This article describes creating an ADRS
ADaM with
oncology endpoint parameters based on iRECIST. It shows a similar way of
deriving the endpoints presented in Creating ADRS
(Including Non-standard Endpoints). Most of the endpoints are
derived by calling admiral::derive_extreme_event()
.
This vignette follows the iRECIST guidelines, for more information user may visit https://recist.eortc.org/irecist/
Examples are currently presented and tested using ADSL
(ADaM) and RS
(SDTM) inputs. However, other domains could
be used. The RS
test data contains iRECIST response for
target, non-target and overall response. Further pre-processing and
considerations may be needed if iRECIST are only collected after RECIST
1.1 progression and input data contains multiple response criteria. The
functions and workflow could similarly be used to create an intermediary
ADEVENT
ADaM.
Note: All examples assume CDISC SDTM and/or ADaM format as input unless otherwise specified.
To start, all data frames needed for the creation of
ADRS
should be read into the environment. This will be a
company specific process. Some of the data frames needed may be
ADSL
, RS
and TU
. For this
vignette we assume that RS
provides the response values
"iCR"
, "iPR"
, "iSD"
,
"NON-iCR/NON-iUPD"
, "iUPD"
,
"iCPD"
, and "NE"
. All examples can be easily
modified to consider other response values (see Handling Different Input Response
Values).
For example purpose, the SDTM and ADaM datasets (based on CDISC Pilot
test data)—which are included in {pharmaversesdtm}
and
{pharmaverseadam}
—are used.
library(admiral)
library(admiralonco)
library(dplyr)
library(pharmaverseadam)
library(pharmaversesdtm)
library(lubridate)
library(stringr)
data("adsl")
# iRECIST oncology sdtm data
data("rs_onco_irecist")
rs <- rs_onco_irecist
rs <- convert_blanks_to_na(rs)
At this step, it may be useful to join ADSL
to your
RS
domain. Only the ADSL
variables used for
derivations are selected at this step. The rest of the relevant
ADSL
would be added later.
adsl_vars <- exprs(RANDDT)
adrs <- derive_vars_merged(
rs,
dataset_add = adsl,
new_vars = adsl_vars,
by_vars = get_admiral_option("subject_keys")
)
USUBJID | RSTESTCD | RSDTC | VISIT | RANDDT |
---|---|---|---|---|
01-701-1015 | OVRLRESP | 2014-02-12 | WEEK 6 | 2014-01-02 |
01-701-1028 | OVRLRESP | 2013-08 | WEEK 6 | 2013-07-19 |
01-701-1028 | OVRLRESP | 2013-10-09 | WEEK 12 | 2013-07-19 |
01-701-1028 | OVRLRESP | 2013-11-20 | WEEK 18 | 2013-07-19 |
01-701-1034 | OVRLRESP | 2014-08-11 | WEEK 6 | 2014-07-01 |
01-701-1034 | OVRLRESP | 2014-09-25 | WEEK 12 | 2014-07-01 |
01-701-1034 | OVRLRESP | 2014-11-04 | WEEK 18 | 2014-07-01 |
01-701-1097 | OVRLRESP | 2014-02-11 | WEEK 6 | 2014-01-01 |
01-701-1115 | OVRLRESP | 2013-01-10 | WEEK 6 | 2012-11-30 |
01-701-1118 | OVRLRESP | 2014-04-23 | WEEK 6 | 2014-03-12 |
The first step involves company-specific pre-processing of records
for the required input to the downstream parameter functions. Note that
this could be needed multiple times (e.g. once for investigator and once
for Independent Review Facility (IRF)/Blinded Independent Central Review
(BICR) records). It could even involve merging input data from other
sources besides RS
, such as ADTR
.
This step would include any required selection/derivation of
ADT
or applying any necessary partial date imputations,
updating AVAL
(e.g. this should be ordered from best to
worst response), and setting analysis flag ANL01FL
. Common
options for ANL01FL
would be to set null for invalid
assessments or those occurring after new anti-cancer therapy, or to only
flag assessments on or after date of first treatment/randomization, or
rules to cover the case when a patient has multiple observations per
visit (e.g. by selecting the worst value). Another consideration could
be extra potential protocol-specific sources of Progressive Disease such
as radiological assessments, which could be pre-processed here to create
a PD record to feed downstream derivations.
For the derivation of the parameters it is expected that the subject
identifier variables (usually STUDYID
and
USUBJID
) and ADT
are a unique key. This can be
achieved by deriving an analysis flag (ANLzzFL
). See Derive ANL01FL
for an example.
The below shows an example of a possible company-specific implementation of this step.
In this case we use the overall response records from RS
from the investigator as our starting point. The parameter details such
as PARAMCD
, PARAM
etc will always be
company-specific, but an example is shown below so that you can trace
through how these records feed into the other parameter derivations.
adrs <- adrs %>%
filter(RSEVAL == "INVESTIGATOR" & RSTESTCD == "OVRLRESP") %>%
mutate(
PARAMCD = "OVR",
PARAM = "Overall Response by Investigator",
PARCAT1 = "Tumor Response",
PARCAT2 = "Investigator",
PARCAT3 = "iRECIST"
)
USUBJID | VISIT | RSTESTCD | RSEVAL | PARAMCD | PARAM | PARCAT1 | PARCAT2 | PARCAT3 |
---|---|---|---|---|---|---|---|---|
01-701-1015 | WEEK 6 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Tumor Response | Investigator | iRECIST |
01-701-1028 | WEEK 6 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Tumor Response | Investigator | iRECIST |
01-701-1028 | WEEK 12 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Tumor Response | Investigator | iRECIST |
01-701-1028 | WEEK 18 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Tumor Response | Investigator | iRECIST |
01-701-1034 | WEEK 6 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Tumor Response | Investigator | iRECIST |
01-701-1034 | WEEK 12 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Tumor Response | Investigator | iRECIST |
01-701-1034 | WEEK 18 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Tumor Response | Investigator | iRECIST |
01-701-1097 | WEEK 6 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Tumor Response | Investigator | iRECIST |
01-701-1115 | WEEK 6 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Tumor Response | Investigator | iRECIST |
01-701-1118 | WEEK 6 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Tumor Response | Investigator | iRECIST |
ADT
,
ADTF
, AVISIT
etcIf your data collection allows for partial dates, you could apply a
company-specific imputation rule at this stage when deriving
ADT
. For this example, here we impute missing day to last
possible date.
adrs <- adrs %>%
derive_vars_dt(
dtc = RSDTC,
new_vars_prefix = "A",
highest_imputation = "D",
date_imputation = "last"
) %>%
mutate(AVISIT = VISIT)
USUBJID | AVISIT | PARAMCD | PARAM | RSSTRESC | RSDTC | ADT | ADTF |
---|---|---|---|---|---|---|---|
01-701-1015 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | 2014-02-12 | 2014-02-12 | NA |
01-701-1028 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | 2013-08 | 2013-08-31 | D |
01-701-1028 | WEEK 12 | OVR | Overall Response by Investigator | iCPD | 2013-10-09 | 2013-10-09 | NA |
01-701-1028 | WEEK 18 | OVR | Overall Response by Investigator | iSD | 2013-11-20 | 2013-11-20 | NA |
01-701-1034 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | 2014-08-11 | 2014-08-11 | NA |
01-701-1034 | WEEK 12 | OVR | Overall Response by Investigator | iSD | 2014-09-25 | 2014-09-25 | NA |
01-701-1034 | WEEK 18 | OVR | Overall Response by Investigator | NON-iCR/NON-iUPD | 2014-11-04 | 2014-11-04 | NA |
01-701-1097 | WEEK 6 | OVR | Overall Response by Investigator | NE | 2014-02-11 | 2014-02-11 | NA |
01-701-1115 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | 2013-01-10 | 2013-01-10 | NA |
01-701-1118 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | 2014-04-23 | 2014-04-23 | NA |
AVALC
and AVAL
Here we populate AVALC
and create the numeric version as
AVAL
(ordered from worst to best response, followed by
NE
and MISSING). The AVAL
values are not
considered in the parameter derivations below, and so changing
AVAL
here would not change the result of those derivations.
However, please note that the ordering of AVAL
will be used
to determine ANL01FL
in the subsequent step, ensure that
the appropriate mode
is being set in the
admiral::derive_var_extreme_flag()
.
iRECIST ordering will be used or if you’d like to provide your own company-specific ordering here you could do this as follows:
aval_resp_new <- function(arg) {
case_when(
arg == "NE" ~ 8,
arg == "MISSING" ~ 7,
arg == "iCR" ~ 6,
arg == "iPR" ~ 5,
arg == "iSD" ~ 4,
arg == "NON-iCR/NON-iUPD" ~ 3,
arg == "iUPD" ~ 2,
arg == "iCPD" ~ 1,
TRUE ~ NA_real_
)
}
adrs <- adrs %>%
mutate(
AVALC = RSSTRESC,
AVAL = aval_resp_new(AVALC)
)
USUBJID | AVISIT | PARAMCD | PARAM | RSSTRESC | AVALC | AVAL |
---|---|---|---|---|---|---|
01-701-1015 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | iUPD | 2 |
01-701-1028 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | iUPD | 2 |
01-701-1028 | WEEK 12 | OVR | Overall Response by Investigator | iCPD | iCPD | 1 |
01-701-1028 | WEEK 18 | OVR | Overall Response by Investigator | iSD | iSD | 4 |
01-701-1034 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | iUPD | 2 |
01-701-1034 | WEEK 12 | OVR | Overall Response by Investigator | iSD | iSD | 4 |
01-701-1034 | WEEK 18 | OVR | Overall Response by Investigator | NON-iCR/NON-iUPD | NON-iCR/NON-iUPD | 3 |
01-701-1097 | WEEK 6 | OVR | Overall Response by Investigator | NE | NE | 8 |
01-701-1115 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | iUPD | 2 |
01-701-1118 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | iUPD | 2 |
ANL01FL
)When deriving ANL01FL
this is an opportunity to exclude
any records that should not contribute to any downstream parameter
derivations. In the below example this includes only selecting valid
assessments and those occurring on or after randomization date. If there
is more than one assessment at a date, the worst one is flagged.
adrs <- adrs %>%
restrict_derivation(
derivation = derive_var_extreme_flag,
args = params(
by_vars = c(get_admiral_option("subject_keys"), exprs(ADT)),
order = exprs(AVAL, RSSEQ),
new_var = ANL01FL,
mode = "first"
),
filter = !is.na(AVAL) & AVALC != "MISSING" & ADT >= RANDDT
)
USUBJID | AVISIT | PARAMCD | PARAM | AVALC | ADT | RANDDT | ANL01FL |
---|---|---|---|---|---|---|---|
01-701-1015 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | 2014-02-12 | 2014-01-02 | Y |
01-701-1028 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | 2013-08-31 | 2013-07-19 | Y |
01-701-1028 | WEEK 12 | OVR | Overall Response by Investigator | iCPD | 2013-10-09 | 2013-07-19 | Y |
01-701-1028 | WEEK 18 | OVR | Overall Response by Investigator | iSD | 2013-11-20 | 2013-07-19 | Y |
01-701-1034 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | 2014-08-11 | 2014-07-01 | Y |
01-701-1034 | WEEK 12 | OVR | Overall Response by Investigator | iSD | 2014-09-25 | 2014-07-01 | Y |
01-701-1034 | WEEK 18 | OVR | Overall Response by Investigator | NON-iCR/NON-iUPD | 2014-11-04 | 2014-07-01 | Y |
01-701-1097 | WEEK 6 | OVR | Overall Response by Investigator | NE | 2014-02-11 | 2014-01-01 | Y |
01-701-1115 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | 2013-01-10 | 2012-11-30 | Y |
01-701-1118 | WEEK 6 | OVR | Overall Response by Investigator | iUPD | 2014-04-23 | 2014-03-12 | Y |
Here is an alternative example where those records occurring after
new anti-cancer therapy are additionally excluded (where
NACTDT
would be pre-derived as first date of new
anti-cancer therapy. See {admiralonco}
Creating and Using New Anti-Cancer Start Date for
deriving this variable).
ANL02FL
)To restrict response data up to and including first reported
progressive disease ANL02FL
flag could be created by using
{admiral}
function
admiral::derive_var_relative_flag()
.
adrs <- adrs %>%
derive_var_relative_flag(
by_vars = get_admiral_option("subject_keys"),
order = exprs(ADT, RSSEQ),
new_var = ANL02FL,
condition = AVALC == "iCPD",
mode = "first",
selection = "before",
inclusive = TRUE
)
USUBJID | AVISIT | PARAMCD | AVALC | ADT | ANL01FL | ANL02FL |
---|---|---|---|---|---|---|
01-701-1015 | WEEK 6 | OVR | iUPD | 2014-02-12 | Y | Y |
01-701-1028 | WEEK 6 | OVR | iUPD | 2013-08-31 | Y | Y |
01-701-1028 | WEEK 12 | OVR | iCPD | 2013-10-09 | Y | Y |
01-701-1028 | WEEK 18 | OVR | iSD | 2013-11-20 | Y | NA |
01-701-1034 | WEEK 6 | OVR | iUPD | 2014-08-11 | Y | Y |
01-701-1034 | WEEK 12 | OVR | iSD | 2014-09-25 | Y | Y |
01-701-1034 | WEEK 18 | OVR | NON-iCR/NON-iUPD | 2014-11-04 | Y | Y |
01-701-1097 | WEEK 6 | OVR | NE | 2014-02-11 | Y | Y |
01-701-1115 | WEEK 6 | OVR | iUPD | 2013-01-10 | Y | Y |
01-701-1118 | WEEK 6 | OVR | iUPD | 2014-04-23 | Y | Y |
For most parameter derivations the post-baseline overall response assessments up to and including first iCPD are considered.
USUBJID | AVISIT | AVALC | ADT | RANDDT |
---|---|---|---|---|
01-701-1015 | WEEK 6 | iUPD | 2014-02-12 | 2014-01-02 |
01-701-1028 | WEEK 6 | iUPD | 2013-08-31 | 2013-07-19 |
01-701-1028 | WEEK 12 | iCPD | 2013-10-09 | 2013-07-19 |
01-701-1034 | WEEK 6 | iUPD | 2014-08-11 | 2014-07-01 |
01-701-1034 | WEEK 12 | iSD | 2014-09-25 | 2014-07-01 |
01-701-1034 | WEEK 18 | NON-iCR/NON-iUPD | 2014-11-04 | 2014-07-01 |
01-701-1097 | WEEK 6 | NE | 2014-02-11 | 2014-01-01 |
01-701-1115 | WEEK 6 | iUPD | 2013-01-10 | 2012-11-30 |
01-701-1118 | WEEK 6 | iUPD | 2014-04-23 | 2014-03-12 |
01-701-1118 | WEEK 12 | iSD | 2014-06-05 | 2014-03-12 |
The building blocks for the events that contribute to deriving common endpoints like what constitutes a responder, or a Best Overall Response of complete response (CR), … are predefined in admiralonco for RECIST 1.1 (see Pre-Defined Response Event Objects). New Response Event Objects are needed for iRECIST and any study-specific needs.
icpd_y <- event_joined(
description = paste(
"Define confirmed progressive disease (iCPD) as",
"iUPD followed by iCPD with only other iUPD and NE responses in between"
),
dataset_name = "ovr",
join_vars = exprs(AVALC, ADT),
join_type = "after",
first_cond_upper = AVALC.join == "iCPD",
condition = AVALC == "iUPD" &
all(AVALC.join %in% c("iCPD", "iUPD", "NE")),
set_values_to = exprs(AVALC = "Y")
)
iupd_y <- event_joined(
description = paste(
"Define unconfirmed progressive disease (iUPD) as",
"iUPD followed only by other iUPD or NE responses"
),
dataset_name = "ovr",
join_vars = exprs(AVALC, ADT),
join_type = "all",
condition = ADT <= ADT.join & AVALC == "iUPD" & all(AVALC.join %in% c("iUPD", "NE")),
set_values_to = exprs(AVALC = "Y")
)
no_data_n <- event(
description = "Define no response for all patients in adsl (should be used as last event)",
dataset_name = "adsl",
condition = TRUE,
set_values_to = exprs(AVALC = "N"),
keep_source_vars = adsl_vars
)
no_data_missing <- event(
description = paste(
"Define missing response (MISSING) for all patients in adsl (should be used",
"as last event)"
),
dataset_name = "adsl",
condition = TRUE,
set_values_to = exprs(AVALC = "MISSING"),
keep_source_vars = adsl_vars
)
If RS
contains other response values than the iRECIST
responses, the event()
and event_joined()
can
be adjusted to cover this scenario. For example, if RECIST responses
("CR"
, "PR"
, "SD"
, …) are
collected up to first PD and iRECIST responses ("iCR"
,
"iPR"
, "iSD"
, …) thereafter, the
event()
object defining unconfirmed response can be
adjusted in the following way.
Now that we have the input records prepared above with any
company-specific requirements, we can start to derive new parameter
records. For the parameter derivations, all values except those
overwritten by set_values_to
argument are kept from the
earliest occurring input record fulfilling the required criteria.
When an iCPD
occurs, the date of progression would be
the first occurrence of iUPD
in that block. For example,
when we have values of iUPD
, iUPD
, and
iCPD
, the iRECIST PD
date would be the first
occurrence of iUPD
. In cases where we have SD
,
SD
, iUPD
, PR
, PR
,
iUPD
, and iCPD
, the iRECIST PD
date would be the second occurrence of iUPD
.
The function admiral::derive_extreme_records()
, in
conjunction with the event icpd_y
, could be used to find
the date of the first iUPD
.
For the Unconfirmed Progressive Disease Parameter, it can be of
interest to look at iUPD
that has never been confirmed and
no subsequent iSD
, iPR
or iCR
has
been observed.
adrs <- adrs %>%
derive_extreme_event(
by_vars = get_admiral_option("subject_keys"),
order = exprs(ADT),
mode = "first",
source_datasets = list(
ovr = ovr,
adsl = adsl
),
events = list(icpd_y, no_data_n),
set_values_to = exprs(
PARAMCD = "ICPD",
PARAM = "iRECIST Confirmation of Disease Progression by Investigator",
PARCAT1 = "Tumor Response",
PARCAT2 = "Investigator",
PARCAT3 = "iRECIST",
AVAL = yn_to_numeric(AVALC),
ANL01FL = "Y"
)
)
ovr_orig <- ovr
ovr <- ovr %>%
group_by(!!!get_admiral_option("subject_keys")) %>%
filter(ADT >= max_cond(var = ADT, cond = AVALC == "iUPD")) %>%
ungroup(!!!get_admiral_option("subject_keys"))
adrs <- adrs %>%
derive_extreme_event(
by_vars = get_admiral_option("subject_keys"),
order = exprs(ADT),
mode = "first",
source_datasets = list(
ovr = ovr,
adsl = adsl
),
events = list(iupd_y, no_data_n),
set_values_to = exprs(
PARAMCD = "IUPD",
PARAM = "iRECIST Unconfirmed Disease Progression by Investigator",
PARCAT1 = "Tumor Response",
PARCAT2 = "Investigator",
PARCAT3 = "iRECIST",
AVAL = yn_to_numeric(AVALC),
ANL01FL = "Y"
)
)
ovr <- ovr_orig
USUBJID | AVISIT | PARAMCD | PARAM | AVALC | ADT | ANL01FL |
---|---|---|---|---|---|---|
01-701-1015 | NA | ICPD | iRECIST Confirmation of Disease Progression by Investigator | N | NA | Y |
01-701-1023 | NA | ICPD | iRECIST Confirmation of Disease Progression by Investigator | N | NA | Y |
01-701-1028 | WEEK 6 | ICPD | iRECIST Confirmation of Disease Progression by Investigator | Y | 2013-08-31 | Y |
01-701-1034 | NA | ICPD | iRECIST Confirmation of Disease Progression by Investigator | N | NA | Y |
01-701-1097 | NA | ICPD | iRECIST Confirmation of Disease Progression by Investigator | N | NA | Y |
01-701-1115 | NA | ICPD | iRECIST Confirmation of Disease Progression by Investigator | N | NA | Y |
01-701-1118 | NA | ICPD | iRECIST Confirmation of Disease Progression by Investigator | N | NA | Y |
01-701-1130 | NA | ICPD | iRECIST Confirmation of Disease Progression by Investigator | N | NA | Y |
01-701-1133 | NA | ICPD | iRECIST Confirmation of Disease Progression by Investigator | N | NA | Y |
01-701-1146 | NA | ICPD | iRECIST Confirmation of Disease Progression by Investigator | N | NA | Y |
For progressive disease and response shown in steps here and below,
in our examples we show these as ADRS
parameters, but they
could equally be achieved via ADSL
dates or
ADEVENT
parameters.If you prefer to store as an ADSL date,
then the function admiral::derive_var_extreme_dt()
could be
used to find the date of first iCPD
as a variable, rather
than as a new parameter record.
The function admiral::derive_extreme_event()
can then be
used to find the date of first response. In the below example, the
response condition has been defined as iCR
or
iPR
via the event irsp_y
that was created for
iRECIST.
irsp_y <- event(
description = "Define iCR or iPR as (unconfirmed) response",
dataset_name = "ovr",
condition = AVALC %in% c("iCR", "iPR"),
set_values_to = exprs(AVALC = "Y")
)
adrs <- adrs %>%
derive_extreme_event(
by_vars = get_admiral_option("subject_keys"),
order = exprs(ADT),
mode = "first",
events = list(irsp_y, no_data_n),
source_datasets = list(
ovr = ovr,
adsl = adsl
),
set_values_to = exprs(
PARAMCD = "IRSP",
PARAM = "iRECIST Response by Investigator (confirmation not required)",
PARCAT1 = "Tumor Response",
PARCAT2 = "Investigator",
PARCAT3 = "iRECIST",
AVAL = yn_to_numeric(AVALC),
ANL01FL = "Y"
)
)
USUBJID | AVISIT | PARAMCD | PARAM | AVALC | ADT | ANL01FL |
---|---|---|---|---|---|---|
01-701-1015 | NA | IRSP | iRECIST Response by Investigator (confirmation not required) | N | NA | Y |
01-701-1023 | NA | IRSP | iRECIST Response by Investigator (confirmation not required) | N | NA | Y |
01-701-1028 | NA | IRSP | iRECIST Response by Investigator (confirmation not required) | N | NA | Y |
01-701-1034 | NA | IRSP | iRECIST Response by Investigator (confirmation not required) | N | NA | Y |
01-701-1097 | NA | IRSP | iRECIST Response by Investigator (confirmation not required) | N | NA | Y |
01-701-1115 | NA | IRSP | iRECIST Response by Investigator (confirmation not required) | N | NA | Y |
01-701-1118 | NA | IRSP | iRECIST Response by Investigator (confirmation not required) | N | NA | Y |
01-701-1130 | WEEK 12 | IRSP | iRECIST Response by Investigator (confirmation not required) | Y | 2014-05-16 | Y |
01-701-1133 | WEEK 12 | IRSP | iRECIST Response by Investigator (confirmation not required) | Y | 2013-01-22 | Y |
01-701-1146 | NA | IRSP | iRECIST Response by Investigator (confirmation not required) | N | NA | Y |
The function admiral::derive_extreme_event()
can then be
used to derive the clinical benefit parameter, which we define as a
patient having had a response or a sustained period of time before first
iUPD
. This could also be known as disease control. In this
example the “sustained period” has been defined as 42 days after
randomization date via the created icb_y
event.
icb_y <- event(
description = paste(
"Define iCR, iPR, iSD, or NON-iCR/NON-iUPD occuring at least 42 days after",
"randomization as clinical benefit"
),
dataset_name = "ovr",
condition = AVALC %in% c("iCR", "iPR", "iSD", "NON-iCR/NON-iUPD") &
ADT >= RANDDT + 42,
set_values_to = exprs(AVALC = "Y")
)
Please note that the result AVALC = "Y"
is defined by
the first two events specified for events
. For
subjects with observations fulfilling both events the one with the
earlier date should be selected (and not the first one in the list).
Thus ignore_event_order
and tmp_event_nr_var
are not specified.
adrs <- adrs %>%
derive_extreme_event(
by_vars = get_admiral_option("subject_keys"),
order = exprs(desc(AVALC), ADT),
mode = "first",
events = list(irsp_y, icb_y, no_data_n),
source_datasets = list(
ovr = ovr,
adsl = adsl
),
set_values_to = exprs(
PARAMCD = "ICB",
PARAM = "iRECIST Clinical Benefit by Investigator (confirmation for response not required)",
PARCAT1 = "Tumor Response",
PARCAT2 = "Investigator",
PARCAT3 = "iRECIST",
AVAL = yn_to_numeric(AVALC),
ANL01FL = "Y"
),
check_type = "none"
)
USUBJID | AVISIT | PARAMCD | PARAM | AVALC | ADT | RANDDT | ANL01FL |
---|---|---|---|---|---|---|---|
01-701-1015 | NA | ICB | iRECIST Clinical Benefit by Investigator (confirmation for response not required) | N | NA | 2014-01-02 | Y |
01-701-1023 | NA | ICB | iRECIST Clinical Benefit by Investigator (confirmation for response not required) | N | NA | 2012-08-05 | Y |
01-701-1028 | NA | ICB | iRECIST Clinical Benefit by Investigator (confirmation for response not required) | N | NA | 2013-07-19 | Y |
01-701-1034 | WEEK 12 | ICB | iRECIST Clinical Benefit by Investigator (confirmation for response not required) | Y | 2014-09-25 | 2014-07-01 | Y |
01-701-1097 | NA | ICB | iRECIST Clinical Benefit by Investigator (confirmation for response not required) | N | NA | 2014-01-01 | Y |
01-701-1115 | NA | ICB | iRECIST Clinical Benefit by Investigator (confirmation for response not required) | N | NA | 2012-11-30 | Y |
01-701-1118 | WEEK 12 | ICB | iRECIST Clinical Benefit by Investigator (confirmation for response not required) | Y | 2014-06-05 | 2014-03-12 | Y |
01-701-1130 | WEEK 12 | ICB | iRECIST Clinical Benefit by Investigator (confirmation for response not required) | Y | 2014-05-16 | 2014-02-15 | Y |
01-701-1133 | WEEK 6 | ICB | iRECIST Clinical Benefit by Investigator (confirmation for response not required) | Y | 2012-12-11 | 2012-10-28 | Y |
01-701-1146 | NA | ICB | iRECIST Clinical Benefit by Investigator (confirmation for response not required) | N | NA | 2013-05-20 | Y |
The function admiral::derive_extreme_event()
can be used
to derive the best overall response (without confirmation required)
parameter. Similar to the above function you can optionally decide what
period would you consider an iSD
or
NON-iCR/NON-iUPD
as being eligible from. In this example,
42 days after randomization date has been used again.
Please note that the order of the events specified for
events
is important. For example, a subject with
iPR
, iPR
, iCR
qualifies for both
ibor_icr
and ibor_ipr
. As
ibor_icr
is listed before ibor_ipr
,
iCR
is selected as best overall response for this
subject.
ibor_icr <- event(
description = "Define complete response (iCR) for best overall response (iBOR)",
dataset_name = "ovr",
condition = AVALC == "iCR",
set_values_to = exprs(AVALC = "iCR")
)
ibor_ipr <- event(
description = "Define partial response (iPR) for best overall response (iBOR)",
dataset_name = "ovr",
condition = AVALC == "iPR",
set_values_to = exprs(AVALC = "iPR")
)
ibor_isd <- event(
description = paste(
"Define stable disease (iSD) for best overall response (iBOR) as iCR, iPR, or iSD",
"occurring at least 42 days after randomization"
),
dataset_name = "ovr",
condition = AVALC %in% c("iCR", "iPR", "iSD") & ADT >= RANDDT + 42,
set_values_to = exprs(AVALC = "iSD")
)
ibor_non_icriupd <- event(
description = paste(
"Define NON-iCR/NON-iUPD for best overall response (iBOR) as NON-iCR/NON-iUPD",
"occuring at least 42 days after randomization"
),
dataset_name = "ovr",
condition = AVALC == "NON-iCR/NON-iUPD" & ADT >= RANDDT + 42,
set_values_to = exprs(AVALC = "NON-iCR/NON-iUPD")
)
ibor_icpd <- event_joined(
description = paste(
"Define confirmed progressive disease (iCPD) for best overall response (iBOR) as",
"iUPD followed by iCPD with only other iUPD and NE responses in between"
),
dataset_name = "ovr",
join_vars = exprs(AVALC, ADT),
join_type = "after",
first_cond_upper = AVALC.join == "iCPD",
condition = AVALC == "iUPD" &
all(AVALC.join %in% c("iCPD", "iUPD", "NE")),
set_values_to = exprs(AVALC = "iCPD")
)
ibor_iupd <- event(
description = "Define unconfirmed progressive disease (iUPD) for best overall response (iBOR)",
dataset_name = "ovr",
condition = AVALC == "iUPD",
set_values_to = exprs(AVALC = "iUPD")
)
ibor_ne <- event(
description = paste(
"Define not evaluable (NE) for best overall response (iBOR) as iCR, iPR, iSD,",
"NON-iCR/NON-iUPD, or NE (should be specified after ibor_isd and ibor_non_icriupd)"
),
dataset_name = "ovr",
condition = AVALC %in% c("iCR", "iPR", "iSD", "NON-iCR/NON-iUPD", "NE"),
set_values_to = exprs(AVALC = "NE")
)
adrs <- adrs %>%
derive_extreme_event(
by_vars = get_admiral_option("subject_keys"),
tmp_event_nr_var = event_nr,
order = exprs(event_nr, ADT),
mode = "first",
source_datasets = list(
ovr = ovr,
adsl = adsl
),
events = list(ibor_icr, ibor_ipr, ibor_isd, ibor_non_icriupd, ibor_icpd, ibor_iupd, ibor_ne, no_data_missing),
set_values_to = exprs(
PARAMCD = "IBOR",
PARAM = "iRECIST Best Overall Response by Investigator (confirmation not required)",
PARCAT1 = "Tumor Response",
PARCAT2 = "Investigator",
PARCAT3 = "iRECIST",
AVAL = aval_resp_new(AVALC),
ANL01FL = "Y"
)
)
USUBJID | AVISIT | PARAMCD | PARAM | AVALC | ADT | RANDDT | ANL01FL |
---|---|---|---|---|---|---|---|
01-701-1015 | WEEK 6 | IBOR | iRECIST Best Overall Response by Investigator (confirmation not required) | iUPD | 2014-02-12 | 2014-01-02 | Y |
01-701-1023 | NA | IBOR | iRECIST Best Overall Response by Investigator (confirmation not required) | MISSING | NA | 2012-08-05 | Y |
01-701-1028 | WEEK 6 | IBOR | iRECIST Best Overall Response by Investigator (confirmation not required) | iCPD | 2013-08-31 | 2013-07-19 | Y |
01-701-1034 | WEEK 12 | IBOR | iRECIST Best Overall Response by Investigator (confirmation not required) | iSD | 2014-09-25 | 2014-07-01 | Y |
01-701-1097 | WEEK 6 | IBOR | iRECIST Best Overall Response by Investigator (confirmation not required) | NE | 2014-02-11 | 2014-01-01 | Y |
01-701-1115 | WEEK 6 | IBOR | iRECIST Best Overall Response by Investigator (confirmation not required) | iUPD | 2013-01-10 | 2012-11-30 | Y |
01-701-1118 | WEEK 12 | IBOR | iRECIST Best Overall Response by Investigator (confirmation not required) | iSD | 2014-06-05 | 2014-03-12 | Y |
01-701-1130 | WEEK 12 | IBOR | iRECIST Best Overall Response by Investigator (confirmation not required) | iCR | 2014-05-16 | 2014-02-15 | Y |
01-701-1133 | WEEK 12 | IBOR | iRECIST Best Overall Response by Investigator (confirmation not required) | iPR | 2013-01-22 | 2012-10-28 | Y |
01-701-1146 | WEEK 6 | IBOR | iRECIST Best Overall Response by Investigator (confirmation not required) | iUPD | 2013-06-30 | 2013-05-20 | Y |
Any of the above response parameters can be repeated for “confirmed”
responses only. For these the function
admiral::derive_extreme_event()
can be used with different
events. Some of the other functions from above can then be re-used
passing in these confirmed response records. See the examples below of
derived parameters requiring confirmation. The assessment and the
confirmatory assessment here need to occur at least 28 days apart
(without any +1 applied to this calculation of days between
visits), using the icrsp_y_cr
,
icrsp_y_ipr
, icbor_icr
, and
icbor_ipr
event. Here the confirmation period and the
keep_source_vars
argument is updated, as well as the
first_cond_upper
and condition
for the iRECIST
values.
confirmation_period <- 28
icrsp_y_icr <- event_joined(
description = paste(
"Define confirmed response as iCR followed by iCR at least",
confirmation_period,
"days later and at most one NE in between"
),
dataset_name = "ovr",
join_vars = exprs(AVALC, ADT),
join_type = "after",
order = exprs(ADT),
first_cond_upper = AVALC.join == "iCR" &
ADT.join >= ADT + days(confirmation_period),
condition = AVALC == "iCR" &
all(AVALC.join %in% c("iCR", "NE")) &
count_vals(var = AVALC.join, val = "NE") <= 1,
set_values_to = exprs(AVALC = "Y")
)
icrsp_y_ipr <- event_joined(
description = paste(
"Define confirmed response as iPR followed by iCR or iPR at least",
confirmation_period,
"days later at most one NE in between, and no iPR after iCR"
),
dataset_name = "ovr",
join_vars = exprs(AVALC, ADT),
join_type = "after",
order = exprs(ADT),
first_cond_upper = AVALC.join %in% c("iCR", "iPR") &
ADT.join >= ADT + days(confirmation_period),
condition = AVALC == "iPR" &
all(AVALC.join %in% c("iCR", "iPR", "NE")) &
count_vals(var = AVALC.join, val = "NE") <= 1 &
(
min_cond(
var = ADT.join,
cond = AVALC.join == "iCR"
) > max_cond(var = ADT.join, cond = AVALC.join == "iPR") |
count_vals(var = AVALC.join, val = "iCR") == 0 |
count_vals(var = AVALC.join, val = "iPR") == 0
),
set_values_to = exprs(AVALC = "Y")
)
icbor_icr <- event_joined(
description = paste(
"Define complete response (iCR) for confirmed best overall response (iCBOR) as",
"iCR followed by iCR at least",
confirmation_period,
"days later and at most one NE in between"
),
dataset_name = "ovr",
join_vars = exprs(AVALC, ADT),
join_type = "after",
first_cond_upper = AVALC.join == "iCR" &
ADT.join >= ADT + confirmation_period,
condition = AVALC == "iCR" &
all(AVALC.join %in% c("iCR", "NE")) &
count_vals(var = AVALC.join, val = "NE") <= 1,
set_values_to = exprs(AVALC = "iCR")
)
icbor_ipr <- event_joined(
description = paste(
"Define partial response (iPR) for confirmed best overall response (iCBOR) as",
"iPR followed by iCR or iPR at least",
confirmation_period,
"days later, at most one NE in between and no iPR after iCR"
),
dataset_name = "ovr",
join_vars = exprs(AVALC, ADT),
join_type = "after",
first_cond_upper = AVALC.join %in% c("iCR", "iPR") &
ADT.join >= ADT + confirmation_period,
condition = AVALC == "iPR" &
all(AVALC.join %in% c("iCR", "iPR", "NE")) &
count_vals(var = AVALC.join, val = "NE") <= 1 &
(
min_cond(
var = ADT.join,
cond = AVALC.join == "iCR"
) > max_cond(var = ADT.join, cond = AVALC.join == "iPR") |
count_vals(var = AVALC.join, val = "iCR") == 0 |
count_vals(var = AVALC.join, val = "iPR") == 0
),
set_values_to = exprs(AVALC = "iPR")
)
Please note that the result AVALC = "Y"
for confirmed
clinical benefit is defined by the first two events specified
for events
. For subjects with observations fulfilling both
events the one with the earlier date should be selected (and not the
first one in the list).
adrs <- adrs %>%
derive_extreme_event(
by_vars = get_admiral_option("subject_keys"),
order = exprs(desc(AVALC), ADT),
mode = "first",
source_datasets = list(
ovr = ovr,
adsl = adsl
),
events = list(icrsp_y_icr, icrsp_y_ipr, no_data_n),
set_values_to = exprs(
PARAMCD = "ICRSP",
PARAM = "iRECIST Confirmed Response by Investigator",
PARCAT1 = "Tumor Response",
PARCAT2 = "Investigator",
PARCAT3 = "iRECIST",
AVAL = yn_to_numeric(AVALC),
ANL01FL = "Y"
)
)
adrs <- adrs %>%
derive_extreme_event(
by_vars = get_admiral_option("subject_keys"),
order = exprs(desc(AVALC), ADT),
mode = "first",
events = list(icrsp_y_icr, icrsp_y_ipr, icb_y, no_data_n),
source_datasets = list(
ovr = ovr,
adsl = adsl
),
set_values_to = exprs(
PARAMCD = "ICCB",
PARAM = "iRECIST Confirmed Clinical Benefit by Investigator",
PARCAT1 = "Tumor Response",
PARCAT2 = "Investigator",
PARCAT3 = "iRECIST",
AVAL = yn_to_numeric(AVALC),
ANL01FL = "Y"
),
check_type = "none"
)
adrs <- adrs %>%
derive_extreme_event(
by_vars = get_admiral_option("subject_keys"),
tmp_event_nr_var = event_nr,
order = exprs(event_nr, ADT),
mode = "first",
events = list(icbor_icr, icbor_ipr, ibor_isd, ibor_non_icriupd, ibor_icpd, ibor_iupd, ibor_ne, no_data_missing),
source_datasets = list(
ovr = ovr,
adsl = adsl
),
set_values_to = exprs(
PARAMCD = "ICBOR",
PARAM = "iRECIST Best Confirmed Overall Response by Investigator",
PARCAT1 = "Tumor Response",
PARCAT2 = "Investigator",
PARCAT3 = "iRECIST",
AVAL = aval_resp(AVALC),
ANL01FL = "Y"
)
)
USUBJID | AVISIT | PARAMCD | PARAM | AVALC | ADT | RANDDT | ANL01FL |
---|---|---|---|---|---|---|---|
01-701-1015 | NA | ICRSP | iRECIST Confirmed Response by Investigator | N | NA | 2014-01-02 | Y |
01-701-1023 | NA | ICRSP | iRECIST Confirmed Response by Investigator | N | NA | 2012-08-05 | Y |
01-701-1028 | NA | ICRSP | iRECIST Confirmed Response by Investigator | N | NA | 2013-07-19 | Y |
01-701-1034 | NA | ICRSP | iRECIST Confirmed Response by Investigator | N | NA | 2014-07-01 | Y |
01-701-1097 | NA | ICRSP | iRECIST Confirmed Response by Investigator | N | NA | 2014-01-01 | Y |
01-701-1115 | NA | ICRSP | iRECIST Confirmed Response by Investigator | N | NA | 2012-11-30 | Y |
01-701-1118 | NA | ICRSP | iRECIST Confirmed Response by Investigator | N | NA | 2014-03-12 | Y |
01-701-1130 | WEEK 12 | ICRSP | iRECIST Confirmed Response by Investigator | Y | 2014-05-16 | 2014-02-15 | Y |
01-701-1133 | WEEK 12 | ICRSP | iRECIST Confirmed Response by Investigator | Y | 2013-01-22 | 2012-10-28 | Y |
01-701-1146 | NA | ICRSP | iRECIST Confirmed Response by Investigator | N | NA | 2013-05-20 | Y |
The following parameters may also be added:
IBCP - iRECIST Best Overall Response of CR/PR by Investigator
(confirmation not required)
ICBCP - iRECIST Best Confirmed Overall
Response of CR/PR by Investigator
IOVRB - iRECIST Overall Response
by BICR
ILSTA - iRECIST Last Disease Assessment by Investigator
IMDIS - iRECIST Measurable Disease at Baseline by Investigator
For examples on the additional endpoints, please see Creating ADRS (Including Non-standard Endpoints).