mutate( STUDYID = "xyz", APERIOD = as.integer(APERIOD), ASPER = as.integer(ASPER), across(matches("ASPR[ES]DT"), ymd) ) derive_vars_period( adsl, dataset_ref = subperiod_ref, new_vars = exprs(PxxSwSDT = ASPRSDT, PxxSwEDT = ASPREDT) ) %>% select(STUDYID, USUBJID, P01S1SDT, P01S1EDT, P01S2SDT, P01S2EDT, P02S1SDT, P02S1EDT)
library(tibble) library(dplyr, warn.conflicts = FALSE) library(lubridate) adsl <- tibble(STUDYID = "xyz", USUBJID = c("1", "2")) # Add period variables to ADSL period_ref <- tribble( ~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT, "1", 1, "2021-01-04", "2021-02-06", "1", 2, "2021-02-07", "2021-03-07", "2", 1, "2021-02-02", "2021-03-02", "2", 2, "2021-03-03", "2021-04-01" ) %>% mutate( STUDYID = "xyz", APERIOD = as.integer(APERIOD), across(matches("APER[ES]DT"), ymd) ) derive_vars_period( adsl, dataset_ref = period_ref, new_vars = exprs(APxxSDT = APERSDT, APxxEDT = APEREDT) ) %>% select(STUDYID, USUBJID, AP01SDT, AP01EDT, AP02SDT, AP02EDT) # Add phase variables to ADSL phase_ref <- tribble( ~USUBJID, ~APHASEN, ~PHSDT, ~PHEDT, ~APHASE, "1", 1, "2021-01-04", "2021-02-06", "TREATMENT", "1", 2, "2021-02-07", "2021-03-07", "FUP", "2", 1, "2021-02-02", "2021-03-02", "TREATMENT" ) %>% mutate( STUDYID = "xyz", APHASEN = as.integer(APHASEN), across(matches("PH[ES]DT"), ymd) ) derive_vars_period( adsl, dataset_ref = phase_ref, new_vars = exprs(PHwSDT = PHSDT, PHwEDT = PHEDT, APHASEw = APHASE) ) %>% select(STUDYID, USUBJID, PH1SDT, PH1EDT, PH2SDT, PH2EDT, APHASE1, APHASE2) # Add subperiod variables to ADSL subperiod_ref <- tribble( ~USUBJID, ~APERIOD, ~ASPER, ~ASPRSDT, ~ASPREDT, "1", 1, 1, "2021-01-04", "2021-01-19", "1", 1, 2, "2021-01-20", "2021-02-06", "1", 2, 1, "2021-02-07", "2021-03-07", "2", 1, 1, "2021-02-02", "2021-03-02", "2", 2, 1, "2021-03-03", "2021-04-01" ) %>% mutate( STUDYID = "xyz", APERIOD = as.integer(APERIOD), ASPER = as.integer(ASPER), across(matches("ASPR[ES]DT"), ymd) ) derive_vars_period( adsl, dataset_ref = subperiod_ref, new_vars = exprs(PxxSwSDT = ASPRSDT, PxxSwEDT = ASPREDT) ) %>% select(STUDYID, USUBJID, P01S1SDT, P01S1EDT, P01S2SDT, P01S2EDT, P02S1SDT, P02S1EDT)
Derive Query Variables
derive_vars_query(dataset, dataset_queries)
derive_vars_query(dataset, dataset_queries)
dataset |
Input dataset |
dataset_queries |
A dataset containing required columns
|
This function can be used to derive CDISC variables such as
SMQzzNAM
, SMQzzCD
, SMQzzSC
, SMQzzSCN
, and CQzzNAM
in ADAE and
ADMH, and variables such as SDGzzNAM
, SDGzzCD
, and SDGzzSC
in ADCM.
An example usage of this function can be found in the
OCCDS vignette.
A query dataset is expected as an input to this function. See the
Queries Dataset Documentation vignette
for descriptions, or call data("queries")
for an example of a query dataset.
For each unique element in PREFIX
, the corresponding "NAM"
variable will be created. For each unique PREFIX
, if GRPID
is
not "" or NA, then the corresponding "CD" variable is created; similarly,
if SCOPE
is not "" or NA, then the corresponding "SC" variable will
be created; if SCOPEN
is not "" or NA, then the corresponding
"SCN" variable will be created.
For each record in dataset
, the "NAM" variable takes the value of
GRPNAME
if the value of TERMCHAR
or TERMNUM
in dataset_queries
matches
the value of the respective SRCVAR in dataset
.
Note that TERMCHAR
in dataset_queries
dataset may be NA only when TERMNUM
is non-NA and vice versa. The matching is case insensitive.
The "CD", "SC", and "SCN" variables are derived accordingly based on
GRPID
, SCOPE
, and SCOPEN
respectively,
whenever not missing.
The input dataset with query variables derived.
OCCDS Functions:
derive_var_trtemfl()
,
derive_vars_atc()
,
get_terms_from_db()
library(tibble) data("queries") adae <- tribble( ~USUBJID, ~ASTDTM, ~AETERM, ~AESEQ, ~AEDECOD, ~AELLT, ~AELLTCD, "01", "2020-06-02 23:59:59", "ALANINE AMINOTRANSFERASE ABNORMAL", 3, "Alanine aminotransferase abnormal", NA_character_, NA_integer_, "02", "2020-06-05 23:59:59", "BASEDOW'S DISEASE", 5, "Basedow's disease", NA_character_, 1L, "03", "2020-06-07 23:59:59", "SOME TERM", 2, "Some query", "Some term", NA_integer_, "05", "2020-06-09 23:59:59", "ALVEOLAR PROTEINOSIS", 7, "Alveolar proteinosis", NA_character_, NA_integer_ ) derive_vars_query(adae, queries)
library(tibble) data("queries") adae <- tribble( ~USUBJID, ~ASTDTM, ~AETERM, ~AESEQ, ~AEDECOD, ~AELLT, ~AELLTCD, "01", "2020-06-02 23:59:59", "ALANINE AMINOTRANSFERASE ABNORMAL", 3, "Alanine aminotransferase abnormal", NA_character_, NA_integer_, "02", "2020-06-05 23:59:59", "BASEDOW'S DISEASE", 5, "Basedow's disease", NA_character_, 1L, "03", "2020-06-07 23:59:59", "SOME TERM", 2, "Some query", "Some term", NA_integer_, "05", "2020-06-09 23:59:59", "ALVEOLAR PROTEINOSIS", 7, "Alveolar proteinosis", NA_character_, NA_integer_ ) derive_vars_query(adae, queries)
Adds variables from a vertical dataset after transposing it into a wide one.
derive_vars_transposed( dataset, dataset_merge, by_vars, id_vars = NULL, key_var, value_var, filter = NULL, relationship = NULL )
derive_vars_transposed( dataset, dataset_merge, by_vars, id_vars = NULL, key_var, value_var, filter = NULL, relationship = NULL )
dataset |
Input dataset The variables specified by the |
dataset_merge |
Dataset to transpose and merge The variables specified by the |
by_vars |
Grouping variables Keys used to merge |
id_vars |
ID variables Variables (excluding by_vars) that uniquely identify each observation in Permitted Values: list of variables created by |
key_var |
The variable of |
value_var |
The variable of |
filter |
Expression used to restrict the records of |
relationship |
Expected merge-relationship between the This argument is passed to the Permitted Values for |
After filtering dataset_merge
based upon the condition provided in filter
, this
dataset is transposed and subsequently merged onto dataset
using by_vars
as
keys.
The input dataset with transposed variables from dataset_merge
added
General Derivation Functions for all ADaMs that returns variable appended to dataset:
derive_var_extreme_flag()
,
derive_var_joined_exist_flag()
,
derive_var_merged_ef_msrc()
,
derive_var_merged_exist_flag()
,
derive_var_merged_summary()
,
derive_var_obs_number()
,
derive_var_relative_flag()
,
derive_vars_cat()
,
derive_vars_computed()
,
derive_vars_joined()
,
derive_vars_merged()
,
derive_vars_merged_lookup()
library(tibble) library(dplyr, warn.conflicts = FALSE) cm <- tribble( ~USUBJID, ~CMGRPID, ~CMREFID, ~CMDECOD, "BP40257-1001", "14", "1192056", "PARACETAMOL", "BP40257-1001", "18", "2007001", "SOLUMEDROL", "BP40257-1002", "19", "2791596", "SPIRONOLACTONE" ) facm <- tribble( ~USUBJID, ~FAGRPID, ~FAREFID, ~FATESTCD, ~FASTRESC, "BP40257-1001", "1", "1192056", "CMATC1CD", "N", "BP40257-1001", "1", "1192056", "CMATC2CD", "N02", "BP40257-1001", "1", "1192056", "CMATC3CD", "N02B", "BP40257-1001", "1", "1192056", "CMATC4CD", "N02BE", "BP40257-1001", "1", "2007001", "CMATC1CD", "D", "BP40257-1001", "1", "2007001", "CMATC2CD", "D10", "BP40257-1001", "1", "2007001", "CMATC3CD", "D10A", "BP40257-1001", "1", "2007001", "CMATC4CD", "D10AA", "BP40257-1001", "2", "2007001", "CMATC1CD", "D", "BP40257-1001", "2", "2007001", "CMATC2CD", "D07", "BP40257-1001", "2", "2007001", "CMATC3CD", "D07A", "BP40257-1001", "2", "2007001", "CMATC4CD", "D07AA", "BP40257-1001", "3", "2007001", "CMATC1CD", "H", "BP40257-1001", "3", "2007001", "CMATC2CD", "H02", "BP40257-1001", "3", "2007001", "CMATC3CD", "H02A", "BP40257-1001", "3", "2007001", "CMATC4CD", "H02AB", "BP40257-1002", "1", "2791596", "CMATC1CD", "C", "BP40257-1002", "1", "2791596", "CMATC2CD", "C03", "BP40257-1002", "1", "2791596", "CMATC3CD", "C03D", "BP40257-1002", "1", "2791596", "CMATC4CD", "C03DA" ) cm %>% derive_vars_transposed( facm, by_vars = exprs(USUBJID, CMREFID = FAREFID), id_vars = exprs(FAGRPID), key_var = FATESTCD, value_var = FASTRESC ) %>% select(USUBJID, CMDECOD, starts_with("CMATC"))
library(tibble) library(dplyr, warn.conflicts = FALSE) cm <- tribble( ~USUBJID, ~CMGRPID, ~CMREFID, ~CMDECOD, "BP40257-1001", "14", "1192056", "PARACETAMOL", "BP40257-1001", "18", "2007001", "SOLUMEDROL", "BP40257-1002", "19", "2791596", "SPIRONOLACTONE" ) facm <- tribble( ~USUBJID, ~FAGRPID, ~FAREFID, ~FATESTCD, ~FASTRESC, "BP40257-1001", "1", "1192056", "CMATC1CD", "N", "BP40257-1001", "1", "1192056", "CMATC2CD", "N02", "BP40257-1001", "1", "1192056", "CMATC3CD", "N02B", "BP40257-1001", "1", "1192056", "CMATC4CD", "N02BE", "BP40257-1001", "1", "2007001", "CMATC1CD", "D", "BP40257-1001", "1", "2007001", "CMATC2CD", "D10", "BP40257-1001", "1", "2007001", "CMATC3CD", "D10A", "BP40257-1001", "1", "2007001", "CMATC4CD", "D10AA", "BP40257-1001", "2", "2007001", "CMATC1CD", "D", "BP40257-1001", "2", "2007001", "CMATC2CD", "D07", "BP40257-1001", "2", "2007001", "CMATC3CD", "D07A", "BP40257-1001", "2", "2007001", "CMATC4CD", "D07AA", "BP40257-1001", "3", "2007001", "CMATC1CD", "H", "BP40257-1001", "3", "2007001", "CMATC2CD", "H02", "BP40257-1001", "3", "2007001", "CMATC3CD", "H02A", "BP40257-1001", "3", "2007001", "CMATC4CD", "H02AB", "BP40257-1002", "1", "2791596", "CMATC1CD", "C", "BP40257-1002", "1", "2791596", "CMATC2CD", "C03", "BP40257-1002", "1", "2791596", "CMATC3CD", "C03D", "BP40257-1002", "1", "2791596", "CMATC4CD", "C03DA" ) cm %>% derive_vars_transposed( facm, by_vars = exprs(USUBJID, CMREFID = FAREFID), id_vars = exprs(FAGRPID), key_var = FATESTCD, value_var = FASTRESC ) %>% select(USUBJID, CMDECOD, starts_with("CMATC"))
These pre-defined dose frequencies are sourced from
CDISC. The
number of rows to generate using create_single_dose_dataset()
arguments
start_date
and end_date
is derived from DOSE_COUNT
, DOSE_WINDOW
, and
CONVERSION_FACTOR
with appropriate functions from lubridate
.
dose_freq_lookup
dose_freq_lookup
An object of class tbl_df
(inherits from tbl
, data.frame
) with 86 rows and 5 columns.
NCI_CODE
and CDISC_VALUE
are included from the CDISC source for
traceability.
DOSE_COUNT
represents the number of doses received in one single unit of
DOSE_WINDOW
. For example, for CDISC_VALUE=="10 DAYS PER MONTH"
,
DOSE_WINDOW=="MONTH"
and DOSE_COUNT==10
. Similarly, for
CDISC_VALUE=="EVERY 2 WEEKS"
, DOSE_WINDOW=="WEEK"
and
DOSE_COUNT==0.5
(to yield one dose every two weeks).
CONVERSION_FACTOR
is used to convert DOSE_WINDOW
units "WEEK"
,
"MONTH"
, and "YEAR"
to the unit "DAY"
.
For example, for CDISC_VALUE=="10 DAYS PER MONTH"
, CONVERSION_FACTOR
is 0.0329
. One day of a month is assumed to be 1 / 30.4375
of a month (one
day is assumed to be 1/365.25
of a year).
Given only start_date
and end_date
in the aggregate dataset, CONVERSION_FACTOR
is used to calculate specific dates forstart_date
and end_date
in the
resulting single dose dataset for the doses that occur. In such cases, doses
are assumed to occur at evenly spaced increments over the interval.
To see the entire table in the console, run print(dose_freq_lookup)
.
Other metadata:
atoxgr_criteria_ctcv4
,
atoxgr_criteria_ctcv5
,
atoxgr_criteria_daids
,
country_code_lookup
dthcaus_source
Object The derive_var_dthcaus()
function and dthcaus_source()
have been superseded in favor of
derive_vars_extreme_event()
.
dthcaus_source( dataset_name, filter, date, order = NULL, mode = "first", dthcaus, set_values_to = NULL )
dthcaus_source( dataset_name, filter, date, order = NULL, mode = "first", dthcaus, set_values_to = NULL )
dataset_name |
The name of the dataset, i.e. a string, used to search for the death cause. |
filter |
An expression used for filtering |
date |
A date or datetime variable or an expression to be used for
sorting |
order |
Sort order Additional variables/expressions to be used for sorting the Permitted Values: list of expressions created by |
mode |
One of |
dthcaus |
A variable name, an expression, or a string literal If a variable name is specified, e.g., |
set_values_to |
Variables to be set to trace the source dataset |
An object of class "dthcaus_source".
Other superseded:
date_source()
,
derive_param_extreme_record()
,
derive_var_dthcaus()
,
derive_var_extreme_dt()
,
derive_var_extreme_dtm()
,
get_summary_records()
# Deaths sourced from AE src_ae <- dthcaus_source( dataset_name = "ae", filter = AEOUT == "FATAL", date = AEDTHDT, mode = "first", dthcaus = AEDECOD ) # Deaths sourced from DS src_ds <- dthcaus_source( dataset_name = "ds", filter = DSDECOD == "DEATH", date = convert_dtc_to_dt(DSSTDTC), mode = "first", dthcaus = DSTERM )
# Deaths sourced from AE src_ae <- dthcaus_source( dataset_name = "ae", filter = AEOUT == "FATAL", date = AEDTHDT, mode = "first", dthcaus = AEDECOD ) # Deaths sourced from DS src_ds <- dthcaus_source( dataset_name = "ds", filter = DSDECOD == "DEATH", date = convert_dtc_to_dt(DSSTDTC), mode = "first", dthcaus = DSTERM )
event
ObjectThe event
object is used to define events as input for the
derive_extreme_event()
and derive_vars_extreme_event()
functions.
event( dataset_name = NULL, condition = NULL, mode = NULL, order = NULL, set_values_to = NULL, keep_source_vars = NULL, description = NULL )
event( dataset_name = NULL, condition = NULL, mode = NULL, order = NULL, set_values_to = NULL, keep_source_vars = NULL, description = NULL )
dataset_name |
Dataset name of the dataset to be used as input for the
event. The name refers to the dataset specified for Permitted Values: a character scalar |
condition |
An unquoted condition for selecting the observations, which
will contribute to the extreme event. If the condition contains summary
functions like Permitted Values: an unquoted condition |
mode |
If specified, the first or last observation with respect to Permitted Values: |
order |
The specified variables or expressions are used to select the
first or last observation if For handling of Permitted Values: list of expressions created by |
set_values_to |
A named list returned by Permitted Values: a named list of expressions, e.g., created by |
keep_source_vars |
Variables to keep from the source dataset The specified variables are kept for the selected observations. The
variables specified for Permitted Values: A list of expressions where each element is
a symbol or a tidyselect expression, e.g., |
description |
Description of the event The description does not affect the derivations where the event is used. It is intended for documentation only. Permitted Values: a character scalar |
An object of class event
derive_extreme_event()
, derive_vars_extreme_event()
, event_joined()
Source Objects:
basket_select()
,
censor_source()
,
death_event
,
event_joined()
,
event_source()
,
flag_event()
,
query()
,
records_source()
,
tte_source()
event_joined
ObjectThe event_joined
object is used to define events as input for the
derive_extreme_event()
and derive_vars_extreme_event()
functions.
This object should be used if the event does not depend on a single
observation of the source dataset but on multiple observations. For example,
if the event needs to be confirmed by a second observation of the source
dataset.
The events are selected by calling filter_joined()
. See its documentation
for more details.
event_joined( dataset_name = NULL, condition, order = NULL, join_vars, join_type, first_cond_lower = NULL, first_cond_upper = NULL, set_values_to = NULL, keep_source_vars = NULL, description = NULL )
event_joined( dataset_name = NULL, condition, order = NULL, join_vars, join_type, first_cond_lower = NULL, first_cond_upper = NULL, set_values_to = NULL, keep_source_vars = NULL, description = NULL )
dataset_name |
Dataset name of the dataset to be used as input for the
event. The name refers to the dataset specified for Permitted Values: a character scalar |
condition |
An unquoted condition for selecting the observations, which will contribute to the extreme event. The condition is applied to the joined dataset for selecting the confirmed
observations. The condition can include summary functions like Permitted Values: an unquoted condition |
order |
If specified, the specified variables or expressions are used to select the first observation. For handling of Permitted Values: list of expressions created by |
join_vars |
Variables to keep from joined dataset The variables needed from the other observations should be specified for
this parameter. The specified variables are added to the joined dataset
with suffix ".join". For example to select all observations with The Permitted Values: a named list of expressions, e.g., created by |
join_type |
Observations to keep after joining The argument determines which of the joined observations are kept with
respect to the original observation. For example, if Permitted Values: |
first_cond_lower |
Condition for selecting range of data (before) If this argument is specified, the other observations are restricted from the first observation before the current observation where the specified condition is fulfilled up to the current observation. If the condition is not fulfilled for any of the other observations, no observations are considered, i.e., the observation is not flagged. This parameter should be specified if Permitted Values: an unquoted condition |
first_cond_upper |
Condition for selecting range of data (after) If this argument is specified, the other observations are restricted up to the first observation where the specified condition is fulfilled. If the condition is not fulfilled for any of the other observations, no observations are considered, i.e., the observation is not flagged. This parameter should be specified if Permitted Values: an unquoted condition |
set_values_to |
A named list returned by Permitted Values: a named list of expressions, e.g., created by |
keep_source_vars |
Variables to keep from the source dataset The specified variables are kept for the selected observations. The
variables specified for Permitted Values: A list of expressions where each element is
a symbol or a tidyselect expression, e.g., |
description |
Description of the event The description does not affect the derivations where the event is used. It is intended for documentation only. Permitted Values: a character scalar |
An object of class event_joined
derive_extreme_event()
, derive_vars_extreme_event()
, event()
Source Objects:
basket_select()
,
censor_source()
,
death_event
,
event()
,
event_source()
,
flag_event()
,
query()
,
records_source()
,
tte_source()
library(tibble) library(dplyr) library(lubridate) # Derive confirmed best overall response (using event_joined()) # CR - complete response, PR - partial response, SD - stable disease # NE - not evaluable, PD - progressive disease adsl <- tribble( ~USUBJID, ~TRTSDTC, "1", "2020-01-01", "2", "2019-12-12", "3", "2019-11-11", "4", "2019-12-30", "5", "2020-01-01", "6", "2020-02-02", "7", "2020-02-02", "8", "2020-02-01" ) %>% mutate(TRTSDT = ymd(TRTSDTC)) adrs <- tribble( ~USUBJID, ~ADTC, ~AVALC, "1", "2020-01-01", "PR", "1", "2020-02-01", "CR", "1", "2020-02-16", "NE", "1", "2020-03-01", "CR", "1", "2020-04-01", "SD", "2", "2020-01-01", "SD", "2", "2020-02-01", "PR", "2", "2020-03-01", "SD", "2", "2020-03-13", "CR", "4", "2020-01-01", "PR", "4", "2020-03-01", "NE", "4", "2020-04-01", "NE", "4", "2020-05-01", "PR", "5", "2020-01-01", "PR", "5", "2020-01-10", "PR", "5", "2020-01-20", "PR", "6", "2020-02-06", "PR", "6", "2020-02-16", "CR", "6", "2020-03-30", "PR", "7", "2020-02-06", "PR", "7", "2020-02-16", "CR", "7", "2020-04-01", "NE", "8", "2020-02-16", "PD" ) %>% mutate( ADT = ymd(ADTC), PARAMCD = "OVR", PARAM = "Overall Response by Investigator" ) %>% derive_vars_merged( dataset_add = adsl, by_vars = exprs(USUBJID), new_vars = exprs(TRTSDT) ) derive_extreme_event( adrs, by_vars = exprs(USUBJID), order = exprs(ADT), mode = "first", source_datasets = list(adsl = adsl), events = list( event_joined( description = paste( "CR needs to be confirmed by a second CR at least 28 days later", "at most one NE is acceptable between the two assessments" ), join_vars = exprs(AVALC, ADT), join_type = "after", first_cond_upper = AVALC.join == "CR" & ADT.join >= ADT + 28, condition = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1, set_values_to = exprs( AVALC = "CR" ) ), event_joined( description = paste( "PR needs to be confirmed by a second CR or PR at least 28 days later,", "at most one NE is acceptable between the two assessments" ), join_vars = exprs(AVALC, ADT), join_type = "after", first_cond_upper = AVALC.join %in% c("CR", "PR") & ADT.join >= ADT + 28, condition = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1, set_values_to = exprs( AVALC = "PR" ) ), event( description = paste( "CR, PR, or SD are considered as SD if occurring at least 28", "after treatment start" ), condition = AVALC %in% c("CR", "PR", "SD") & ADT >= TRTSDT + 28, set_values_to = exprs( AVALC = "SD" ) ), event( condition = AVALC == "PD", set_values_to = exprs( AVALC = "PD" ) ), event( condition = AVALC %in% c("CR", "PR", "SD", "NE"), set_values_to = exprs( AVALC = "NE" ) ), event( description = "set response to MISSING for patients without records in ADRS", dataset_name = "adsl", condition = TRUE, set_values_to = exprs( AVALC = "MISSING" ), keep_source_vars = exprs(TRTSDT) ) ), set_values_to = exprs( PARAMCD = "CBOR", PARAM = "Best Confirmed Overall Response by Investigator" ) ) %>% filter(PARAMCD == "CBOR")
library(tibble) library(dplyr) library(lubridate) # Derive confirmed best overall response (using event_joined()) # CR - complete response, PR - partial response, SD - stable disease # NE - not evaluable, PD - progressive disease adsl <- tribble( ~USUBJID, ~TRTSDTC, "1", "2020-01-01", "2", "2019-12-12", "3", "2019-11-11", "4", "2019-12-30", "5", "2020-01-01", "6", "2020-02-02", "7", "2020-02-02", "8", "2020-02-01" ) %>% mutate(TRTSDT = ymd(TRTSDTC)) adrs <- tribble( ~USUBJID, ~ADTC, ~AVALC, "1", "2020-01-01", "PR", "1", "2020-02-01", "CR", "1", "2020-02-16", "NE", "1", "2020-03-01", "CR", "1", "2020-04-01", "SD", "2", "2020-01-01", "SD", "2", "2020-02-01", "PR", "2", "2020-03-01", "SD", "2", "2020-03-13", "CR", "4", "2020-01-01", "PR", "4", "2020-03-01", "NE", "4", "2020-04-01", "NE", "4", "2020-05-01", "PR", "5", "2020-01-01", "PR", "5", "2020-01-10", "PR", "5", "2020-01-20", "PR", "6", "2020-02-06", "PR", "6", "2020-02-16", "CR", "6", "2020-03-30", "PR", "7", "2020-02-06", "PR", "7", "2020-02-16", "CR", "7", "2020-04-01", "NE", "8", "2020-02-16", "PD" ) %>% mutate( ADT = ymd(ADTC), PARAMCD = "OVR", PARAM = "Overall Response by Investigator" ) %>% derive_vars_merged( dataset_add = adsl, by_vars = exprs(USUBJID), new_vars = exprs(TRTSDT) ) derive_extreme_event( adrs, by_vars = exprs(USUBJID), order = exprs(ADT), mode = "first", source_datasets = list(adsl = adsl), events = list( event_joined( description = paste( "CR needs to be confirmed by a second CR at least 28 days later", "at most one NE is acceptable between the two assessments" ), join_vars = exprs(AVALC, ADT), join_type = "after", first_cond_upper = AVALC.join == "CR" & ADT.join >= ADT + 28, condition = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1, set_values_to = exprs( AVALC = "CR" ) ), event_joined( description = paste( "PR needs to be confirmed by a second CR or PR at least 28 days later,", "at most one NE is acceptable between the two assessments" ), join_vars = exprs(AVALC, ADT), join_type = "after", first_cond_upper = AVALC.join %in% c("CR", "PR") & ADT.join >= ADT + 28, condition = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1, set_values_to = exprs( AVALC = "PR" ) ), event( description = paste( "CR, PR, or SD are considered as SD if occurring at least 28", "after treatment start" ), condition = AVALC %in% c("CR", "PR", "SD") & ADT >= TRTSDT + 28, set_values_to = exprs( AVALC = "SD" ) ), event( condition = AVALC == "PD", set_values_to = exprs( AVALC = "PD" ) ), event( condition = AVALC %in% c("CR", "PR", "SD", "NE"), set_values_to = exprs( AVALC = "NE" ) ), event( description = "set response to MISSING for patients without records in ADRS", dataset_name = "adsl", condition = TRUE, set_values_to = exprs( AVALC = "MISSING" ), keep_source_vars = exprs(TRTSDT) ) ), set_values_to = exprs( PARAMCD = "CBOR", PARAM = "Best Confirmed Overall Response by Investigator" ) ) %>% filter(PARAMCD == "CBOR")
event_source
Objectevent_source
objects are used to define events as input for the
derive_param_tte()
function.
Note: This is a wrapper function for the more generic tte_source()
.
event_source(dataset_name, filter = NULL, date, set_values_to = NULL)
event_source(dataset_name, filter = NULL, date, set_values_to = NULL)
dataset_name |
The name of the source dataset The name refers to the dataset provided by the |
filter |
An unquoted condition for selecting the observations from
|
date |
A variable or expression providing the date of the event or censoring. A date, or a datetime can be specified. An unquoted symbol or expression is expected. Refer to |
set_values_to |
A named list returned by |
An object of class event_source
, inheriting from class tte_source
derive_param_tte()
, censor_source()
Source Objects:
basket_select()
,
censor_source()
,
death_event
,
event()
,
event_joined()
,
flag_event()
,
query()
,
records_source()
,
tte_source()
# Death event event_source( dataset_name = "adsl", filter = DTHFL == "Y", date = DTHDT, set_values_to = exprs( EVNTDESC = "DEATH", SRCDOM = "ADSL", SRCVAR = "DTHDT" ) )
# Death event event_source( dataset_name = "adsl", filter = DTHFL == "Y", date = DTHDT, set_values_to = exprs( EVNTDESC = "DEATH", SRCDOM = "ADSL", SRCVAR = "DTHDT" ) )
A derived dataset with single dose per date.
ex_single
ex_single
An object of class tbl_df
(inherits from tbl
, data.frame
) with 22439 rows and 17 columns.
Derived from the ex
dataset using {admiral}
and {dplyr}
(https://github.com/pharmaverse/admiral/blob/main/inst/example_scripts/derive_single_dose.R)
Other datasets:
admiral_adlb
,
admiral_adsl
,
example_qs
,
queries
,
queries_mh
QS
DatasetAn example QS
dataset based on the examples from the CDISC ADaM Supplements
Generalized Anxiety Disorder 7-Item Version 2 (GAD-7)
and Geriatric Depression Scale Short Form (GDS-SF).
example_qs
example_qs
An object of class tbl_df
(inherits from tbl
, data.frame
) with 161 rows and 11 columns.
Created by (https://github.com/pharmaverse/admiral/blob/main/inst/example_scripts/example_qs.R)
Other datasets:
admiral_adlb
,
admiral_adsl
,
ex_single
,
queries
,
queries_mh
Extract the unit of a parameter from a description like "Param (unit)".
extract_unit(x)
extract_unit(x)
x |
A parameter description |
A string
Utilities used within Derivation functions:
call_user_fun()
,
get_flagged_records()
,
get_not_mapped()
,
get_vars_query()
extract_unit("Height (cm)") extract_unit("Diastolic Blood Pressure (mmHg)")
extract_unit("Height (cm)") extract_unit("Diastolic Blood Pressure (mmHg)")
Returns all records in the input dataset that belong to by groups that are present in a source dataset, after the source dataset is optionally filtered. For example, this could be used to return ADSL records for subjects that experienced a certain adverse event during the course of the study (as per records in ADAE).
filter_exist(dataset, dataset_add, by_vars, filter_add = NULL)
filter_exist(dataset, dataset_add, by_vars, filter_add = NULL)
dataset |
Input dataset The variables specified by the |
dataset_add |
Source dataset The source dataset, which determines the by groups returned in the input dataset,
based on the groups that exist in this dataset after being subset by The variables specified in the |
by_vars |
Grouping variables Permitted Values: list of variables created by |
filter_add |
Filter for the source dataset The filter condition which will be used to subset the source dataset. Alternatively, if no filter condition is supplied, no subsetting of the source dataset will be performed. Default: |
Returns the records in dataset
which match an existing by group in dataset_add
,
after being filtered according to filter_add
. If there are no by groups that exist
in both datasets, an empty dataset will be returned.
The records in the input dataset which are contained within an existing by group in the filtered source dataset.
Utilities for Filtering Observations:
count_vals()
,
filter_extreme()
,
filter_joined()
,
filter_not_exist()
,
filter_relative()
,
max_cond()
,
min_cond()
# Get demographic information about subjects who have suffered from moderate or # severe fatigue library(tibble) adsl <- tribble( ~USUBJID, ~AGE, ~SEX, "01-701-1015", 63, "F", "01-701-1034", 77, "F", "01-701-1115", 84, "M", "01-701-1146", 75, "F", "01-701-1444", 63, "M" ) adae <- tribble( ~USUBJID, ~AEDECOD, ~AESEV, ~AESTDTC, "01-701-1015", "DIARRHOEA", "MODERATE", "2014-01-09", "01-701-1034", "FATIGUE", "SEVERE", "2014-11-02", "01-701-1034", "APPLICATION SITE PRURITUS", "MODERATE", "2014-08-27", "01-701-1115", "FATIGUE", "MILD", "2013-01-14", "01-701-1146", "FATIGUE", "MODERATE", "2013-06-03" ) filter_exist( dataset = adsl, dataset_add = adae, by_vars = exprs(USUBJID), filter_add = AEDECOD == "FATIGUE" & AESEV %in% c("MODERATE", "SEVERE") )
# Get demographic information about subjects who have suffered from moderate or # severe fatigue library(tibble) adsl <- tribble( ~USUBJID, ~AGE, ~SEX, "01-701-1015", 63, "F", "01-701-1034", 77, "F", "01-701-1115", 84, "M", "01-701-1146", 75, "F", "01-701-1444", 63, "M" ) adae <- tribble( ~USUBJID, ~AEDECOD, ~AESEV, ~AESTDTC, "01-701-1015", "DIARRHOEA", "MODERATE", "2014-01-09", "01-701-1034", "FATIGUE", "SEVERE", "2014-11-02", "01-701-1034", "APPLICATION SITE PRURITUS", "MODERATE", "2014-08-27", "01-701-1115", "FATIGUE", "MILD", "2013-01-14", "01-701-1146", "FATIGUE", "MODERATE", "2013-06-03" ) filter_exist( dataset = adsl, dataset_add = adae, by_vars = exprs(USUBJID), filter_add = AEDECOD == "FATIGUE" & AESEV %in% c("MODERATE", "SEVERE") )
Filters the first or last observation for each by group.
filter_extreme(dataset, by_vars = NULL, order, mode, check_type = "warning")
filter_extreme(dataset, by_vars = NULL, order, mode, check_type = "warning")
dataset |
Input dataset The variables specified by the |
by_vars |
Grouping variables Default: Permitted Values: list of variables created by |
order |
Sort order Within each by group the observations are ordered by the specified order. Permitted Values: list of expressions created by |
mode |
Selection mode (first or last) If Permitted Values: |
check_type |
Check uniqueness? If Default: Permitted Values: |
For each group (with respect to the variables specified for the
by_vars
parameter) the first or last observation (with respect to the
order specified for the order
parameter and the mode specified for the
mode
parameter) is included in the output dataset.
A dataset containing the first or last observation of each by group
Utilities for Filtering Observations:
count_vals()
,
filter_exist()
,
filter_joined()
,
filter_not_exist()
,
filter_relative()
,
max_cond()
,
min_cond()
library(dplyr, warn.conflicts = FALSE) ex <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~EXSEQ, ~EXDOSE, ~EXTRT, "PILOT01", "EX", "01-1442", 1, 54, "XANO", "PILOT01", "EX", "01-1442", 2, 54, "XANO", "PILOT01", "EX", "01-1442", 3, 54, "XANO", "PILOT01", "EX", "01-1444", 1, 54, "XANO", "PILOT01", "EX", "01-1444", 2, 81, "XANO", "PILOT01", "EX", "05-1382", 1, 54, "XANO", "PILOT01", "EX", "08-1213", 1, 54, "XANO", "PILOT01", "EX", "10-1053", 1, 54, "XANO", "PILOT01", "EX", "10-1053", 2, 54, "XANO", "PILOT01", "EX", "10-1183", 1, 0, "PLACEBO", "PILOT01", "EX", "10-1183", 2, 0, "PLACEBO", "PILOT01", "EX", "10-1183", 3, 0, "PLACEBO", "PILOT01", "EX", "11-1036", 1, 0, "PLACEBO", "PILOT01", "EX", "11-1036", 2, 0, "PLACEBO", "PILOT01", "EX", "11-1036", 3, 0, "PLACEBO", "PILOT01", "EX", "14-1425", 1, 54, "XANO", "PILOT01", "EX", "15-1319", 1, 54, "XANO", "PILOT01", "EX", "15-1319", 2, 81, "XANO", "PILOT01", "EX", "16-1151", 1, 54, "XANO", "PILOT01", "EX", "16-1151", 2, 54, "XANO" ) # Select first dose for each patient ex %>% filter_extreme( by_vars = exprs(USUBJID), order = exprs(EXSEQ), mode = "first" ) %>% select(USUBJID, EXSEQ) # Select highest dose for each patient on the active drug ex %>% filter(EXTRT != "PLACEBO") %>% filter_extreme( by_vars = exprs(USUBJID), order = exprs(EXDOSE), mode = "last", check_type = "none" ) %>% select(USUBJID, EXTRT, EXDOSE)
library(dplyr, warn.conflicts = FALSE) ex <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~EXSEQ, ~EXDOSE, ~EXTRT, "PILOT01", "EX", "01-1442", 1, 54, "XANO", "PILOT01", "EX", "01-1442", 2, 54, "XANO", "PILOT01", "EX", "01-1442", 3, 54, "XANO", "PILOT01", "EX", "01-1444", 1, 54, "XANO", "PILOT01", "EX", "01-1444", 2, 81, "XANO", "PILOT01", "EX", "05-1382", 1, 54, "XANO", "PILOT01", "EX", "08-1213", 1, 54, "XANO", "PILOT01", "EX", "10-1053", 1, 54, "XANO", "PILOT01", "EX", "10-1053", 2, 54, "XANO", "PILOT01", "EX", "10-1183", 1, 0, "PLACEBO", "PILOT01", "EX", "10-1183", 2, 0, "PLACEBO", "PILOT01", "EX", "10-1183", 3, 0, "PLACEBO", "PILOT01", "EX", "11-1036", 1, 0, "PLACEBO", "PILOT01", "EX", "11-1036", 2, 0, "PLACEBO", "PILOT01", "EX", "11-1036", 3, 0, "PLACEBO", "PILOT01", "EX", "14-1425", 1, 54, "XANO", "PILOT01", "EX", "15-1319", 1, 54, "XANO", "PILOT01", "EX", "15-1319", 2, 81, "XANO", "PILOT01", "EX", "16-1151", 1, 54, "XANO", "PILOT01", "EX", "16-1151", 2, 54, "XANO" ) # Select first dose for each patient ex %>% filter_extreme( by_vars = exprs(USUBJID), order = exprs(EXSEQ), mode = "first" ) %>% select(USUBJID, EXSEQ) # Select highest dose for each patient on the active drug ex %>% filter(EXTRT != "PLACEBO") %>% filter_extreme( by_vars = exprs(USUBJID), order = exprs(EXDOSE), mode = "last", check_type = "none" ) %>% select(USUBJID, EXTRT, EXDOSE)
The function filters observation using a condition taking other observations
into account. For example, it could select all observations with AVALC == "Y"
and AVALC == "Y"
for at least one subsequent observation. The input
dataset is joined with itself to enable conditions taking variables from both
the current observation and the other observations into account. The suffix
".join" is added to the variables from the subsequent observations.
An example usage might be checking if a patient received two required medications within a certain timeframe of each other.
In the oncology setting, for example, we use such processing to check if a response value can be confirmed by a subsequent assessment. This is commonly used in endpoints such as best overall response.
filter_joined( dataset, dataset_add, by_vars, join_vars, join_type, first_cond_lower = NULL, first_cond_upper = NULL, order, tmp_obs_nr_var = NULL, filter_add = NULL, filter_join, check_type = "warning" )
filter_joined( dataset, dataset_add, by_vars, join_vars, join_type, first_cond_lower = NULL, first_cond_upper = NULL, order, tmp_obs_nr_var = NULL, filter_add = NULL, filter_join, check_type = "warning" )
dataset |
Input dataset The variables specified by the |
dataset_add |
Additional dataset The variables specified for |
by_vars |
By variables The specified variables are used as by variables for joining the input dataset with itself. Permitted Values: list of variables created by |
join_vars |
Variables to keep from joined dataset The variables needed from the other observations should be specified for
this parameter. The specified variables are added to the joined dataset
with suffix ".join". For example to select all observations with The |
join_type |
Observations to keep after joining The argument determines which of the joined observations are kept with
respect to the original observation. For example, if For example for confirmed response or BOR in the oncology setting or
confirmed deterioration in questionnaires the confirmatory assessment must
be after the assessment. Thus Whereas, sometimes you might allow for confirmatory observations to occur
prior to the observation. For example, to identify AEs occurring on or
after seven days before a COVID AE. Thus Permitted Values: |
first_cond_lower |
Condition for selecting range of data (before) If this argument is specified, the other observations are restricted from the first observation before the current observation where the specified condition is fulfilled up to the current observation. If the condition is not fulfilled for any of the other observations, no observations are considered, i.e., the observation is not flagged. This parameter should be specified if |
first_cond_upper |
Condition for selecting range of data (after) If this argument is specified, the other observations are restricted up to the first observation where the specified condition is fulfilled. If the condition is not fulfilled for any of the other observations, no observations are considered, i.e., the observation is not flagged. This parameter should be specified if |
order |
Order The observations are ordered by the specified order. For handling of Permitted Values: list of expressions created by |
tmp_obs_nr_var |
Temporary observation number The specified variable is added to the input dataset ( |
filter_add |
Filter for additional dataset ( Only observations from Variables created by the The condition can include summary functions. The additional dataset is
grouped by the by variables ( |
filter_join |
Condition for selecting observations The filter is applied to the joined dataset for selecting the confirmed
observations. The condition can include summary functions like |
check_type |
Check uniqueness? If Permitted Values: |
The following steps are performed to produce the output dataset.
The variables specified by order
are added to the additional dataset
(dataset_add
).
The variables specified by join_vars
are added to the additional dataset
(dataset_add
).
The records from the additional dataset (dataset_add
) are restricted to
those matching the filter_add
condition.
Then the input dataset (dataset
) is joined with the restricted
additional dataset by the variables specified for by_vars
. From the
additional dataset only the variables specified for join_vars
are kept.
The suffix ".join" is added to those variables which are also present in
the input dataset.
For example, for by_vars = USUBJID
, join_vars = exprs(AVISITN, AVALC)
and input dataset and additional dataset
# A tibble: 2 x 4 USUBJID AVISITN AVALC AVAL <chr> <dbl> <chr> <dbl> 1 1 Y 1 1 2 N 0
the joined dataset is
A tibble: 4 x 6 USUBJID AVISITN AVALC AVAL AVISITN.join AVALC.join <chr> <dbl> <chr> <dbl> <dbl> <chr> 1 1 Y 1 1 Y 1 1 Y 1 2 N 1 2 N 0 1 Y 1 2 N 0 2 N
The joined dataset is restricted to observations with respect to
join_type
and order
.
The dataset from the example in the previous step with join_type = "after"
and order = exprs(AVISITN)
is restricted to
A tibble: 4 x 6 USUBJID AVISITN AVALC AVAL AVISITN.join AVALC.join <chr> <dbl> <chr> <dbl> <dbl> <chr> 1 1 Y 1 2 N
If first_cond_lower
is specified, for each observation of the input
dataset the joined dataset is restricted to observations from the first
observation where first_cond_lower
is fulfilled (the observation
fulfilling the condition is included) up to the observation of the input
dataset. If for an observation of the input dataset the condition is not
fulfilled, the observation is removed.
If first_cond_upper
is specified, for each observation of the input
dataset the joined dataset is restricted to observations up to the first
observation where first_cond_upper
is fulfilled (the observation
fulfilling the condition is included). If for an observation of the input
dataset the condition is not fulfilled, the observation is removed.
For an example see the last example in the "Examples" section.
The joined dataset is grouped by the observations from the input dataset
and restricted to the observations fulfilling the condition specified by
filter_join
.
The first observation of each group is selected and the *.join
variables
are dropped.
A subset of the observations of the input dataset. All variables of the input dataset are included in the output dataset.
count_vals()
, min_cond()
, max_cond()
Utilities for Filtering Observations:
count_vals()
,
filter_exist()
,
filter_extreme()
,
filter_not_exist()
,
filter_relative()
,
max_cond()
,
min_cond()
library(tibble) library(admiral) # filter observations with a duration longer than 30 and # on or after 7 days before a COVID AE (ACOVFL == "Y") adae <- tribble( ~USUBJID, ~ADY, ~ACOVFL, ~ADURN, "1", 10, "N", 1, "1", 21, "N", 50, "1", 23, "Y", 14, "1", 32, "N", 31, "1", 42, "N", 20, "2", 11, "Y", 13, "2", 23, "N", 2, "3", 13, "Y", 12, "4", 14, "N", 32, "4", 21, "N", 41 ) filter_joined( adae, dataset_add = adae, by_vars = exprs(USUBJID), join_vars = exprs(ACOVFL, ADY), join_type = "all", order = exprs(ADY), filter_join = ADURN > 30 & ACOVFL.join == "Y" & ADY >= ADY.join - 7 ) # filter observations with AVALC == "Y" and AVALC == "Y" at a subsequent visit data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "Y", "1", 2, "N", "1", 3, "Y", "1", 4, "N", "2", 1, "Y", "2", 2, "N", "3", 1, "Y", "4", 1, "N", "4", 2, "N", ) filter_joined( data, dataset_add = data, by_vars = exprs(USUBJID), join_vars = exprs(AVALC, AVISITN), join_type = "after", order = exprs(AVISITN), filter_join = AVALC == "Y" & AVALC.join == "Y" & AVISITN < AVISITN.join ) # select observations with AVALC == "CR", AVALC == "CR" at a subsequent visit, # only "CR" or "NE" in between, and at most one "NE" in between data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "PR", "1", 2, "CR", "1", 3, "NE", "1", 4, "CR", "1", 5, "NE", "2", 1, "CR", "2", 2, "PR", "2", 3, "CR", "3", 1, "CR", "4", 1, "CR", "4", 2, "NE", "4", 3, "NE", "4", 4, "CR", "4", 5, "PR" ) filter_joined( data, dataset_add = data, by_vars = exprs(USUBJID), join_vars = exprs(AVALC), join_type = "after", order = exprs(AVISITN), first_cond_upper = AVALC.join == "CR", filter_join = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1 ) # select observations with AVALC == "PR", AVALC == "CR" or AVALC == "PR" # at a subsequent visit at least 20 days later, only "CR", "PR", or "NE" # in between, at most one "NE" in between, and "CR" is not followed by "PR" data <- tribble( ~USUBJID, ~ADY, ~AVALC, "1", 6, "PR", "1", 12, "CR", "1", 24, "NE", "1", 32, "CR", "1", 48, "PR", "2", 3, "PR", "2", 21, "CR", "2", 33, "PR", "3", 11, "PR", "4", 7, "PR", "4", 12, "NE", "4", 24, "NE", "4", 32, "PR", "4", 55, "PR" ) filter_joined( data, dataset_add = data, by_vars = exprs(USUBJID), join_vars = exprs(AVALC, ADY), join_type = "after", order = exprs(ADY), first_cond_upper = AVALC.join %in% c("CR", "PR") & ADY.join - ADY >= 20, filter_join = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1 & ( min_cond(var = ADY.join, cond = AVALC.join == "CR") > max_cond(var = ADY.join, cond = AVALC.join == "PR") | count_vals(var = AVALC.join, val = "CR") == 0 ) ) # select observations with CRIT1FL == "Y" at two consecutive visits or at the last visit data <- tribble( ~USUBJID, ~AVISITN, ~CRIT1FL, "1", 1, "Y", "1", 2, "N", "1", 3, "Y", "1", 5, "N", "2", 1, "Y", "2", 3, "Y", "2", 5, "N", "3", 1, "Y", "4", 1, "Y", "4", 2, "N", ) filter_joined( data, dataset_add = data, by_vars = exprs(USUBJID), tmp_obs_nr_var = tmp_obs_nr, join_vars = exprs(CRIT1FL), join_type = "all", order = exprs(AVISITN), filter_join = CRIT1FL == "Y" & CRIT1FL.join == "Y" & (tmp_obs_nr + 1 == tmp_obs_nr.join | tmp_obs_nr == max(tmp_obs_nr.join)) ) # first_cond_lower and first_cond_upper argument myd <- tribble( ~subj, ~day, ~val, "1", 1, "++", "1", 2, "-", "1", 3, "0", "1", 4, "+", "1", 5, "++", "1", 6, "-", "2", 1, "-", "2", 2, "++", "2", 3, "+", "2", 4, "0", "2", 5, "-", "2", 6, "++" ) # select "0" where all results from the first "++" before the "0" up to the "0" # (excluding the "0") are "+" or "++" filter_joined( myd, dataset_add = myd, by_vars = exprs(subj), order = exprs(day), join_vars = exprs(val), join_type = "before", first_cond_lower = val.join == "++", filter_join = val == "0" & all(val.join %in% c("+", "++")) ) # select "0" where all results from the "0" (excluding the "0") up to the first # "++" after the "0" are "+" or "++" filter_joined( myd, dataset_add = myd, by_vars = exprs(subj), order = exprs(day), join_vars = exprs(val), join_type = "after", first_cond_upper = val.join == "++", filter_join = val == "0" & all(val.join %in% c("+", "++")) )
library(tibble) library(admiral) # filter observations with a duration longer than 30 and # on or after 7 days before a COVID AE (ACOVFL == "Y") adae <- tribble( ~USUBJID, ~ADY, ~ACOVFL, ~ADURN, "1", 10, "N", 1, "1", 21, "N", 50, "1", 23, "Y", 14, "1", 32, "N", 31, "1", 42, "N", 20, "2", 11, "Y", 13, "2", 23, "N", 2, "3", 13, "Y", 12, "4", 14, "N", 32, "4", 21, "N", 41 ) filter_joined( adae, dataset_add = adae, by_vars = exprs(USUBJID), join_vars = exprs(ACOVFL, ADY), join_type = "all", order = exprs(ADY), filter_join = ADURN > 30 & ACOVFL.join == "Y" & ADY >= ADY.join - 7 ) # filter observations with AVALC == "Y" and AVALC == "Y" at a subsequent visit data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "Y", "1", 2, "N", "1", 3, "Y", "1", 4, "N", "2", 1, "Y", "2", 2, "N", "3", 1, "Y", "4", 1, "N", "4", 2, "N", ) filter_joined( data, dataset_add = data, by_vars = exprs(USUBJID), join_vars = exprs(AVALC, AVISITN), join_type = "after", order = exprs(AVISITN), filter_join = AVALC == "Y" & AVALC.join == "Y" & AVISITN < AVISITN.join ) # select observations with AVALC == "CR", AVALC == "CR" at a subsequent visit, # only "CR" or "NE" in between, and at most one "NE" in between data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "PR", "1", 2, "CR", "1", 3, "NE", "1", 4, "CR", "1", 5, "NE", "2", 1, "CR", "2", 2, "PR", "2", 3, "CR", "3", 1, "CR", "4", 1, "CR", "4", 2, "NE", "4", 3, "NE", "4", 4, "CR", "4", 5, "PR" ) filter_joined( data, dataset_add = data, by_vars = exprs(USUBJID), join_vars = exprs(AVALC), join_type = "after", order = exprs(AVISITN), first_cond_upper = AVALC.join == "CR", filter_join = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1 ) # select observations with AVALC == "PR", AVALC == "CR" or AVALC == "PR" # at a subsequent visit at least 20 days later, only "CR", "PR", or "NE" # in between, at most one "NE" in between, and "CR" is not followed by "PR" data <- tribble( ~USUBJID, ~ADY, ~AVALC, "1", 6, "PR", "1", 12, "CR", "1", 24, "NE", "1", 32, "CR", "1", 48, "PR", "2", 3, "PR", "2", 21, "CR", "2", 33, "PR", "3", 11, "PR", "4", 7, "PR", "4", 12, "NE", "4", 24, "NE", "4", 32, "PR", "4", 55, "PR" ) filter_joined( data, dataset_add = data, by_vars = exprs(USUBJID), join_vars = exprs(AVALC, ADY), join_type = "after", order = exprs(ADY), first_cond_upper = AVALC.join %in% c("CR", "PR") & ADY.join - ADY >= 20, filter_join = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1 & ( min_cond(var = ADY.join, cond = AVALC.join == "CR") > max_cond(var = ADY.join, cond = AVALC.join == "PR") | count_vals(var = AVALC.join, val = "CR") == 0 ) ) # select observations with CRIT1FL == "Y" at two consecutive visits or at the last visit data <- tribble( ~USUBJID, ~AVISITN, ~CRIT1FL, "1", 1, "Y", "1", 2, "N", "1", 3, "Y", "1", 5, "N", "2", 1, "Y", "2", 3, "Y", "2", 5, "N", "3", 1, "Y", "4", 1, "Y", "4", 2, "N", ) filter_joined( data, dataset_add = data, by_vars = exprs(USUBJID), tmp_obs_nr_var = tmp_obs_nr, join_vars = exprs(CRIT1FL), join_type = "all", order = exprs(AVISITN), filter_join = CRIT1FL == "Y" & CRIT1FL.join == "Y" & (tmp_obs_nr + 1 == tmp_obs_nr.join | tmp_obs_nr == max(tmp_obs_nr.join)) ) # first_cond_lower and first_cond_upper argument myd <- tribble( ~subj, ~day, ~val, "1", 1, "++", "1", 2, "-", "1", 3, "0", "1", 4, "+", "1", 5, "++", "1", 6, "-", "2", 1, "-", "2", 2, "++", "2", 3, "+", "2", 4, "0", "2", 5, "-", "2", 6, "++" ) # select "0" where all results from the first "++" before the "0" up to the "0" # (excluding the "0") are "+" or "++" filter_joined( myd, dataset_add = myd, by_vars = exprs(subj), order = exprs(day), join_vars = exprs(val), join_type = "before", first_cond_lower = val.join == "++", filter_join = val == "0" & all(val.join %in% c("+", "++")) ) # select "0" where all results from the "0" (excluding the "0") up to the first # "++" after the "0" are "+" or "++" filter_joined( myd, dataset_add = myd, by_vars = exprs(subj), order = exprs(day), join_vars = exprs(val), join_type = "after", first_cond_upper = val.join == "++", filter_join = val == "0" & all(val.join %in% c("+", "++")) )
Returns all records in the input dataset that belong to by groups that are not present in a source dataset, after the source dataset is optionally filtered. For example, this could be used to return ADSL records for subjects that didn't take certain concomitant medications during the course of the study (as per records in ADCM).
filter_not_exist(dataset, dataset_add, by_vars, filter_add = NULL)
filter_not_exist(dataset, dataset_add, by_vars, filter_add = NULL)
dataset |
Input dataset The variables specified by the |
dataset_add |
Source dataset The source dataset, which determines the by groups returned in the input dataset,
based on the groups that don't exist in this dataset after being subset by The variables specified in the |
by_vars |
Grouping variables Permitted Values: list of variables created by |
filter_add |
Filter for the source dataset The filter condition which will be used to subset the source dataset. Alternatively, if no filter condition is supplied, no subsetting of the source dataset will be performed. Default: |
Returns the records in dataset
which don't match any existing by groups in
dataset_add
, after being filtered according to filter_add
. If all by
groups that exist in dataset
don't exist in dataset_add
, an empty dataset will
be returned.
The records in the input dataset which are not contained within any existing by group in the filtered source dataset.
Utilities for Filtering Observations:
count_vals()
,
filter_exist()
,
filter_extreme()
,
filter_joined()
,
filter_relative()
,
max_cond()
,
min_cond()
# Get demographic information about subjects who didn't take vitamin supplements # during the study library(tibble) adsl <- tribble( ~USUBJID, ~AGE, ~SEX, "01-701-1015", 63, "F", "01-701-1023", 64, "M", "01-701-1034", 77, "F", "01-701-1118", 52, "M" ) adcm <- tribble( ~USUBJID, ~CMTRT, ~CMSTDTC, "01-701-1015", "ASPIRIN", "2013-05-14", "01-701-1023", "MYLANTA", "2014-01-04", "01-701-1023", "CALCIUM", "2014-02-25", "01-701-1034", "VITAMIN C", "2013-12-12", "01-701-1034", "CALCIUM", "2013-03-27", "01-701-1118", "MULTIVITAMIN", "2013-02-21" ) filter_not_exist( dataset = adsl, dataset_add = adcm, by_vars = exprs(USUBJID), filter_add = str_detect(CMTRT, "VITAMIN") )
# Get demographic information about subjects who didn't take vitamin supplements # during the study library(tibble) adsl <- tribble( ~USUBJID, ~AGE, ~SEX, "01-701-1015", 63, "F", "01-701-1023", 64, "M", "01-701-1034", 77, "F", "01-701-1118", 52, "M" ) adcm <- tribble( ~USUBJID, ~CMTRT, ~CMSTDTC, "01-701-1015", "ASPIRIN", "2013-05-14", "01-701-1023", "MYLANTA", "2014-01-04", "01-701-1023", "CALCIUM", "2014-02-25", "01-701-1034", "VITAMIN C", "2013-12-12", "01-701-1034", "CALCIUM", "2013-03-27", "01-701-1118", "MULTIVITAMIN", "2013-02-21" ) filter_not_exist( dataset = adsl, dataset_add = adcm, by_vars = exprs(USUBJID), filter_add = str_detect(CMTRT, "VITAMIN") )
Filters the observations before or after the observation where a specified condition is fulfilled for each by group. For example, the function could be called to select for each subject all observations before the first disease progression.
filter_relative( dataset, by_vars, order, condition, mode, selection, inclusive, keep_no_ref_groups = TRUE, check_type = "warning" )
filter_relative( dataset, by_vars, order, condition, mode, selection, inclusive, keep_no_ref_groups = TRUE, check_type = "warning" )
dataset |
Input dataset The variables specified by the |
by_vars |
Grouping variables Permitted Values: list of variables created by |
order |
Sort order Within each by group the observations are ordered by the specified order. For handling of Permitted Values: list of expressions created by |
condition |
Condition for Reference Observation The specified condition determines the reference observation. The output
dataset contains all observations before or after ( |
mode |
Selection mode (first or last) If Permitted Values: |
selection |
Select observations before or after the reference observation? Permitted Values: |
inclusive |
Include the reference observation? Permitted Values: |
keep_no_ref_groups |
Should by groups without reference observation be kept? Permitted Values: |
check_type |
Check uniqueness? If Permitted Values: |
For each by group ( by_vars
parameter) the observations before or
after (selection
parameter) the observations where the condition
(condition
parameter) is fulfilled the first or last time (order
parameter and mode
parameter) is included in the output dataset.
A dataset containing for each by group the observations before or after the observation where the condition was fulfilled the first or last time
Utilities for Filtering Observations:
count_vals()
,
filter_exist()
,
filter_extreme()
,
filter_joined()
,
filter_not_exist()
,
max_cond()
,
min_cond()
library(tibble) response <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "PR", "1", 2, "CR", "1", 3, "CR", "1", 4, "SD", "1", 5, "NE", "2", 1, "SD", "2", 2, "PD", "2", 3, "PD", "3", 1, "SD", "4", 1, "SD", "4", 2, "PR", "4", 3, "PD", "4", 4, "SD", "4", 5, "PR" ) # Select observations up to first PD for each patient response %>% filter_relative( by_vars = exprs(USUBJID), order = exprs(AVISITN), condition = AVALC == "PD", mode = "first", selection = "before", inclusive = TRUE ) # Select observations after last CR, PR, or SD for each patient response %>% filter_relative( by_vars = exprs(USUBJID), order = exprs(AVISITN), condition = AVALC %in% c("CR", "PR", "SD"), mode = "last", selection = "after", inclusive = FALSE ) # Select observations from first response to first PD response %>% filter_relative( by_vars = exprs(USUBJID), order = exprs(AVISITN), condition = AVALC %in% c("CR", "PR"), mode = "first", selection = "after", inclusive = TRUE, keep_no_ref_groups = FALSE ) %>% filter_relative( by_vars = exprs(USUBJID), order = exprs(AVISITN), condition = AVALC == "PD", mode = "first", selection = "before", inclusive = TRUE )
library(tibble) response <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "PR", "1", 2, "CR", "1", 3, "CR", "1", 4, "SD", "1", 5, "NE", "2", 1, "SD", "2", 2, "PD", "2", 3, "PD", "3", 1, "SD", "4", 1, "SD", "4", 2, "PR", "4", 3, "PD", "4", 4, "SD", "4", 5, "PR" ) # Select observations up to first PD for each patient response %>% filter_relative( by_vars = exprs(USUBJID), order = exprs(AVISITN), condition = AVALC == "PD", mode = "first", selection = "before", inclusive = TRUE ) # Select observations after last CR, PR, or SD for each patient response %>% filter_relative( by_vars = exprs(USUBJID), order = exprs(AVISITN), condition = AVALC %in% c("CR", "PR", "SD"), mode = "last", selection = "after", inclusive = FALSE ) # Select observations from first response to first PD response %>% filter_relative( by_vars = exprs(USUBJID), order = exprs(AVISITN), condition = AVALC %in% c("CR", "PR"), mode = "first", selection = "after", inclusive = TRUE, keep_no_ref_groups = FALSE ) %>% filter_relative( by_vars = exprs(USUBJID), order = exprs(AVISITN), condition = AVALC == "PD", mode = "first", selection = "before", inclusive = TRUE )
flag_event
ObjectThe flag_event
object is used to define events as input for the
derive_var_merged_ef_msrc()
function.
flag_event(dataset_name, condition = NULL, by_vars = NULL)
flag_event(dataset_name, condition = NULL, by_vars = NULL)
dataset_name |
Dataset name of the dataset to be used as input for the
event. The name refers to the dataset specified for Permitted Values: a character scalar |
condition |
Condition The condition is evaluated at the dataset referenced by |
by_vars |
Grouping variables If specified, the dataset is grouped by the specified variables before the
condition is evaluated. If named elements are used in |
Source Objects:
basket_select()
,
censor_source()
,
death_event
,
event()
,
event_joined()
,
event_source()
,
query()
,
records_source()
,
tte_source()
Get the Value of an Admiral Option Which Can Be Modified for Advanced Users.
get_admiral_option(option)
get_admiral_option(option)
option |
A character scalar of commonly used admiral function inputs. As of now, support only available for
"subject_keys" and "signif_digits".
See |
This function allows flexibility for function inputs that may need to be repeated
multiple times in a script, such as subject_keys
.
The value of the specified option.
set_admiral_options()
, derive_param_exist_flag()
, derive_param_tte()
derive_var_dthcaus()
, derive_var_extreme_dtm()
, derive_vars_period()
,
create_period_dataset()
Other admiral_options:
set_admiral_options()
library(dplyr, warn.conflicts = FALSE) dm <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "DM", "01-1302", 61, "YEARS", "PILOT01", "DM", "17-1344", 64, "YEARS" ) vs <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~VSTESTCD, ~VISIT, ~VSTPT, ~VSSTRESN, "PILOT01", "VS", "01-1302", "DIABP", "BASELINE", "LYING", 76, "PILOT01", "VS", "01-1302", "DIABP", "BASELINE", "STANDING", 87, "PILOT01", "VS", "01-1302", "DIABP", "WEEK 2", "LYING", 71, "PILOT01", "VS", "01-1302", "DIABP", "WEEK 2", "STANDING", 79, "PILOT01", "VS", "17-1344", "DIABP", "BASELINE", "LYING", 88, "PILOT01", "VS", "17-1344", "DIABP", "BASELINE", "STANDING", 86, "PILOT01", "VS", "17-1344", "DIABP", "WEEK 2", "LYING", 84, "PILOT01", "VS", "17-1344", "DIABP", "WEEK 2", "STANDING", 82 ) # Merging all dm variables to vs derive_vars_merged( vs, dataset_add = select(dm, -DOMAIN), by_vars = get_admiral_option("subject_keys") )
library(dplyr, warn.conflicts = FALSE) dm <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AGE, ~AGEU, "PILOT01", "DM", "01-1302", 61, "YEARS", "PILOT01", "DM", "17-1344", 64, "YEARS" ) vs <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~VSTESTCD, ~VISIT, ~VSTPT, ~VSSTRESN, "PILOT01", "VS", "01-1302", "DIABP", "BASELINE", "LYING", 76, "PILOT01", "VS", "01-1302", "DIABP", "BASELINE", "STANDING", 87, "PILOT01", "VS", "01-1302", "DIABP", "WEEK 2", "LYING", 71, "PILOT01", "VS", "01-1302", "DIABP", "WEEK 2", "STANDING", 79, "PILOT01", "VS", "17-1344", "DIABP", "BASELINE", "LYING", 88, "PILOT01", "VS", "17-1344", "DIABP", "BASELINE", "STANDING", 86, "PILOT01", "VS", "17-1344", "DIABP", "WEEK 2", "LYING", 84, "PILOT01", "VS", "17-1344", "DIABP", "WEEK 2", "STANDING", 82 ) # Merging all dm variables to vs derive_vars_merged( vs, dataset_add = select(dm, -DOMAIN), by_vars = get_admiral_option("subject_keys") )
Get Duplicate Records that Led to a Prior Error
get_duplicates_dataset()
get_duplicates_dataset()
Many {admiral}
function check that the input dataset contains only one record
per by_vars
group and throw an error otherwise. The get_duplicates_dataset()
function allows one to retrieve the duplicate records that lead to an error.
Note that the function always returns the dataset of duplicates from the last
error that has been thrown in the current R session. Thus, after restarting the
R sessions get_duplicates_dataset()
will return NULL
and after a second error
has been thrown, the dataset of the first error can no longer be accessed (unless
it has been saved in a variable).
A data.frame
or NULL
Utilities for Dataset Checking:
get_many_to_one_dataset()
,
get_one_to_many_dataset()
data(admiral_adsl) # Duplicate the first record adsl <- rbind(admiral_adsl[1L, ], admiral_adsl) signal_duplicate_records(adsl, exprs(USUBJID), cnd_type = "warning") get_duplicates_dataset()
data(admiral_adsl) # Duplicate the first record adsl <- rbind(admiral_adsl[1L, ], admiral_adsl) signal_duplicate_records(adsl, exprs(USUBJID), cnd_type = "warning") get_duplicates_dataset()
Create a flag variable for the input dataset which indicates if there exists at least one observation in the input dataset fulfilling a certain condition.
Note: This is a helper function for derive_vars_merged_exist_flag()
which
inputs this result into derive_vars_merged()
.
get_flagged_records(dataset, new_var, condition, filter = NULL)
get_flagged_records(dataset, new_var, condition, filter = NULL)
dataset |
Input dataset |
new_var |
New variable The specified variable is added to the input dataset. |
condition |
Condition The condition is evaluated at the dataset ( |
filter |
Filter for additional data Only observations fulfilling the specified condition are taken into account for flagging. If the argument is not specified, all observations are considered. Permitted Values: a condition |
The output dataset is the input dataset filtered by the filter
condition
and with the variable specified for new_var
representing a flag for the condition.
Utilities used within Derivation functions:
call_user_fun()
,
extract_unit()
,
get_not_mapped()
,
get_vars_query()
library(dplyr, warn.conflicts = FALSE) ae <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AETERM, ~AEREL, "PILOT01", "AE", "01-1028", "ERYTHEMA", "POSSIBLE", "PILOT01", "AE", "01-1028", "PRURITUS", "PROBABLE", "PILOT01", "AE", "06-1049", "SYNCOPE", "POSSIBLE", "PILOT01", "AE", "06-1049", "SYNCOPE", "PROBABLE" ) get_flagged_records( dataset = ae, new_var = AERELFL, condition = AEREL == "PROBABLE" ) %>% select(STUDYID, USUBJID, AERELFL) vs <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~VISIT, ~VSTESTCD, ~VSSTRESN, ~VSBLFL, "PILOT01", "VS", "01-1028", "SCREENING", "HEIGHT", 177.8, NA, "PILOT01", "VS", "01-1028", "SCREENING", "WEIGHT", 98.88, NA, "PILOT01", "VS", "01-1028", "BASELINE", "WEIGHT", 99.34, "Y", "PILOT01", "VS", "01-1028", "WEEK 4", "WEIGHT", 98.88, NA, "PILOT01", "VS", "04-1127", "SCREENING", "HEIGHT", 165.1, NA, "PILOT01", "VS", "04-1127", "SCREENING", "WEIGHT", 42.87, NA, "PILOT01", "VS", "04-1127", "BASELINE", "WEIGHT", 41.05, "Y", "PILOT01", "VS", "04-1127", "WEEK 4", "WEIGHT", 41.73, NA, "PILOT01", "VS", "06-1049", "SCREENING", "HEIGHT", 167.64, NA, "PILOT01", "VS", "06-1049", "SCREENING", "WEIGHT", 57.61, NA, "PILOT01", "VS", "06-1049", "BASELINE", "WEIGHT", 57.83, "Y", "PILOT01", "VS", "06-1049", "WEEK 4", "WEIGHT", 58.97, NA ) get_flagged_records( dataset = vs, new_var = WTBLHIFL, condition = VSSTRESN > 90, filter = VSTESTCD == "WEIGHT" & VSBLFL == "Y" ) %>% select(STUDYID, USUBJID, WTBLHIFL)
library(dplyr, warn.conflicts = FALSE) ae <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AETERM, ~AEREL, "PILOT01", "AE", "01-1028", "ERYTHEMA", "POSSIBLE", "PILOT01", "AE", "01-1028", "PRURITUS", "PROBABLE", "PILOT01", "AE", "06-1049", "SYNCOPE", "POSSIBLE", "PILOT01", "AE", "06-1049", "SYNCOPE", "PROBABLE" ) get_flagged_records( dataset = ae, new_var = AERELFL, condition = AEREL == "PROBABLE" ) %>% select(STUDYID, USUBJID, AERELFL) vs <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~VISIT, ~VSTESTCD, ~VSSTRESN, ~VSBLFL, "PILOT01", "VS", "01-1028", "SCREENING", "HEIGHT", 177.8, NA, "PILOT01", "VS", "01-1028", "SCREENING", "WEIGHT", 98.88, NA, "PILOT01", "VS", "01-1028", "BASELINE", "WEIGHT", 99.34, "Y", "PILOT01", "VS", "01-1028", "WEEK 4", "WEIGHT", 98.88, NA, "PILOT01", "VS", "04-1127", "SCREENING", "HEIGHT", 165.1, NA, "PILOT01", "VS", "04-1127", "SCREENING", "WEIGHT", 42.87, NA, "PILOT01", "VS", "04-1127", "BASELINE", "WEIGHT", 41.05, "Y", "PILOT01", "VS", "04-1127", "WEEK 4", "WEIGHT", 41.73, NA, "PILOT01", "VS", "06-1049", "SCREENING", "HEIGHT", 167.64, NA, "PILOT01", "VS", "06-1049", "SCREENING", "WEIGHT", 57.61, NA, "PILOT01", "VS", "06-1049", "BASELINE", "WEIGHT", 57.83, "Y", "PILOT01", "VS", "06-1049", "WEEK 4", "WEIGHT", 58.97, NA ) get_flagged_records( dataset = vs, new_var = WTBLHIFL, condition = VSSTRESN > 90, filter = VSTESTCD == "WEIGHT" & VSBLFL == "Y" ) %>% select(STUDYID, USUBJID, WTBLHIFL)
Get Many to One Values that Led to a Prior Error
get_many_to_one_dataset()
get_many_to_one_dataset()
If assert_one_to_one()
detects an issue, the many to one values are stored
in a dataset. This dataset can be retrieved by get_many_to_one_dataset()
.
Note that the function always returns the many to one values from the last
error that has been thrown in the current R session. Thus, after restarting
the R sessions get_many_to_one_dataset()
will return NULL
and after a
second error has been thrown, the dataset of the first error can no longer be
accessed (unless it has been saved in a variable).
A data.frame
or NULL
Utilities for Dataset Checking:
get_duplicates_dataset()
,
get_one_to_many_dataset()
library(admiraldev, warn.conflicts = FALSE) data(admiral_adsl) try( assert_one_to_one(admiral_adsl, exprs(SITEID), exprs(STUDYID)) ) get_many_to_one_dataset()
library(admiraldev, warn.conflicts = FALSE) data(admiral_adsl) try( assert_one_to_one(admiral_adsl, exprs(SITEID), exprs(STUDYID)) ) get_many_to_one_dataset()
Get list of records not mapped from the lookup table.
get_not_mapped()
get_not_mapped()
A data.frame
or NULL
Utilities used within Derivation functions:
call_user_fun()
,
extract_unit()
,
get_flagged_records()
,
get_vars_query()
Get One to Many Values that Led to a Prior Error
get_one_to_many_dataset()
get_one_to_many_dataset()
If assert_one_to_one()
detects an issue, the one to many values are stored
in a dataset. This dataset can be retrieved by get_one_to_many_dataset()
.
Note that the function always returns the one to many values from the last
error that has been thrown in the current R session. Thus, after restarting
the R sessions get_one_to_many_dataset()
will return NULL
and after a
second error has been thrown, the dataset of the first error can no longer be
accessed (unless it has been saved in a variable).
A data.frame
or NULL
Utilities for Dataset Checking:
get_duplicates_dataset()
,
get_many_to_one_dataset()
library(admiraldev, warn.conflicts = FALSE) data(admiral_adsl) try( assert_one_to_one(admiral_adsl, exprs(STUDYID), exprs(SITEID)) ) get_one_to_many_dataset()
library(admiraldev, warn.conflicts = FALSE) data(admiral_adsl) try( assert_one_to_one(admiral_adsl, exprs(STUDYID), exprs(SITEID)) ) get_one_to_many_dataset()
Development on get_summary_records()
is complete, and for new code we recommend
switching to using the dataset_add
argument in derive_summary_records()
.
It is not uncommon to have an analysis need whereby one needs to derive an
analysis value (AVAL
) from multiple records. The ADaM basic dataset
structure variable DTYPE
is available to indicate when a new derived
records has been added to a dataset.
get_summary_records( dataset, by_vars, filter = NULL, analysis_var, summary_fun, set_values_to = NULL )
get_summary_records( dataset, by_vars, filter = NULL, analysis_var, summary_fun, set_values_to = NULL )
This function only creates derived observations and does not append them
to the original dataset observations. If you would like to this instead,
see the derive_summary_records()
function.
A data frame of derived records.
derive_summary_records()
, derive_var_merged_summary()
Other superseded:
date_source()
,
derive_param_extreme_record()
,
derive_var_dthcaus()
,
derive_var_extreme_dt()
,
derive_var_extreme_dtm()
,
dthcaus_source()
library(tibble) adeg <- tribble( ~USUBJID, ~EGSEQ, ~PARAM, ~AVISIT, ~EGDTC, ~AVAL, ~TRTA, "XYZ-1001", 1, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385, NA_character_, "XYZ-1001", 2, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:52", 399, NA_character_, "XYZ-1001", 3, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:56", 396, NA_character_, "XYZ-1001", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:45", 384, "Placebo", "XYZ-1001", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:48", 393, "Placebo", "XYZ-1001", 6, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:51", 388, "Placebo", "XYZ-1001", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:45", 385, "Placebo", "XYZ-1001", 8, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:48", 394, "Placebo", "XYZ-1001", 9, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:51", 402, "Placebo", "XYZ-1002", 1, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 399, NA_character_, "XYZ-1002", 2, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 410, NA_character_, "XYZ-1002", 3, "QTcF Int. (msec)", "Baseline", "2016-02-22T08:01", 392, NA_character_, "XYZ-1002", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:50", 401, "Active 20mg", "XYZ-1002", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:53", 407, "Active 20mg", "XYZ-1002", 6, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:56", 400, "Active 20mg", "XYZ-1002", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:50", 412, "Active 20mg", "XYZ-1002", 8, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:53", 414, "Active 20mg", "XYZ-1002", 9, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:56", 402, "Active 20mg" ) # Summarize the average of the triplicate ECG interval values (AVAL) get_summary_records( adeg, by_vars = exprs(USUBJID, PARAM, AVISIT), set_values_to = exprs( AVAL = mean(AVAL, na.rm = TRUE), DTYPE = "AVERAGE" ) ) # Derive more than one summary variable get_summary_records( adeg, by_vars = exprs(USUBJID, PARAM, AVISIT), set_values_to = exprs( AVAL = mean(AVAL), ASTDTM = min(convert_dtc_to_dtm(EGDTC)), AENDTM = max(convert_dtc_to_dtm(EGDTC)), DTYPE = "AVERAGE" ) ) # Sample ADEG dataset with triplicate record for only AVISIT = 'Baseline' adeg <- tribble( ~USUBJID, ~EGSEQ, ~PARAM, ~AVISIT, ~EGDTC, ~AVAL, ~TRTA, "XYZ-1001", 1, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385, NA_character_, "XYZ-1001", 2, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:52", 399, NA_character_, "XYZ-1001", 3, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:56", 396, NA_character_, "XYZ-1001", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:48", 393, "Placebo", "XYZ-1001", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:51", 388, "Placebo", "XYZ-1001", 6, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:48", 394, "Placebo", "XYZ-1001", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:51", 402, "Placebo", "XYZ-1002", 1, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 399, NA_character_, "XYZ-1002", 2, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 410, NA_character_, "XYZ-1002", 3, "QTcF Int. (msec)", "Baseline", "2016-02-22T08:01", 392, NA_character_, "XYZ-1002", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:53", 407, "Active 20mg", "XYZ-1002", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:56", 400, "Active 20mg", "XYZ-1002", 6, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:53", 414, "Active 20mg", "XYZ-1002", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:56", 402, "Active 20mg" ) # Compute the average of AVAL only if there are more than 2 records within the # by group get_summary_records( adeg, by_vars = exprs(USUBJID, PARAM, AVISIT), filter = n() > 2, set_values_to = exprs( AVAL = mean(AVAL, na.rm = TRUE), DTYPE = "AVERAGE" ) )
library(tibble) adeg <- tribble( ~USUBJID, ~EGSEQ, ~PARAM, ~AVISIT, ~EGDTC, ~AVAL, ~TRTA, "XYZ-1001", 1, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385, NA_character_, "XYZ-1001", 2, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:52", 399, NA_character_, "XYZ-1001", 3, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:56", 396, NA_character_, "XYZ-1001", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:45", 384, "Placebo", "XYZ-1001", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:48", 393, "Placebo", "XYZ-1001", 6, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:51", 388, "Placebo", "XYZ-1001", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:45", 385, "Placebo", "XYZ-1001", 8, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:48", 394, "Placebo", "XYZ-1001", 9, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:51", 402, "Placebo", "XYZ-1002", 1, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 399, NA_character_, "XYZ-1002", 2, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 410, NA_character_, "XYZ-1002", 3, "QTcF Int. (msec)", "Baseline", "2016-02-22T08:01", 392, NA_character_, "XYZ-1002", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:50", 401, "Active 20mg", "XYZ-1002", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:53", 407, "Active 20mg", "XYZ-1002", 6, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:56", 400, "Active 20mg", "XYZ-1002", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:50", 412, "Active 20mg", "XYZ-1002", 8, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:53", 414, "Active 20mg", "XYZ-1002", 9, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:56", 402, "Active 20mg" ) # Summarize the average of the triplicate ECG interval values (AVAL) get_summary_records( adeg, by_vars = exprs(USUBJID, PARAM, AVISIT), set_values_to = exprs( AVAL = mean(AVAL, na.rm = TRUE), DTYPE = "AVERAGE" ) ) # Derive more than one summary variable get_summary_records( adeg, by_vars = exprs(USUBJID, PARAM, AVISIT), set_values_to = exprs( AVAL = mean(AVAL), ASTDTM = min(convert_dtc_to_dtm(EGDTC)), AENDTM = max(convert_dtc_to_dtm(EGDTC)), DTYPE = "AVERAGE" ) ) # Sample ADEG dataset with triplicate record for only AVISIT = 'Baseline' adeg <- tribble( ~USUBJID, ~EGSEQ, ~PARAM, ~AVISIT, ~EGDTC, ~AVAL, ~TRTA, "XYZ-1001", 1, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385, NA_character_, "XYZ-1001", 2, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:52", 399, NA_character_, "XYZ-1001", 3, "QTcF Int. (msec)", "Baseline", "2016-02-24T07:56", 396, NA_character_, "XYZ-1001", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:48", 393, "Placebo", "XYZ-1001", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-08T09:51", 388, "Placebo", "XYZ-1001", 6, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:48", 394, "Placebo", "XYZ-1001", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-22T10:51", 402, "Placebo", "XYZ-1002", 1, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 399, NA_character_, "XYZ-1002", 2, "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 410, NA_character_, "XYZ-1002", 3, "QTcF Int. (msec)", "Baseline", "2016-02-22T08:01", 392, NA_character_, "XYZ-1002", 4, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:53", 407, "Active 20mg", "XYZ-1002", 5, "QTcF Int. (msec)", "Visit 2", "2016-03-06T09:56", 400, "Active 20mg", "XYZ-1002", 6, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:53", 414, "Active 20mg", "XYZ-1002", 7, "QTcF Int. (msec)", "Visit 3", "2016-03-24T10:56", 402, "Active 20mg" ) # Compute the average of AVAL only if there are more than 2 records within the # by group get_summary_records( adeg, by_vars = exprs(USUBJID, PARAM, AVISIT), filter = n() > 2, set_values_to = exprs( AVAL = mean(AVAL, na.rm = TRUE), DTYPE = "AVERAGE" ) )
The function checks if all requirements to access the database are fulfilled
(version and access function are available, see assert_db_requirements()
),
reads the terms from the database, and checks if the dataset with the terms
is in the expected format (see assert_terms()
).
get_terms_from_db( version, fun, queries, definition, expect_grpname = FALSE, expect_grpid = FALSE, i, temp_env )
get_terms_from_db( version, fun, queries, definition, expect_grpname = FALSE, expect_grpid = FALSE, i, temp_env )
version |
Version The version must be non null. Otherwise, an error is issued. The value is
passed to the access function ( |
fun |
Access function The access function must be non null. Otherwise, an error is issued. The function is called to retrieve the terms. |
queries |
Queries List of all queries passed to |
definition |
Definition of the query The definition is passed to the access function. It defines which terms are returned. |
expect_grpname |
Is |
expect_grpid |
Is |
i |
Index of The value is used for error messages. |
temp_env |
Temporary environment The value is passed to the access function. |
Output dataset of the access function
OCCDS Functions:
derive_var_trtemfl()
,
derive_vars_atc()
,
derive_vars_query()
Create a table for the input dataset which binds the necessary
rows for a derive_vars_query()
call with the relevant SRCVAR
, TERM_NAME_ID
and a temporary index if it is necessary
Note: This function is the first step performed in derive_vars_query()
requested by some users to be present independently from it.
get_vars_query(dataset, dataset_queries)
get_vars_query(dataset, dataset_queries)
dataset |
Input dataset |
dataset_queries |
A dataset containing required columns
|
This function can be used to derive CDISC variables such as
SMQzzNAM
, SMQzzCD
, SMQzzSC
, SMQzzSCN
, and CQzzNAM
in ADAE and
ADMH, and variables such as SDGzzNAM
, SDGzzCD
, and SDGzzSC
in ADCM.
An example usage of this function can be found in the
OCCDS vignette.
A query dataset is expected as an input to this function. See the
Queries Dataset Documentation vignette
for descriptions, or call data("queries")
for an example of a query dataset.
For each unique element in PREFIX
, the corresponding "NAM"
variable will be created. For each unique PREFIX
, if GRPID
is
not "" or NA, then the corresponding "CD" variable is created; similarly,
if SCOPE
is not "" or NA, then the corresponding "SC" variable will
be created; if SCOPEN
is not "" or NA, then the corresponding
"SCN" variable will be created.
For each record in dataset
, the "NAM" variable takes the value of
GRPNAME
if the value of TERMCHAR
or TERMNUM
in dataset_queries
matches
the value of the respective SRCVAR in dataset
.
Note that TERMCHAR
in dataset_queries
dataset may be NA only when TERMNUM
is non-NA and vice versa. The matching is case insensitive.
The "CD", "SC", and "SCN" variables are derived accordingly based on
GRPID
, SCOPE
, and SCOPEN
respectively,
whenever not missing.
The processed query dataset with SRCVAR
and TERM_NAME_ID
so that
that can be merged to the input dataset to execute the derivations outlined by dataset_queries
.
Utilities used within Derivation functions:
call_user_fun()
,
extract_unit()
,
get_flagged_records()
,
get_not_mapped()
library(tibble) data("queries") adae <- tribble( ~USUBJID, ~ASTDTM, ~AETERM, ~AESEQ, ~AEDECOD, ~AELLT, ~AELLTCD, "01", "2020-06-02 23:59:59", "ALANINE AMINOTRANSFERASE ABNORMAL", 3, "Alanine aminotransferase abnormal", NA_character_, NA_integer_, "02", "2020-06-05 23:59:59", "BASEDOW'S DISEASE", 5, "Basedow's disease", NA_character_, 1L, "03", "2020-06-07 23:59:59", "SOME TERM", 2, "Some query", "Some term", NA_integer_, "05", "2020-06-09 23:59:59", "ALVEOLAR PROTEINOSIS", 7, "Alveolar proteinosis", NA_character_, NA_integer_ ) get_vars_query(adae, queries)
library(tibble) data("queries") adae <- tribble( ~USUBJID, ~ASTDTM, ~AETERM, ~AESEQ, ~AEDECOD, ~AELLT, ~AELLTCD, "01", "2020-06-02 23:59:59", "ALANINE AMINOTRANSFERASE ABNORMAL", 3, "Alanine aminotransferase abnormal", NA_character_, NA_integer_, "02", "2020-06-05 23:59:59", "BASEDOW'S DISEASE", 5, "Basedow's disease", NA_character_, 1L, "03", "2020-06-07 23:59:59", "SOME TERM", 2, "Some query", "Some term", NA_integer_, "05", "2020-06-09 23:59:59", "ALVEOLAR PROTEINOSIS", 7, "Alveolar proteinosis", NA_character_, NA_integer_ ) get_vars_query(adae, queries)
'--DTC'
VariableImputation partial date portion of a '--DTC'
variable based on user input.
impute_dtc_dt( dtc, highest_imputation = "n", date_imputation = "first", min_dates = NULL, max_dates = NULL, preserve = FALSE )
impute_dtc_dt( dtc, highest_imputation = "n", date_imputation = "first", min_dates = NULL, max_dates = NULL, preserve = FALSE )
dtc |
The A character date is expected in a format like |
highest_imputation |
Highest imputation level The If a component at a higher level than the highest imputation level is
missing, If If Permitted Values: |
date_imputation |
The value to impute the day/month when a datepart is missing. A character value is expected, either as a
The argument is ignored if |
min_dates |
Minimum dates A list of dates is expected. It is ensured that the imputed date is not
before any of the specified dates, e.g., that the imputed adverse event start
date is not before the first treatment date. Only dates which are in the
range of possible dates of the impute_dtc_dtm( "2020-11", min_dates = list( ymd_hms("2020-12-06T12:12:12"), ymd_hms("2020-11-11T11:11:11") ), highest_imputation = "M" ) returns |
max_dates |
Maximum dates A list of dates is expected. It is ensured that the imputed date is not after any of the specified dates, e.g., that the imputed date is not after the data cut off date. Only dates which are in the range of possible dates are considered. A date or date-time object is expected. |
preserve |
Preserve day if month is missing and day is present For example Permitted Values: |
Usually this computation function can not be used with %>%
.
A character vector
Date/Time Computation Functions that returns a vector:
compute_age_years()
,
compute_dtf()
,
compute_duration()
,
compute_tmf()
,
convert_date_to_dtm()
,
convert_dtc_to_dt()
,
convert_dtc_to_dtm()
,
impute_dtc_dtm()
library(lubridate) dates <- c( "2019-07-18T15:25:40", "2019-07-18T15:25", "2019-07-18T15", "2019-07-18", "2019-02", "2019", "2019", "2019---07", "" ) # No date imputation (highest_imputation defaulted to "n") impute_dtc_dt(dtc = dates) # Impute to first day/month if date is partial impute_dtc_dt( dtc = dates, highest_imputation = "M" ) # Same as above impute_dtc_dt( dtc = dates, highest_imputation = "M", date_imputation = "01-01" ) # Impute to last day/month if date is partial impute_dtc_dt( dtc = dates, highest_imputation = "M", date_imputation = "last", ) # Impute to mid day/month if date is partial impute_dtc_dt( dtc = dates, highest_imputation = "M", date_imputation = "mid" ) # Impute a date and ensure that the imputed date is not before a list of # minimum dates impute_dtc_dt( "2020-12", min_dates = list( ymd("2020-12-06"), ymd("2020-11-11") ), highest_imputation = "M" ) # Impute completely missing dates (only possible if min_dates or max_dates is specified) impute_dtc_dt( c("2020-12", NA_character_), min_dates = list( ymd("2020-12-06", "2020-01-01"), ymd("2020-11-11", NA) ), highest_imputation = "Y" )
library(lubridate) dates <- c( "2019-07-18T15:25:40", "2019-07-18T15:25", "2019-07-18T15", "2019-07-18", "2019-02", "2019", "2019", "2019---07", "" ) # No date imputation (highest_imputation defaulted to "n") impute_dtc_dt(dtc = dates) # Impute to first day/month if date is partial impute_dtc_dt( dtc = dates, highest_imputation = "M" ) # Same as above impute_dtc_dt( dtc = dates, highest_imputation = "M", date_imputation = "01-01" ) # Impute to last day/month if date is partial impute_dtc_dt( dtc = dates, highest_imputation = "M", date_imputation = "last", ) # Impute to mid day/month if date is partial impute_dtc_dt( dtc = dates, highest_imputation = "M", date_imputation = "mid" ) # Impute a date and ensure that the imputed date is not before a list of # minimum dates impute_dtc_dt( "2020-12", min_dates = list( ymd("2020-12-06"), ymd("2020-11-11") ), highest_imputation = "M" ) # Impute completely missing dates (only possible if min_dates or max_dates is specified) impute_dtc_dt( c("2020-12", NA_character_), min_dates = list( ymd("2020-12-06", "2020-01-01"), ymd("2020-11-11", NA) ), highest_imputation = "Y" )
'--DTC'
VariableImputation partial date/time portion of a '--DTC'
variable. based on user
input.
impute_dtc_dtm( dtc, highest_imputation = "h", date_imputation = "first", time_imputation = "first", min_dates = NULL, max_dates = NULL, preserve = FALSE )
impute_dtc_dtm( dtc, highest_imputation = "h", date_imputation = "first", time_imputation = "first", min_dates = NULL, max_dates = NULL, preserve = FALSE )
dtc |
The A character date is expected in a format like |
highest_imputation |
Highest imputation level The If a component at a higher level than the highest imputation level is
missing, If If Permitted Values: |
date_imputation |
The value to impute the day/month when a datepart is missing. A character value is expected, either as a
The argument is ignored if |
time_imputation |
The value to impute the time when a timepart is missing. A character value is expected, either as a
The argument is ignored if |
min_dates |
Minimum dates A list of dates is expected. It is ensured that the imputed date is not
before any of the specified dates, e.g., that the imputed adverse event start
date is not before the first treatment date. Only dates which are in the
range of possible dates of the impute_dtc_dtm( "2020-11", min_dates = list( ymd_hms("2020-12-06T12:12:12"), ymd_hms("2020-11-11T11:11:11") ), highest_imputation = "M" ) returns For date variables (not datetime) in the list the time is imputed to
|
max_dates |
Maximum dates A list of dates is expected. It is ensured that the imputed date is not after any of the specified dates, e.g., that the imputed date is not after the data cut off date. Only dates which are in the range of possible dates are considered. A date or date-time object is expected. For date variables (not datetime) in the list the time is imputed to
|
preserve |
Preserve lower level date/time part when higher order part is missing, e.g. preserve day if month is missing or preserve minute when hour is missing. For example Permitted Values: |
Usually this computation function can not be used with %>%
.
A character vector
Date/Time Computation Functions that returns a vector:
compute_age_years()
,
compute_dtf()
,
compute_duration()
,
compute_tmf()
,
convert_date_to_dtm()
,
convert_dtc_to_dt()
,
convert_dtc_to_dtm()
,
impute_dtc_dt()
library(lubridate) dates <- c( "2019-07-18T15:25:40", "2019-07-18T15:25", "2019-07-18T15", "2019-07-18", "2019-02", "2019", "2019", "2019---07", "" ) # No date imputation (highest_imputation defaulted to "h") # Missing time part imputed with 00:00:00 portion by default impute_dtc_dtm(dtc = dates) # No date imputation (highest_imputation defaulted to "h") # Missing time part imputed with 23:59:59 portion impute_dtc_dtm( dtc = dates, time_imputation = "23:59:59" ) # Same as above impute_dtc_dtm( dtc = dates, time_imputation = "last" ) # Impute to first day/month if date is partial # Missing time part imputed with 00:00:00 portion by default impute_dtc_dtm( dtc = dates, highest_imputation = "M" ) # same as above impute_dtc_dtm( dtc = dates, highest_imputation = "M", date_imputation = "01-01" ) # Impute to last day/month if date is partial # Missing time part imputed with 23:59:59 portion impute_dtc_dtm( dtc = dates, date_imputation = "last", time_imputation = "last" ) # Impute to mid day/month if date is partial # Missing time part imputed with 00:00:00 portion by default impute_dtc_dtm( dtc = dates, highest_imputation = "M", date_imputation = "mid" ) # Impute a date and ensure that the imputed date is not before a list of # minimum dates impute_dtc_dtm( "2020-12", min_dates = list( ymd_hms("2020-12-06T12:12:12"), ymd_hms("2020-11-11T11:11:11") ), highest_imputation = "M" ) # Impute completely missing dates (only possible if min_dates or max_dates is specified) impute_dtc_dtm( c("2020-12", NA_character_), min_dates = list( ymd_hms("2020-12-06T12:12:12", "2020-01-01T01:01:01"), ymd_hms("2020-11-11T11:11:11", NA) ), highest_imputation = "Y" )
library(lubridate) dates <- c( "2019-07-18T15:25:40", "2019-07-18T15:25", "2019-07-18T15", "2019-07-18", "2019-02", "2019", "2019", "2019---07", "" ) # No date imputation (highest_imputation defaulted to "h") # Missing time part imputed with 00:00:00 portion by default impute_dtc_dtm(dtc = dates) # No date imputation (highest_imputation defaulted to "h") # Missing time part imputed with 23:59:59 portion impute_dtc_dtm( dtc = dates, time_imputation = "23:59:59" ) # Same as above impute_dtc_dtm( dtc = dates, time_imputation = "last" ) # Impute to first day/month if date is partial # Missing time part imputed with 00:00:00 portion by default impute_dtc_dtm( dtc = dates, highest_imputation = "M" ) # same as above impute_dtc_dtm( dtc = dates, highest_imputation = "M", date_imputation = "01-01" ) # Impute to last day/month if date is partial # Missing time part imputed with 23:59:59 portion impute_dtc_dtm( dtc = dates, date_imputation = "last", time_imputation = "last" ) # Impute to mid day/month if date is partial # Missing time part imputed with 00:00:00 portion by default impute_dtc_dtm( dtc = dates, highest_imputation = "M", date_imputation = "mid" ) # Impute a date and ensure that the imputed date is not before a list of # minimum dates impute_dtc_dtm( "2020-12", min_dates = list( ymd_hms("2020-12-06T12:12:12"), ymd_hms("2020-11-11T11:11:11") ), highest_imputation = "M" ) # Impute completely missing dates (only possible if min_dates or max_dates is specified) impute_dtc_dtm( c("2020-12", NA_character_), min_dates = list( ymd_hms("2020-12-06T12:12:12", "2020-01-01T01:01:01"), ymd_hms("2020-11-11T11:11:11", NA) ), highest_imputation = "Y" )
List All Available ADaM Templates
list_all_templates(package = "admiral")
list_all_templates(package = "admiral")
package |
The R package in which to look for templates. By default |
A character
vector of all available templates
Utilities used for examples and template scripts:
use_ad_template()
list_all_templates()
list_all_templates()
tte_source
Objects Available in a PackageList all tte_source
Objects Available in a Package
list_tte_source_objects(package = "admiral")
list_tte_source_objects(package = "admiral")
package |
The name of the package in which to search for |
A data.frame
where each row corresponds to one tte_source
object or NULL
if package
does not contain any tte_source
objects
Other Advanced Functions:
params()
list_tte_source_objects()
list_tte_source_objects()
The function derives the maximum value of a vector/column on a subset of entries/observations.
max_cond(var, cond)
max_cond(var, cond)
var |
A vector |
cond |
A condition |
Utilities for Filtering Observations:
count_vals()
,
filter_exist()
,
filter_extreme()
,
filter_joined()
,
filter_not_exist()
,
filter_relative()
,
min_cond()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(admiral) data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "PR", "1", 2, "CR", "1", 3, "NE", "1", 4, "CR", "1", 5, "NE", "2", 1, "CR", "2", 2, "PR", "2", 3, "CR", ) # In oncology setting, when needing to check the first time a patient had # a Complete Response (CR) to compare to see if any Partial Response (PR) # occurred after this add variable indicating if PR occurred after CR group_by(data, USUBJID) %>% mutate( first_cr_vis = min_cond(var = AVISITN, cond = AVALC == "CR"), last_pr_vis = max_cond(var = AVISITN, cond = AVALC == "PR"), pr_after_cr = last_pr_vis > first_cr_vis )
library(tibble) library(dplyr, warn.conflicts = FALSE) library(admiral) data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "PR", "1", 2, "CR", "1", 3, "NE", "1", 4, "CR", "1", 5, "NE", "2", 1, "CR", "2", 2, "PR", "2", 3, "CR", ) # In oncology setting, when needing to check the first time a patient had # a Complete Response (CR) to compare to see if any Partial Response (PR) # occurred after this add variable indicating if PR occurred after CR group_by(data, USUBJID) %>% mutate( first_cr_vis = min_cond(var = AVISITN, cond = AVALC == "CR"), last_pr_vis = max_cond(var = AVISITN, cond = AVALC == "PR"), pr_after_cr = last_pr_vis > first_cr_vis )
The function derives the minimum value of a vector/column on a subset of entries/observations.
min_cond(var, cond)
min_cond(var, cond)
var |
A vector |
cond |
A condition |
Utilities for Filtering Observations:
count_vals()
,
filter_exist()
,
filter_extreme()
,
filter_joined()
,
filter_not_exist()
,
filter_relative()
,
max_cond()
library(tibble) library(dplyr, warn.conflicts = FALSE) library(admiral) data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "PR", "1", 2, "CR", "1", 3, "NE", "1", 4, "CR", "1", 5, "NE", "2", 1, "CR", "2", 2, "PR", "2", 3, "CR", ) # In oncology setting, when needing to check the first time a patient had # a Complete Response (CR) to compare to see if any Partial Response (PR) # occurred after this add variable indicating if PR occurred after CR group_by(data, USUBJID) %>% mutate( first_cr_vis = min_cond(var = AVISITN, cond = AVALC == "CR"), last_pr_vis = max_cond(var = AVISITN, cond = AVALC == "PR"), pr_after_cr = last_pr_vis > first_cr_vis )
library(tibble) library(dplyr, warn.conflicts = FALSE) library(admiral) data <- tribble( ~USUBJID, ~AVISITN, ~AVALC, "1", 1, "PR", "1", 2, "CR", "1", 3, "NE", "1", 4, "CR", "1", 5, "NE", "2", 1, "CR", "2", 2, "PR", "2", 3, "CR", ) # In oncology setting, when needing to check the first time a patient had # a Complete Response (CR) to compare to see if any Partial Response (PR) # occurred after this add variable indicating if PR occurred after CR group_by(data, USUBJID) %>% mutate( first_cr_vis = min_cond(var = AVISITN, cond = AVALC == "CR"), last_pr_vis = max_cond(var = AVISITN, cond = AVALC == "PR"), pr_after_cr = last_pr_vis > first_cr_vis )
The function adds a minus sign as prefix to each variable.
negate_vars(vars = NULL)
negate_vars(vars = NULL)
vars |
List of variables created by |
This is useful if a list of variables should be removed from a dataset,
e.g., select(!!!negate_vars(by_vars))
removes all by variables.
A list of expressions
Utilities for working with quosures/list of expressions:
chr2vars()
negate_vars(exprs(USUBJID, STUDYID))
negate_vars(exprs(USUBJID, STUDYID))
Create a set of variable parameters/function arguments to be used in call_derivation()
.
params(...)
params(...)
... |
One or more named arguments |
An object of class params
Other Advanced Functions:
list_tte_source_objects()
library(dplyr, warn.conflicts = FALSE) adsl <- tribble( ~STUDYID, ~USUBJID, ~TRTSDT, ~TRTEDT, "PILOT01", "01-1307", NA, NA, "PILOT01", "05-1377", "2014-01-04", "2014-01-25", "PILOT01", "06-1384", "2012-09-15", "2012-09-24", "PILOT01", "15-1085", "2013-02-16", "2013-08-18", "PILOT01", "16-1298", "2013-04-08", "2013-06-28" ) %>% mutate( across(TRTSDT:TRTEDT, as.Date) ) ae <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AESTDTC, ~AEENDTC, "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "16-1298", "2013-06-08", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-06-08", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06" ) adae <- ae %>% select(USUBJID, AESTDTC, AEENDTC) %>% derive_vars_merged( dataset_add = adsl, new_vars = exprs(TRTSDT, TRTEDT), by_vars = exprs(USUBJID) ) ## In order to derive both `ASTDT` and `AENDT` in `ADAE`, one can use `derive_vars_dt()` adae %>% derive_vars_dt( new_vars_prefix = "AST", dtc = AESTDTC, date_imputation = "first", min_dates = exprs(TRTSDT), max_dates = exprs(TRTEDT) ) %>% derive_vars_dt( new_vars_prefix = "AEN", dtc = AEENDTC, date_imputation = "last", min_dates = exprs(TRTSDT), max_dates = exprs(TRTEDT) ) ## While `derive_vars_dt()` can only add one variable at a time, using `call_derivation()` ## one can add multiple variables in one go. ## The function arguments which are different from a variable to another (e.g. `new_vars_prefix`, ## `dtc`, and `date_imputation`) are specified as a list of `params()` in the `variable_params` ## argument of `call_derivation()`. All other arguments which are common to all variables ## (e.g. `min_dates` and `max_dates`) are specified outside of `variable_params` (i.e. in `...`). call_derivation( dataset = adae, derivation = derive_vars_dt, variable_params = list( params(dtc = AESTDTC, date_imputation = "first", new_vars_prefix = "AST"), params(dtc = AEENDTC, date_imputation = "last", new_vars_prefix = "AEN") ), min_dates = exprs(TRTSDT), max_dates = exprs(TRTEDT) ) ## The above call using `call_derivation()` is equivalent to the call using `derive_vars_dt()` ## to derive variables `ASTDT` and `AENDT` separately at the beginning.
library(dplyr, warn.conflicts = FALSE) adsl <- tribble( ~STUDYID, ~USUBJID, ~TRTSDT, ~TRTEDT, "PILOT01", "01-1307", NA, NA, "PILOT01", "05-1377", "2014-01-04", "2014-01-25", "PILOT01", "06-1384", "2012-09-15", "2012-09-24", "PILOT01", "15-1085", "2013-02-16", "2013-08-18", "PILOT01", "16-1298", "2013-04-08", "2013-06-28" ) %>% mutate( across(TRTSDT:TRTEDT, as.Date) ) ae <- tribble( ~STUDYID, ~DOMAIN, ~USUBJID, ~AESTDTC, ~AEENDTC, "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29", "PILOT01", "AE", "16-1298", "2013-06-08", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-06-08", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06", "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06" ) adae <- ae %>% select(USUBJID, AESTDTC, AEENDTC) %>% derive_vars_merged( dataset_add = adsl, new_vars = exprs(TRTSDT, TRTEDT), by_vars = exprs(USUBJID) ) ## In order to derive both `ASTDT` and `AENDT` in `ADAE`, one can use `derive_vars_dt()` adae %>% derive_vars_dt( new_vars_prefix = "AST", dtc = AESTDTC, date_imputation = "first", min_dates = exprs(TRTSDT), max_dates = exprs(TRTEDT) ) %>% derive_vars_dt( new_vars_prefix = "AEN", dtc = AEENDTC, date_imputation = "last", min_dates = exprs(TRTSDT), max_dates = exprs(TRTEDT) ) ## While `derive_vars_dt()` can only add one variable at a time, using `call_derivation()` ## one can add multiple variables in one go. ## The function arguments which are different from a variable to another (e.g. `new_vars_prefix`, ## `dtc`, and `date_imputation`) are specified as a list of `params()` in the `variable_params` ## argument of `call_derivation()`. All other arguments which are common to all variables ## (e.g. `min_dates` and `max_dates`) are specified outside of `variable_params` (i.e. in `...`). call_derivation( dataset = adae, derivation = derive_vars_dt, variable_params = list( params(dtc = AESTDTC, date_imputation = "first", new_vars_prefix = "AST"), params(dtc = AEENDTC, date_imputation = "last", new_vars_prefix = "AEN") ), min_dates = exprs(TRTSDT), max_dates = exprs(TRTEDT) ) ## The above call using `call_derivation()` is equivalent to the call using `derive_vars_dt()` ## to derive variables `ASTDT` and `AENDT` separately at the beginning.
Queries Dataset
queries
queries
An object of class tbl_df
(inherits from tbl
, data.frame
) with 15 rows and 8 columns.
An example of standard query dataset to be used in deriving variables in ADAE and ADCM
Other datasets:
admiral_adlb
,
admiral_adsl
,
ex_single
,
example_qs
,
queries_mh
Queries MH Dataset
queries_mh
queries_mh
An object of class tbl_df
(inherits from tbl
, data.frame
) with 14 rows and 8 columns.
An example of standard query MH dataset to be used in deriving variables in ADMH
Other datasets:
admiral_adlb
,
admiral_adsl
,
ex_single
,
example_qs
,
queries
query
objectA query
object defines a query, e.g., a Standard MedDRA Query (SMQ), a
Standardized Drug Grouping (SDG), or a customized query (CQ). It is used
as input to create_query_data()
.
query(prefix, name = auto, id = NULL, add_scope_num = FALSE, definition = NULL)
query(prefix, name = auto, id = NULL, add_scope_num = FALSE, definition = NULL)
prefix |
The value is used to populate |
name |
The value is used to populate Permitted Values: A character scalar or the |
id |
The value is used to populate Permitted Values: A integer scalar or the |
add_scope_num |
Determines if If the parameter is set to Default: Permitted Values: |
definition |
Definition of terms belonging to the query There are three different ways to define the terms:
Permitted Values: an |
An object of class query
.
create_query_data()
, basket_select()
, Queries Dataset Documentation
Source Objects:
basket_select()
,
censor_source()
,
death_event
,
event()
,
event_joined()
,
event_source()
,
flag_event()
,
records_source()
,
tte_source()
# create a query for an SMQ library(tibble) library(dplyr, warn.conflicts = FALSE) # create a query for a SMQ query( prefix = "SMQ02", id = auto, definition = basket_select( name = "Pregnancy and neonatal topics (SMQ)", scope = "NARROW", type = "smq" ) ) # create a query for an SDG query( prefix = "SDG01", id = auto, definition = basket_select( name = "5-aminosalicylates for ulcerative colitis", scope = NA_character_, type = "sdg" ) ) # creating a query for a customized query cqterms <- tribble( ~TERMCHAR, ~TERMNUM, "APPLICATION SITE ERYTHEMA", 10003041L, "APPLICATION SITE PRURITUS", 10003053L ) %>% mutate(SRCVAR = "AEDECOD") query( prefix = "CQ01", name = "Application Site Issues", definition = cqterms ) # creating a customized query based on SMQs and additional terms query( prefix = "CQ03", name = "Special issues of interest", definition = list( cqterms, basket_select( name = "Pregnancy and neonatal topics (SMQ)", scope = "NARROW", type = "smq" ), basket_select( id = 8050L, scope = "BROAD", type = "smq" ) ) )
# create a query for an SMQ library(tibble) library(dplyr, warn.conflicts = FALSE) # create a query for a SMQ query( prefix = "SMQ02", id = auto, definition = basket_select( name = "Pregnancy and neonatal topics (SMQ)", scope = "NARROW", type = "smq" ) ) # create a query for an SDG query( prefix = "SDG01", id = auto, definition = basket_select( name = "5-aminosalicylates for ulcerative colitis", scope = NA_character_, type = "sdg" ) ) # creating a query for a customized query cqterms <- tribble( ~TERMCHAR, ~TERMNUM, "APPLICATION SITE ERYTHEMA", 10003041L, "APPLICATION SITE PRURITUS", 10003053L ) %>% mutate(SRCVAR = "AEDECOD") query( prefix = "CQ01", name = "Application Site Issues", definition = cqterms ) # creating a customized query based on SMQs and additional terms query( prefix = "CQ03", name = "Special issues of interest", definition = list( cqterms, basket_select( name = "Pregnancy and neonatal topics (SMQ)", scope = "NARROW", type = "smq" ), basket_select( id = 8050L, scope = "BROAD", type = "smq" ) ) )
records_source
ObjectThe records_source
object is used to find extreme records of interest.
records_source(dataset_name, filter = NULL, new_vars)
records_source(dataset_name, filter = NULL, new_vars)
dataset_name |
The name of the source dataset The name refers to the dataset provided by the |
filter |
An unquoted condition for selecting the observations from
|
new_vars |
Variables to add The specified variables from the source datasets are added to the output
dataset. Variables can be renamed by naming the element, i.e., For example And Permitted Values: list of expressions created by |
An object of class records_source
Source Objects:
basket_select()
,
censor_source()
,
death_event
,
event()
,
event_joined()
,
event_source()
,
flag_event()
,
query()
,
tte_source()
Execute a derivation on a subset of the input dataset.
restrict_derivation(dataset, derivation, args = NULL, filter)
restrict_derivation(dataset, derivation, args = NULL, filter)
dataset |
Input dataset |
derivation |
Derivation A function that performs a specific derivation is expected. A derivation
adds variables or observations to a dataset. The first argument of a
derivation must expect a dataset and the derivation must return a dataset.
The function must provide the |
args |
Arguments of the derivation A |
filter |
Filter condition |
Higher Order Functions:
call_derivation()
,
derivation_slice()
,
slice_derivation()
library(tibble) adlb <- tribble( ~USUBJID, ~AVISITN, ~AVAL, ~ABLFL, "1", -1, 113, NA_character_, "1", 0, 113, "Y", "1", 3, 117, NA_character_, "2", 0, 95, "Y", "3", 0, 111, "Y", "3", 1, 101, NA_character_, "3", 2, 123, NA_character_ ) # Derive BASE for post-baseline records only (derive_var_base() can not be used in this case # as it requires the baseline observation to be in the input dataset) restrict_derivation( adlb, derivation = derive_vars_merged, args = params( by_vars = exprs(USUBJID), dataset_add = adlb, filter_add = ABLFL == "Y", new_vars = exprs(BASE = AVAL) ), filter = AVISITN > 0 ) # Derive BASE for baseline and post-baseline records only restrict_derivation( adlb, derivation = derive_var_base, args = params( by_vars = exprs(USUBJID) ), filter = AVISITN >= 0 ) %>% # Derive CHG for post-baseline records only restrict_derivation( derivation = derive_var_chg, filter = AVISITN > 0 )
library(tibble) adlb <- tribble( ~USUBJID, ~AVISITN, ~AVAL, ~ABLFL, "1", -1, 113, NA_character_, "1", 0, 113, "Y", "1", 3, 117, NA_character_, "2", 0, 95, "Y", "3", 0, 111, "Y", "3", 1, 101, NA_character_, "3", 2, 123, NA_character_ ) # Derive BASE for post-baseline records only (derive_var_base() can not be used in this case # as it requires the baseline observation to be in the input dataset) restrict_derivation( adlb, derivation = derive_vars_merged, args = params( by_vars = exprs(USUBJID), dataset_add = adlb, filter_add = ABLFL == "Y", new_vars = exprs(BASE = AVAL) ), filter = AVISITN > 0 ) # Derive BASE for baseline and post-baseline records only restrict_derivation( adlb, derivation = derive_var_base, args = params( by_vars = exprs(USUBJID) ), filter = AVISITN >= 0 ) %>% # Derive CHG for post-baseline records only restrict_derivation( derivation = derive_var_chg, filter = AVISITN > 0 )
Set the Values of Admiral Options That Can Be Modified for Advanced Users.
set_admiral_options(subject_keys, signif_digits)
set_admiral_options(subject_keys, signif_digits)
subject_keys |
Variables to uniquely identify a subject, defaults to
|
signif_digits |
Holds number of significant digits when comparing to numeric variables,
defaults to |
Modify an admiral option, e.g subject_keys
, such that it automatically affects downstream
function inputs where get_admiral_option()
is called such as derive_param_exist_flag()
.
No return value, called for side effects.
get_admiral_option()
, derive_param_exist_flag()
,derive_param_tte()
,
derive_var_dthcaus()
, derive_var_extreme_dtm()
, derive_vars_period()
,
create_period_dataset()
, derive_var_atoxgr_dir()
, derive_var_anrind()
Other admiral_options:
get_admiral_option()
library(lubridate) library(dplyr, warn.conflicts = FALSE) library(tibble) set_admiral_options(subject_keys = exprs(STUDYID, USUBJID2)) # Derive a new parameter for measurable disease at baseline adsl <- tribble( ~USUBJID2, "1", "2", "3" ) %>% mutate(STUDYID = "XX1234") tu <- tribble( ~USUBJID2, ~VISIT, ~TUSTRESC, "1", "SCREENING", "TARGET", "1", "WEEK 1", "TARGET", "1", "WEEK 5", "TARGET", "1", "WEEK 9", "NON-TARGET", "2", "SCREENING", "NON-TARGET", "2", "SCREENING", "NON-TARGET" ) %>% mutate( STUDYID = "XX1234", TUTESTCD = "TUMIDENT" ) derive_param_exist_flag( dataset_ref = adsl, dataset_add = tu, filter_add = TUTESTCD == "TUMIDENT" & VISIT == "SCREENING", condition = TUSTRESC == "TARGET", false_value = "N", missing_value = "N", set_values_to = exprs( PARAMCD = "MDIS", PARAM = "Measurable Disease at Baseline" ) ) set_admiral_options(signif_digits = 14) # Derive ANRIND for ADVS advs <- tribble( ~PARAMCD, ~AVAL, ~ANRLO, ~ANRHI, "DIABP", 59, 60, 80, "SYSBP", 120, 90, 130, "RESP", 21, 8, 20, ) derive_var_anrind(advs)
library(lubridate) library(dplyr, warn.conflicts = FALSE) library(tibble) set_admiral_options(subject_keys = exprs(STUDYID, USUBJID2)) # Derive a new parameter for measurable disease at baseline adsl <- tribble( ~USUBJID2, "1", "2", "3" ) %>% mutate(STUDYID = "XX1234") tu <- tribble( ~USUBJID2, ~VISIT, ~TUSTRESC, "1", "SCREENING", "TARGET", "1", "WEEK 1", "TARGET", "1", "WEEK 5", "TARGET", "1", "WEEK 9", "NON-TARGET", "2", "SCREENING", "NON-TARGET", "2", "SCREENING", "NON-TARGET" ) %>% mutate( STUDYID = "XX1234", TUTESTCD = "TUMIDENT" ) derive_param_exist_flag( dataset_ref = adsl, dataset_add = tu, filter_add = TUTESTCD == "TUMIDENT" & VISIT == "SCREENING", condition = TUSTRESC == "TARGET", false_value = "N", missing_value = "N", set_values_to = exprs( PARAMCD = "MDIS", PARAM = "Measurable Disease at Baseline" ) ) set_admiral_options(signif_digits = 14) # Derive ANRIND for ADVS advs <- tribble( ~PARAMCD, ~AVAL, ~ANRLO, ~ANRHI, "DIABP", 59, 60, 80, "SYSBP", 120, 90, 130, "RESP", 21, 8, 20, ) derive_var_anrind(advs)
The input dataset is split into slices (subsets) and for each slice the derivation is called separately. Some or all arguments of the derivation may vary depending on the slice.
slice_derivation(dataset, derivation, args = NULL, ...)
slice_derivation(dataset, derivation, args = NULL, ...)
dataset |
Input dataset |
derivation |
Derivation A function that performs a specific derivation is expected. A derivation
adds variables or observations to a dataset. The first argument of a
derivation must expect a dataset and the derivation must return a dataset.
The function must provide the Please note that it is not possible to specify |
args |
Arguments of the derivation A |
... |
A Each slice defines a subset of the input dataset and some of the parameters
for the derivation. The derivation is called on the subset with the
parameters specified by the |
For each slice the derivation is called on the subset defined by the
filter
field of the derivation_slice()
object and with the parameters
specified by the args
parameter and the args
field of the
derivation_slice()
object. If a parameter is specified for both, the
value in derivation_slice()
overwrites the one in args
.
Observations that match with more than one slice are only considered for the first matching slice.
Observations with no match to any of the slices are included in the output dataset but the derivation is not called for them.
The input dataset with the variables derived by the derivation added
params()
restrict_derivation()
Higher Order Functions:
call_derivation()
,
derivation_slice()
,
restrict_derivation()
library(tibble) library(stringr) advs <- tribble( ~USUBJID, ~VSDTC, ~VSTPT, "1", "2020-04-16", NA_character_, "1", "2020-04-16", "BEFORE TREATMENT" ) # For the second slice filter is set to TRUE. Thus derive_vars_dtm is called # with time_imputation = "last" for all observations which do not match for the # first slice. slice_derivation( advs, derivation = derive_vars_dtm, args = params( dtc = VSDTC, new_vars_prefix = "A" ), derivation_slice( filter = str_detect(VSTPT, "PRE|BEFORE"), args = params(time_imputation = "first") ), derivation_slice( filter = TRUE, args = params(time_imputation = "last") ) )
library(tibble) library(stringr) advs <- tribble( ~USUBJID, ~VSDTC, ~VSTPT, "1", "2020-04-16", NA_character_, "1", "2020-04-16", "BEFORE TREATMENT" ) # For the second slice filter is set to TRUE. Thus derive_vars_dtm is called # with time_imputation = "last" for all observations which do not match for the # first slice. slice_derivation( advs, derivation = derive_vars_dtm, args = params( dtc = VSDTC, new_vars_prefix = "A" ), derivation_slice( filter = str_detect(VSTPT, "PRE|BEFORE"), args = params(time_imputation = "first") ), derivation_slice( filter = TRUE, args = params(time_imputation = "last") ) )
tte_source
ObjectThe tte_source
object is used to define events and possible censorings.
tte_source(dataset_name, filter = NULL, date, censor = 0, set_values_to = NULL)
tte_source(dataset_name, filter = NULL, date, censor = 0, set_values_to = NULL)
dataset_name |
The name of the source dataset The name refers to the dataset provided by the |
filter |
An unquoted condition for selecting the observations from
|
date |
A variable or expression providing the date of the event or censoring. A date, or a datetime can be specified. An unquoted symbol or expression is expected. Refer to |
censor |
Censoring value CDISC strongly recommends using |
set_values_to |
A named list returned by |
An object of class tte_source
derive_param_tte()
, censor_source()
, event_source()
Source Objects:
basket_select()
,
censor_source()
,
death_event
,
event()
,
event_joined()
,
event_source()
,
flag_event()
,
query()
,
records_source()
Open an ADaM Template Script
use_ad_template( adam_name = "adsl", save_path = paste0("./", adam_name, ".R"), package = "admiral", overwrite = FALSE, open = interactive() )
use_ad_template( adam_name = "adsl", save_path = paste0("./", adam_name, ".R"), package = "admiral", overwrite = FALSE, open = interactive() )
adam_name |
An ADaM dataset name. You can use any of the available
dataset names
|
save_path |
Path to save the script. |
package |
The R package in which to look for templates. By default |
overwrite |
Whether to overwrite an existing file named |
open |
Whether to open the script right away. |
Running without any arguments such as use_ad_template()
auto-generates adsl.R
in
the current path. Use list_all_templates()
to discover which templates are available.
No return values, called for side effects
Utilities used for examples and template scripts:
list_all_templates()
if (interactive()) { use_ad_template("adsl") }
if (interactive()) { use_ad_template("adsl") }
"Y"
and "N"
to Numeric ValuesMap "Y"
and "N"
to numeric values.
yn_to_numeric(arg)
yn_to_numeric(arg)
arg |
Character vector |
1
if arg
equals "Y"
, 0
if arg
equals "N"
, NA_real_
otherwise
Utilities for Formatting Observations:
convert_blanks_to_na()
,
convert_na_to_blanks()
yn_to_numeric(c("Y", "N", NA_character_))
yn_to_numeric(c("Y", "N", NA_character_))