Package 'xportr'

Analysis Dataset Subject Level

Description

An example dataset containing subject level data

Usage

data("adsl_xportr")

Format

adsl_xportr

A data frame with 306 rows and 51 columns:

STUDYID

Study Identifier

USUBJID

Unique Subject Identifier

SUBJID

Subject Identifier for the Study

RFSTDTC

Subject Reference Start Date/Time

RFENDTC

Subject Reference End Date/Time

RFXSTDTC

Date/Time of First Study Treatment

RFXENDTC

Date/Time of Last Study Treatment

RFICDTC

Date/Time of Informed Consent

RFPENDTC

Date/Time of End of Participation

DTHDTC

Date/Time of Death

DTHFL

Subject Death Flag

SITEID

Study Site Identifier

AGE

Age

AGEU

Age Units

SEX

Sex

RACE

Race

ETHNIC

Ethnicity

ARMCD

Planned Arm Code

ARM

Description of Planned Arm

ACTARMCD

Actual Arm Code

ACTARM

Description of Actual Arm

COUNTRY

Country

DMDTC

Date/Time of Collection

DMDY

Study Day of Collection

TRT01P

Planned Treatment for Period 01

TRT01A

Actual Treatment for Period 01

TRTSDTM

Datetime of First Exposure to Treatment

TRTSTMF

Time of First Exposure Imputation Flag

TRTEDTM

Datetime of Last Exposure to Treatment

TRTETMF

Time of Last Exposure Imputation Flag

TRTSDT

Date of First Exposure to Treatment

TRTEDT

Date of Last Exposure to Treatment

TRTDURD

Total Treatment Duration (Days)

SCRFDT

Screen Failure Date

EOSDT

End of Study Date

EOSSTT

End of Study Status

FRVDT

Final Retrieval Visit Date

RANDDT

Date of Randomization

DTHDT

Date of Death

DTHDTF

Date of Death Imputation Flag

DTHADY

Relative Day of Death

LDDTHELD

Elapsed Days from Last Dose to Death

LSTALVDT

Date Last Known Alive

SAFFL

Safety Population Flag

RACEGR1

Pooled Race Group 1

AGEGR1

Pooled Age Group 1

REGION1

Geographic Region 1

LDDTHGR1

Last Dose to Death - Days Elapsed Group 1

DTH30FL

Death Within 30 Days of Last Trt Flag

DTHA30FL

Death After 30 Days from Last Trt Flag

DTHB30FL

Death Within 30 Days of First Trt Flag

Source

Dataset created by admiral::use_ad_template("adsl")

---

Example Dataset Specification

Description

Example Dataset Specification

Usage

data("dataset_spec")

Format

dataset_spec

A data frame with 1 row and 9 columns:

Dataset

chr: Dataset

Description

chr: Dataset description

Class

chr: Dataset class

Structure

lgl: Logical, indicating if there's a specific structure

Purpose

chr: Purpose of the dataset

Key, Variables

chr: Join Key variables in the dataset

Repeating

chr: Indicates if the dataset is repeating

Reference Data

lgl: Reference Data

Comment

chr: Additional comment

---

Example Dataset Variable Specification

Description

Example Dataset Variable Specification

Usage

data("var_spec")

Format

var_spec

A data frame with 216 rows and 19 columns:

Order

Order of variable

Dataset

Dataset

Variable

Variable

Label

Variable Label

Data Type

Data Type

Length

Variable Length

Significant Digits

Significant Digits

Format

Variable Format

Mandatory

Mandatory Variable Flag

Assigned Value

Variable Assigned Value

Codelist

Variable Codelist

Common

Common Variable Flag

Origin

Variable Origin

Pages

Pages

Method

Variable Method

Predecessor

Variable Predecessor

Role

Variable Role

Comment

Comment

Developer Notes

Developer Notes

---

Wrapper to apply all core xportr functions and write xpt

Description

Wrapper to apply all core xportr functions and write xpt

Usage

xportr(
  .df,
  var_metadata = NULL,
  df_metadata = NULL,
  domain = NULL,
  verbose = NULL,
  path,
  strict_checks = FALSE
)

Arguments

.df	A data frame of CDISC standard.
var_metadata	A data frame containing variable level metadata
df_metadata	A data frame containing dataset level metadata.
domain	Appropriate CDISC dataset name, e.g. ADAE, DM. Used to subset the metadata object.
verbose	The action this function takes when an action is taken on the dataset or function validation finds an issue. See 'Messaging' section for details. Options are 'stop', 'warn', 'message', and 'none'
path	Path where transport file will be written. File name sans will be used as xpt name.
strict_checks	If TRUE, xpt validation will report errors and not write out the dataset. If FALSE, xpt validation will report warnings and continue with writing out the dataset. Defaults to FALSE

Value

Returns the input dataframe invisibly

Examples

data("adsl_xportr", "dataset_spec", "var_spec")
adsl <- adsl_xportr

library(magrittr)
test_dir <- tempdir()

pipeline_path <- file.path(test_dir, "adslpipe.xpt")
xportr_path <- file.path(test_dir, "adslxptr.xpt")

dataset_spec_low <- setNames(dataset_spec, tolower(names(dataset_spec)))
names(dataset_spec_low)[[2]] <- "label"

var_spec_low <- setNames(var_spec, tolower(names(var_spec)))
names(var_spec_low)[[5]] <- "type"

adsl %>%
  xportr_metadata(var_spec_low, "ADSL", verbose = "none") %>%
  xportr_type() %>%
  xportr_length() %>%
  xportr_label() %>%
  xportr_order() %>%
  xportr_format() %>%
  xportr_df_label(dataset_spec_low) %>%
  xportr_write(pipeline_path)

# `xportr()` can be used to apply a whole pipeline at once
xportr(
  adsl,
  var_metadata = var_spec_low,
  df_metadata = dataset_spec_low,
  domain = "ADSL",
  verbose = "none",
  path = xportr_path
)

---

Assign Dataset Label

Description

Assigns dataset label from a dataset level metadata to a given data frame. This is stored in the 'label' attribute of the dataframe.

Usage

xportr_df_label(.df, metadata = NULL, domain = NULL, metacore = deprecated())

Arguments

.df	A data frame of CDISC standard.
metadata	A data frame containing dataset. See 'Metadata' section for details.
domain	Appropriate CDISC dataset name, e.g. ADAE, DM. Used to subset the metadata object.
metacore	Previously used to pass metadata now renamed with metadata

Value

Data frame with label attributes.

Metadata

The argument passed in the 'metadata' argument can either be a metacore object, or a data.frame containing the data listed below. If metacore is used, no changes to options are required.

For data.frame 'metadata' arguments two columns must be present:

1. Domain Name - passed as the 'xportr.df_domain_name' option. Default: "dataset". This is the column subset by the 'domain' argument in the function.

2. Label Name - passed as the 'xportr.df_label' option. Default: "label". Character values to update the 'label' attribute of the dataframe This is passed to haven::write_xpt to note the label.

Examples

adsl <- data.frame(
  USUBJID = c(1001, 1002, 1003),
  SITEID = c(001, 002, 003),
  AGE = c(63, 35, 27),
  SEX = c("M", "F", "M")
)

metadata <- data.frame(
  dataset = c("adsl", "adae"),
  label = c("Subject-Level Analysis", "Adverse Events Analysis")
)

adsl <- xportr_df_label(adsl, metadata, domain = "adsl")

---

Assign SAS Format

Description

Assigns a SAS format from a variable level metadata to a given data frame. If no format is found for a given variable, it is set as an empty character vector. This is stored in the 'format.sas' attribute.

Usage

xportr_format(
  .df,
  metadata = NULL,
  domain = NULL,
  verbose = NULL,
  metacore = deprecated()
)

Arguments

.df	A data frame of CDISC standard.
metadata	A data frame containing variable level metadata. See 'Metadata' section for details.
domain	Appropriate CDISC dataset name, e.g. ADAE, DM. Used to subset the metadata object.
verbose	The action this function takes when an action is taken on the dataset or function validation finds an issue. See 'Messaging' section for details. Options are 'stop', 'warn', 'message', and 'none'
metacore	Previously used to pass metadata now renamed with metadata

Value

Data frame with SASformat attributes for each variable.

Format Checks

This function carries out a series of basic checks to ensure the formats being applied make sense.

Note, the 'type' of message that is generated will depend on the value passed to the verbose argument: with 'stop' producing an error, 'warn' producing a warning, or 'message' producing a message. A value of 'none' will not output any messages.

1. If the variable has a suffix of DT, DTM, TM (indicating a numeric date/time variable) then a message will be shown if there is no format associated with it.

2. If a variable is character then a message will be shown if there is no $ prefix in the associated format.

3. If a variable is character then a message will be shown if the associated format has greater than 31 characters (excluding the $).

4. If a variable is numeric then a message will be shown if there is a $ prefix in the associated format.

5. If a variable is numeric then a message will be shown if the associated format has greater than 32 characters.

6. All formats will be checked against a list of formats considered 'standard' as part of an ADaM dataset. Note, however, this list is not exhaustive (it would not be feasible to check all the functions within the scope of this package). If the format is not found in the 'standard' list, then a message is created advising the user to check.

Format Name	w Values	d Values
w.d	1 - 32	., 0 - 31
$w.	1 - 200
DATEw.	., 5 - 11
DATETIMEw.	7 - 40
DDMMYYw.	., 2 - 10
HHMM.
MMDDYYw.	., 2 - 10
TIMEw.	., 2 - 20
WEEKDATEw.	., 3 - 37
YYMMDDw.	., 2 - 10
B8601DAw.	., 8 - 10
B8601DTw.d	., 15 - 26	., 0 - 6
B8601TM.
IS8601DA.
IS8601TM.
E8601DAw.	., 10
E8601DNw.	., 10
E8601DTw.d	., 16 - 26	., 0 - 6
E8601DXw.	., 20 - 35
E8601LXw.	., 20 - 35
E8601LZw.	., 9 - 20
E8601TMw.d	., 8 - 15	., 0 - 6
E8601TXw.	., 9 - 20
E8601TZw.d	., 9 - 20	., 0 - 6

Metadata

The argument passed in the 'metadata' argument can either be a metacore object, or a data.frame containing the data listed below. If metacore is used, no changes to options are required.

For data.frame 'metadata' arguments three columns must be present:

1. Domain Name - passed as the 'xportr.domain_name' option. Default: "dataset". This is the column subset by the 'domain' argument in the function.

2. Format Name - passed as the 'xportr.format_name' option. Default: "format". Character values to update the 'format.sas' attribute of the column. This is passed to haven::write to note the format.

3. Variable Name - passed as the 'xportr.variable_name' option. Default: "variable". This is used to match columns in '.df' argument and the metadata.

Examples

adsl <- data.frame(
  USUBJID = c(1001, 1002, 1003),
  BRTHDT = c(1, 1, 2)
)

metadata <- data.frame(
  dataset = c("adsl", "adsl"),
  variable = c("USUBJID", "BRTHDT"),
  format = c(NA, "DATE9.")
)

adsl <- xportr_format(adsl, metadata, domain = "adsl")

---

Assign Variable Label

Description

Assigns variable label from a variable level metadata to a given data frame. This function will give detect if a label is greater than 40 characters which isn't allowed in XPT v5. If labels aren't present for the variable it will be assigned an empty character value. Labels are stored in the 'label' attribute of the column.

Usage

xportr_label(
  .df,
  metadata = NULL,
  domain = NULL,
  verbose = NULL,
  metacore = deprecated()
)

Arguments

.df	A data frame of CDISC standard.
metadata	A data frame containing variable level metadata. See 'Metadata' section for details.
domain	Appropriate CDISC dataset name, e.g. ADAE, DM. Used to subset the metadata object.
verbose	The action this function takes when an action is taken on the dataset or function validation finds an issue. See 'Messaging' section for details. Options are 'stop', 'warn', 'message', and 'none'
metacore	Previously used to pass metadata now renamed with metadata

Value

Data frame with label attributes for each variable.

Messaging

label_log() is the primary messaging tool for xportr_label(). If there are any columns present in the '.df' that are not noted in the metadata, they cannot be assigned a label and a message will be generated noting the number or variables that have not been assigned a label.

If variables were not found in the metadata and the value passed to the 'verbose' argument is 'stop', 'warn', or 'message', a message will be generated detailing the variables that were missing in metadata.

Metadata

The argument passed in the 'metadata' argument can either be a metacore object, or a data.frame containing the data listed below. If metacore is used, no changes to options are required.

For data.frame 'metadata' arguments three columns must be present:

1. Domain Name - passed as the 'xportr.domain_name' option. Default: "dataset". This is the column subset by the 'domain' argument in the function.

2. Variable Name - passed as the 'xportr.variable_name' option. Default: "variable". This is used to match columns in '.df' argument and the metadata.

3. Variable Label - passed as the 'xportr.label' option. Default: "label". These character values to update the 'label' attribute of the column. This is passed to haven::write to note the label.

Examples

adsl <- data.frame(
  USUBJID = c(1001, 1002, 1003),
  SITEID = c(001, 002, 003),
  AGE = c(63, 35, 27),
  SEX = c("M", "F", "M")
)

metadata <- data.frame(
  dataset = "adsl",
  variable = c("USUBJID", "SITEID", "AGE", "SEX"),
  label = c("Unique Subject Identifier", "Study Site Identifier", "Age", "Sex")
)

adsl <- xportr_label(adsl, metadata, domain = "adsl")

---

Assign SAS Length

Description

Assigns the SAS length to a specified data frame, either from a metadata object or based on the calculated maximum data length. If a length isn't present for a variable the length value is set to maximum data length for character columns, and 8 for non-character columns. This value is stored in the 'width' attribute of the column.

Usage

xportr_length(
  .df,
  metadata = NULL,
  domain = NULL,
  verbose = NULL,
  length_source = c("metadata", "data"),
  metacore = deprecated()
)

Arguments

.df	A data frame of CDISC standard.
metadata	A data frame containing variable level metadata. See 'Metadata' section for details.
domain	Appropriate CDISC dataset name, e.g. ADAE, DM. Used to subset the metadata object.
verbose	The action this function takes when an action is taken on the dataset or function validation finds an issue. See 'Messaging' section for details. Options are 'stop', 'warn', 'message', and 'none'
length_source	Choose the assigned length from either metadata or data. If "metadata" is specified, the assigned length is from the metadata length. If "data" is specified, the assigned length is determined by the calculated maximum data length. Permitted Values: "metadata", "data"
metacore	Previously used to pass metadata now renamed with metadata

Value

Data frame with SAS default length attributes for each variable.

Messaging

length_log is the primary messaging tool for xportr_length. If there are any columns present in the '.df' that are not noted in the metadata, they cannot be assigned a length and a message will be generated noting the number or variables that have not been assigned a length.

If variables were not found in the metadata and the value passed to the 'verbose' argument is 'stop', 'warn', or 'message', a message will be generated detailing the variables that were missing in the metadata.

Metadata

The argument passed in the 'metadata' argument can either be a {metacore} object, or a data.frame containing the data listed below. If metacore is used, no changes to options are required.

For data.frame 'metadata' arguments three columns must be present:

1. Domain Name - passed as the 'xportr.domain_name' option. Default: "dataset". This is the column subset by the 'domain' argument in the function.

2. Variable Name - passed as the 'xportr.variable_name' option. Default: "variable". This is used to match columns in '.df' argument and the metadata.

3. Variable Label - passed as the 'xportr.length' option. Default: "length". These numeric values to update the 'width' attribute of the column. This is passed to haven::write to note the variable length.

Examples

adsl <- data.frame(
  USUBJID = c(1001, 1002, 1003),
  BRTHDT = c(1, 1, 2)
)

metadata <- data.frame(
  dataset = c("adsl", "adsl"),
  variable = c("USUBJID", "BRTHDT"),
  length = c(10, 8)
)

adsl <- xportr_length(adsl, metadata, domain = "adsl", length_source = "metadata")

---

Set variable specifications and domain

Description

Sets metadata and/or domain for a dataset in a way that can be accessed by other xportr functions. If used at the start of an xportr pipeline, it removes the need to set metadata and domain at each step individually. For details on the format of the metadata, see the 'Metadata' section for each function in question.

Usage

xportr_metadata(.df, metadata = NULL, domain = NULL, verbose = NULL)

Arguments

.df	A data frame of CDISC standard.
metadata	A data frame containing variable level metadata. See 'Metadata' section for details.
domain	Appropriate CDISC dataset name, e.g. ADAE, DM. Used to subset the metadata object.
verbose	The action this function takes when an action is taken on the dataset or function validation finds an issue. See 'Messaging' section for details. Options are 'stop', 'warn', 'message', and 'none'

Value

.df dataset with metadata and domain attributes set

Examples

metadata <- data.frame(
  dataset = "test",
  variable = c("Subj", "Param", "Val", "NotUsed"),
  type = c("numeric", "character", "numeric", "character"),
  format = NA,
  order = c(1, 3, 4, 2)
)

adlb <- data.frame(
  Subj = as.character(123, 456, 789),
  Different = c("a", "b", "c"),
  Val = c("1", "2", "3"),
  Param = c("param1", "param2", "param3")
)

xportr_metadata(adlb, metadata, "test")

library(magrittr)

adlb %>%
  xportr_metadata(metadata, "test") %>%
  xportr_type() %>%
  xportr_order()

---

Get or set xportr options

Description

There are two mechanisms for working with options for xportr. One is the options() function, which is part of base R, and the other is the xportr_options() function, which is in the xportr package. The reason for these two mechanisms is has to do with legacy code and scoping.

The options() function sets options globally, for the duration of the R process. The getOption() function retrieves the value of an option. All xportr related options of this type are prefixed with "xportr.".

Usage

xportr_options(...)

Arguments

...	Options to set, with the form name = value or a character vector of option names.

Options with options()

xportr.df_domain_name

defaults to "dataset"
The name of the domain "name" column in dataset metadata.

xportr.df_label

defaults to "label"
The column noting the dataset label in dataset metadata.

xportr.domain_name

defaults to "dataset"
The name of the domain "name" column in variable metadata.

xportr.variable_name

defaults to "variable"
The name of the variable "name" in variable metadata.

xportr.type_name

defaults to "type"
The name of the variable type column in variable metadata.

xportr.label

defaults to "label"
The name of the variable label column in variable metadata.

xportr.length

defaults to "length"
The name of the variable length column in variable metadata.

xportr.order_name

defaults to "order"
The name of the variable order column in variable metadata.

xportr.format_name

defaults to "format"
The name of the variable format column in variable metadata.

xportr.format_verbose

defaults to "none"
The default argument for the 'verbose' argument for xportr_format.

xportr.label_verbose

defaults to "none"
The default argument for the 'verbose' argument for xportr_label.

xportr.length_verbose

defaults to "none"
The default argument for the 'verbose' argument for xportr_length.

xportr.type_verbose

defaults to "label"
The default argument for the 'verbose' argument for xportr_type.

xportr.character_types

defaults to "character"
The default character vector used to explicitly coerce R classes to character XPT types.

xportr.character_metadata_types

defaults to c("character", "char", "text", "date", "posixct", "posixt", "datetime", "time", "partialdate", "partialtime", "partialdatetime", "incompletedatetime", "durationdatetime", "intervaldatetime")
The default character vector used to explicitly coerce R classes to character XPT types.

xportr.numeric_metadata_types

defaults to c("integer", "numeric", "num", "float")
The default character vector used to explicitly coerce R classes to numeric XPT types.

xportr.numeric_types

defaults to c("integer", "float", "numeric", "posixct", "posixt", "time", "date", "hms")
The default character vector used to explicitly coerce R classes to numeric XPT types.

Options with xportr_options()

Alternative to the options(), the xportr_options() function can be used to set the options. The xportr_options() function also returns the current options when a character vector of the options keys are passed into it. If nothing is passed into it, it returns the state of all xportr options.

Examples

xportr_options("xportr.df_label")
xportr_options(xportr.df_label = "data_label", xportr.label = "custom_label")
xportr_options(c("xportr.label", "xportr.df_label"))
xportr_options()

---

Order variables of a dataset according to Spec

Description

The dplyr::arrange() function is used to order the columns of the dataframe. Any variables that are missing an order value are appended to the end of the dataframe after all of the variables that have an order.

Usage

xportr_order(
  .df,
  metadata = NULL,
  domain = NULL,
  verbose = NULL,
  metacore = deprecated()
)

Arguments

.df	A data frame of CDISC standard.
metadata	A data frame containing variable level metadata. See 'Metadata' section for details.
domain	Appropriate CDISC dataset name, e.g. ADAE, DM. Used to subset the metadata object.
verbose	The action this function takes when an action is taken on the dataset or function validation finds an issue. See 'Messaging' section for details. Options are 'stop', 'warn', 'message', and 'none'
metacore	Previously used to pass metadata now renamed with metadata

Value

Dataframe that has been re-ordered according to spec

Messaging

var_ord_msg() is the primary messaging tool for xportr_order(). There are two primary messages that are output from var_ord_msg(). The first is the "moved" variables. These are the variables that were not found in the metadata file and moved to the end of the dataset. A message will be generated noting the number, if any, of variables that were moved to the end of the dataset. If any variables were moved, and the 'verbose' argument is 'stop', 'warn', or 'message', a message will be generated detailing the variables that were moved.

The second primary message is the number of variables that were in the dataset, but not in the correct order. A message will be generated noting the number, if any, of variables that have been reordered. If any variables were reordered, and the 'verbose' argument is 'stop', 'warn', or 'message', a message will be generated detailing the variables that were reordered.

Metadata

The argument passed in the 'metadata' argument can either be a metacore object, or a data.frame containing the data listed below. If metacore is used, no changes to options are required.

For data.frame 'metadata' arguments three columns must be present:

1. Domain Name - passed as the 'xportr.domain_name' option. Default: "dataset". This is the column subset by the 'domain' argument in the function.

2. Variable Name - passed as the 'xportr.variable_name' option. Default: "variable". This is used to match columns in '.df' argument and the metadata.

3. Variable Order - passed as the 'xportr.order_name' option. Default: "order". These values used to arrange the order of the variables. If the values of order metadata are not numeric, they will be coerced to prevent alphabetical sorting of numeric values.

Examples

adsl <- data.frame(
  BRTHDT = c(1, 1, 2),
  STUDYID = c("mid987650", "mid987650", "mid987650"),
  TRT01A = c("Active", "Active", "Placebo"),
  USUBJID = c(1001, 1002, 1003)
)

metadata <- data.frame(
  dataset = c("adsl", "adsl", "adsl", "adsl"),
  variable = c("STUDYID", "USUBJID", "TRT01A", "BRTHDT"),
  order = 1:4
)

adsl <- xportr_order(adsl, metadata, domain = "adsl")

---

Deprecated - Split xpt file output

Description

This function is deprecated. Please use the argument max_gb_size in the function xportr_write()' instead.

Per the FDA Study Data Technical Conformance Guide(https://www.fda.gov/media/88173/download) section 3.3.2, dataset files sizes shouldn't exceed 5 GB. If datasets are large enough, they should be split based on a variable. For example, laboratory readings in ADLB can be split by LBCAT to split up hematology and chemistry data.

This function will tell xportr_write() to split the data frame based on the variable passed in split_by. When written, the file name will be prepended with a number for uniqueness. These files should be noted in the Reviewer Guides per CDISC guidance to note how you split your files.

Usage

xportr_split(.df, split_by = NULL)

Arguments

.df	A data frame of CDISC standard.
split_by	A quoted variable that will be passed to base::split().

Value

A data frame with an additional attribute added so xportr_write() knows how to split the data frame.

Examples

adlb <- data.frame(
  USUBJID = c(1001, 1002, 1003),
  LBCAT = c("HEMATOLOGY", "HEMATOLOGY", "CHEMISTRY")
)

adlb <- xportr_split(adlb, "LBCAT")

---

Coerce variable type

Description

XPT v5 datasets only have data types of character and numeric. xportr_type() attempts to collapse R classes to those two XPT types. The 'xportr.character_types' option is used to explicitly collapse the class of a column to character using as.character(). Similarly, 'xportr.numeric_types' will collapse a column to a numeric type. (See xportr_options() for default values of these options.) If no type is passed for a variable, it is assumed to be numeric and coerced with as.numeric().

Usage

xportr_type(
  .df,
  metadata = NULL,
  domain = NULL,
  verbose = NULL,
  metacore = deprecated()
)

Arguments

.df	A data frame of CDISC standard.
metadata	A data frame containing variable level metadata. See 'Metadata' section for details.
domain	Appropriate CDISC dataset name, e.g. ADAE, DM. Used to subset the metadata object.
verbose	The action this function takes when an action is taken on the dataset or function validation finds an issue. See 'Messaging' section for details. Options are 'stop', 'warn', 'message', and 'none'
metacore	Previously used to pass metadata now renamed with metadata

Details

Certain care should be taken when using timing variables. R serializes dates based on a reference date of 01/01/1970 where XPT uses 01/01/1960. This can result in dates being 10 years off when outputting from R to XPT if you're using a date class. For this reason, xportr will try to determine what should happen with variables that appear to be used to denote time.

Value

Returns the modified table.

Messaging

type_log() is the primary messaging tool for xportr_type(). The number of column types that mismatch the reported type in the metadata, if any, is reported by xportr_type(). If there are any type mismatches, and the 'verbose' argument is 'stop', 'warn', or 'message', each mismatch will be detailed with the actual type in the data and the type noted in the metadata.

Metadata

The argument passed in the 'metadata' argument can either be a metacore object, or a data.frame containing the data listed below. If metacore is used, no changes to options are required.

For data.frame 'metadata' arguments four columns must be present:

1. Domain Name - passed as the 'xportr.domain_name' option. Default: "dataset". This is the column subset by the 'domain' argument in the function.

2. Variable Name - passed as the 'xportr.variable_name' option. Default: "variable". This is used to match columns in '.df' argument and the metadata.

3. Variable Type - passed as the 'xportr.type_name'. Default: "type". This is used to note the XPT variable "type" options are numeric or character.

4. (Option only) Character Types - The list of classes that should be explicitly coerced to a XPT Character type. Default: c( "character", "char", "text", "date", "posixct", "posixt", "datetime", "time", "partialdate", "partialtime", "partialdatetime", "incompletedatetime", "durationdatetime", "intervaldatetime")'

5. (Option only) Numeric Types - The list of classes that should be explicitly coerced to a XPT numeric type. Default: c("integer", "numeric", "num", "float")

Examples

metadata <- data.frame(
  dataset = "test",
  variable = c("Subj", "Param", "Val", "NotUsed"),
  type = c("numeric", "character", "numeric", "character")
)

.df <- data.frame(
  Subj = as.character(123, 456, 789),
  Different = c("a", "b", "c"),
  Val = c("1", "2", "3"),
  Param = c("param1", "param2", "param3")
)

df2 <- xportr_type(.df, metadata, "test")

---

Write xpt v5 transport file

Description

Writes a local data frame into SAS transport file of version 5. The SAS transport format is an open format, as is required for submission of the data to the FDA.

Usage

xportr_write(
  .df,
  path,
  max_size_gb = NULL,
  metadata = NULL,
  domain = NULL,
  strict_checks = FALSE,
  label = deprecated()
)

Arguments

.df	A data frame to write.
path	Path where transport file will be written. File name sans will be used as xpt name.
max_size_gb	Maximum size in GB of the exported file(s). If size of xpt file exceeds the specified maximum, it will split the data frame into multiple exported chunk(s).
metadata	A data frame containing dataset. See 'Metadata' section for details.
domain	Appropriate CDISC dataset name, e.g. ADAE, DM. Used to subset the metadata object.
strict_checks	If TRUE, xpt validation will report errors and not write out the dataset. If FALSE, xpt validation will report warnings and continue with writing out the dataset. Defaults to FALSE
label	Previously used to to set the Dataset label. Use the metadata argument to set the dataset label.

Details

• Variable and dataset labels are stored in the "label" attribute.

• SAS format are stored in the "SASformat" attribute.

• SAS type are based on the metadata attribute.

Value

A data frame. xportr_write() returns the input data invisibly.

Metadata

The argument passed in the 'metadata' argument can either be a metacore object, or a data.frame containing the data listed below. If metacore is used, no changes to options are required.

For data.frame 'metadata' arguments two columns must be present:

1. Domain Name - passed as the 'xportr.df_domain_name' option. Default: "dataset". This is the column subset by the 'domain' argument in the function.

2. Label Name - passed as the 'xportr.df_label' option. Default: "label". Character values to update the 'label' attribute of the dataframe This is passed to haven::write_xpt to note the label.

Examples

adsl <- data.frame(
  SUBL = as.character(123, 456, 789),
  DIFF = c("a", "b", "c"),
  VAL = c("1", "2", "3"),
  PARAM = c("param1", "param2", "param3")
)

var_spec <- data.frame(
  dataset = "adsl",
  label = "Subject-Level Analysis Dataset",
  data_label = "ADSL"
)
xportr_write(adsl,
  path = paste0(tempdir(), "/adsl.xpt"),
  domain = "adsl",
  metadata = var_spec,
  strict_checks = FALSE
)

---

Validate Dataset Can be Written to xpt

Description

Function used to validate dataframes before they are sent to haven::write_xpt for writing.

Usage

xpt_validate(data)

Arguments

data	Dataset to be exported as xpt file

Value

Returns a character vector of failed conditions

---