Merge branch 'main' into 2546_update_ABLFL_example_derive_var_base

pharmaverse · Nov 13, 2024 · 63902f3 · 63902f3
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: admiral
 Title: ADaM in R Asset Library
-Version: 1.1.1.9021
+Version: 1.1.1.9022
 Authors@R: c(
     person("Ben", "Straub", , "ben.x.straub@gsk.com", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut",

diff --git a/NEWS.md b/NEWS.md
@@ -32,6 +32,10 @@ or that the queries dataset contains duplicates. (#2543)
 wrongly using `x ULN`, for first part of criteria for grades 1 to 3. For
 example, `">2.5 x ULN"` changed to `">2.5"` for grade 3. (#2534)
 
+- `derive_vars_atc()` and `create_single_dose_dataset()` `by_vars` argument updated to use `get_admiral_option("subject_keys")` instead of  `USUBJID` or `STUDYID` in `bds_exposure.Rmd`. (#2501)
+
+- test scripts, R, and markdown files for `create_single_dose_dataset` and `occds.Rmd` updated to include a `STUDYID` column because of `get_admiral_option("subject_keys")` update above. (#2501)
+
 ## Breaking Changes
 
 - The following function arguments are entering the next phase of the deprecation process: (#2487)
@@ -58,6 +62,8 @@ example, `">2.5 x ULN"` changed to `">2.5"` for grade 3. (#2534)
 
 ## Documentation
 
+- `derive_locf_records()` documentation example was fixed to display LOCF records. (#2461)
+
 ## Various
 
 <details>
@@ -70,12 +76,9 @@ example, `">2.5 x ULN"` changed to `">2.5"` for grade 3. (#2534)
 </details>
 
 # admiral 1.1.1
-
 - `derive_extreme_event()` was fixed such that `check_type = "none"` is accepted
 again. (#2462)
 
-- `derive_locf_records()` documentation example was fixed to display LOCF records. (#2461)
-
 # admiral 1.1.0
 
 ## New Features
@@ -87,6 +90,7 @@ again. (#2462)
 
 ## Updates of Existing Functions
 
+
 - `group_var` (optional) parameter is added to `derive_var_trtemfl()` to derive `TRTEMFL` for AE data if the data are collected as one episode of AE with multiple lines. (#2302)
 
 - Templates for ADPC, ADPPK and ADPP are updated to handle urine records. (#2392)

diff --git a/R/create_single_dose_dataset.R b/R/create_single_dose_dataset.R
@@ -287,12 +287,12 @@ dose_freq_lookup <- tribble(
 #' library(dplyr)
 #'
 #' data <- tribble(
-#'   ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
-#'   "P01", "Q2D", ymd("2021-01-01"), ymd_hms("2021-01-01 10:30:00"),
+#'   ~STUDYID, ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
+#'   "STUDY01", "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"),
+#'   "STUDY01", "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"),
+#'   "STUDY01", "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")
 #' )
 #'
@@ -307,10 +307,10 @@ dose_freq_lookup <- tribble(
 #' )
 #'
 #' data <- tribble(
-#'   ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
-#'   "P01", "Q30MIN", ymd("2021-01-01"), ymd_hms("2021-01-01T06:00:00"),
+#'   ~STUDYID, ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
+#'   "STUDY01", "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"),
+#'   "STUDY02", "P02", "Q90MIN", ymd("2021-01-01"), ymd_hms("2021-01-01T06:00:00"),
 #'   ymd("2021-01-01"), ymd_hms("2021-01-01T09:00:00")
 #' )
 #'
@@ -323,12 +323,12 @@ dose_freq_lookup <- tribble(
 #' # 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"),
+#'   ~STUDYID, ~USUBJID, ~EXDOSFRQ, ~NFRLT, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
+#'   "STUDY01", "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"),
+#'   "STUDY01", "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"),
+#'   "STUDY01", "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")
 #' )
 #'
@@ -397,7 +397,7 @@ dose_freq_lookup <- tribble(
 #' # 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)) %>%
+#'   derive_vars_merged(adsl_death, by_vars = get_admiral_option("subject_keys")) %>%
 #'   # 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)) %>%
@@ -450,7 +450,8 @@ create_single_dose_dataset <- function(dataset,
                                        lookup_column = CDISC_VALUE,
                                        nominal_time = NULL,
                                        keep_source_vars = expr_c(
-                                         exprs(USUBJID), dose_freq, start_date, start_datetime,
+                                         get_admiral_option("subject_keys"), dose_freq,
+                                         start_date, start_datetime,
                                          end_date, end_datetime
                                        )) {
   dose_freq <- assert_symbol(enexpr(dose_freq))

diff --git a/R/derive_vars_transposed.R b/R/derive_vars_transposed.R
@@ -56,33 +56,33 @@
 #' 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"
+#'   ~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"
+#'   ~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 %>%
@@ -226,39 +226,42 @@ derive_vars_transposed <- function(dataset,
 #' library(tibble)
 #'
 #' cm <- tribble(
-#'   ~USUBJID, ~CMGRPID, ~CMREFID, ~CMDECOD,
-#'   "BP40257-1001", "14", "1192056", "PARACETAMOL",
-#'   "BP40257-1001", "18", "2007001", "SOLUMEDROL",
-#'   "BP40257-1002", "19", "2791596", "SPIRONOLACTONE"
+#'   ~STUDYID,  ~USUBJID,       ~CMGRPID, ~CMREFID,  ~CMDECOD,
+#'   "STUDY01", "BP40257-1001", "14",     "1192056", "PARACETAMOL",
+#'   "STUDY01", "BP40257-1001", "18",     "2007001", "SOLUMEDROL",
+#'   "STUDY01", "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"
+#'   ~STUDYID,  ~USUBJID,       ~FAGRPID, ~FAREFID,  ~FATESTCD,  ~FASTRESC,
+#'   "STUDY01", "BP40257-1001", "1",      "1192056", "CMATC1CD", "N",
+#'   "STUDY01", "BP40257-1001", "1",      "1192056", "CMATC2CD", "N02",
+#'   "STUDY01", "BP40257-1001", "1",      "1192056", "CMATC3CD", "N02B",
+#'   "STUDY01", "BP40257-1001", "1",      "1192056", "CMATC4CD", "N02BE",
+#'   "STUDY01", "BP40257-1001", "1",      "2007001", "CMATC1CD", "D",
+#'   "STUDY01", "BP40257-1001", "1",      "2007001", "CMATC2CD", "D10",
+#'   "STUDY01", "BP40257-1001", "1",      "2007001", "CMATC3CD", "D10A",
+#'   "STUDY01", "BP40257-1001", "1",      "2007001", "CMATC4CD", "D10AA",
+#'   "STUDY01", "BP40257-1001", "2",      "2007001", "CMATC1CD", "D",
+#'   "STUDY01", "BP40257-1001", "2",      "2007001", "CMATC2CD", "D07",
+#'   "STUDY01", "BP40257-1001", "2",      "2007001", "CMATC3CD", "D07A",
+#'   "STUDY01", "BP40257-1001", "2",      "2007001", "CMATC4CD", "D07AA",
+#'   "STUDY01", "BP40257-1001", "3",      "2007001", "CMATC1CD", "H",
+#'   "STUDY01", "BP40257-1001", "3",      "2007001", "CMATC2CD", "H02",
+#'   "STUDY01", "BP40257-1001", "3",      "2007001", "CMATC3CD", "H02A",
+#'   "STUDY01", "BP40257-1001", "3",      "2007001", "CMATC4CD", "H02AB",
+#'   "STUDY01", "BP40257-1002", "1",      "2791596", "CMATC1CD", "C",
+#'   "STUDY01", "BP40257-1002", "1",      "2791596", "CMATC2CD", "C03",
+#'   "STUDY01", "BP40257-1002", "1",      "2791596", "CMATC3CD", "C03D",
+#'   "STUDY01", "BP40257-1002", "1",      "2791596", "CMATC4CD", "C03DA"
 #' )
 #'
 #' derive_vars_atc(cm, facm)
 derive_vars_atc <- function(dataset,
                             dataset_facm,
-                            by_vars = exprs(USUBJID, CMREFID = FAREFID),
+                            by_vars = exprs(
+                              !!!get_admiral_option("subject_keys"),
+                              CMREFID = FAREFID
+                            ),
                             id_vars = NULL,
                             value_var = FASTRESC) {
   value_var <- assert_symbol(enexpr(value_var))

diff --git a/man/create_single_dose_dataset.Rd b/man/create_single_dose_dataset.Rd
diff --git a/man/derive_vars_atc.Rd b/man/derive_vars_atc.Rd