closes #41 create a basic ADSL for peds test subjects (#43)

* #41 create a basic ADSL for peds test subjects

* #41 add adsl_peds dataset and man files

* #41 add missing variable labels

* #41 remove redundant comment

* #41 remove redundant comments

* #41 spelling

R/data.R

@@ -226,10 +226,16 @@
 #' @family datasets
 "dm_peds"
 
-
 #' Vital signs Dataset-updated
 #'
 #' An updated SDTM VS dataset with anthropometric measurements for pediatric patients
 #' @keywords datasets
 #' @family datasets
 "vs_peds"
+
+#' Subject Level Analysis Dataset-updated
+#'
+#' An updated ADaM ADSL dataset with pediatric patients
+#' @keywords datasets
+#' @family datasets
+"adsl_peds"

data-raw/adsl_peds.R

@@ -0,0 +1,75 @@
+# Dataset: adsl_peds
+# Description: Create ADSL test ADaM dataset for pediatric studies
+
+# Load libraries -----
+library(pharmaversesdtm)
+library(admiral)
+library(dplyr)
+library(lubridate)
+library(stringr)
+
+# Create a basic ADSL for pediatrics ----
+
+# Read in input data ----
+data("dm_peds")
+data("ex")
+
+# Derivations ----
+
+# impute start and end time of exposure to first and last respectively, do not impute date
+ex_ext <- ex %>%
+  derive_vars_dtm(
+    dtc = EXSTDTC,
+    new_vars_prefix = "EXST"
+  ) %>%
+  derive_vars_dtm(
+    dtc = EXENDTC,
+    new_vars_prefix = "EXEN",
+    time_imputation = "last"
+  )
+
+adsl_peds <- dm_peds %>%
+  ## derive treatment variables (TRT01P, TRT01A) ----
+  mutate(TRT01P = ARM, TRT01A = ACTARM) %>%
+  ## derive treatment start date (TRTSDTM) ----
+  derive_vars_merged(
+    dataset_add = ex_ext,
+    filter_add = (EXDOSE > 0 |
+      (EXDOSE == 0 &
+        str_detect(EXTRT, "PLACEBO"))) &
+      !is.na(EXSTDTM),
+    new_vars = exprs(TRTSDTM = EXSTDTM, TRTSTMF = EXSTTMF),
+    order = exprs(EXSTDTM, EXSEQ),
+    mode = "first",
+    by_vars = exprs(STUDYID, USUBJID)
+  ) %>%
+  ## derive treatment end date (TRTEDTM) ----
+  derive_vars_merged(
+    dataset_add = ex_ext,
+    filter_add = (EXDOSE > 0 |
+      (EXDOSE == 0 &
+        str_detect(EXTRT, "PLACEBO"))) & !is.na(EXENDTM),
+    new_vars = exprs(TRTEDTM = EXENDTM, TRTETMF = EXENTMF),
+    order = exprs(EXENDTM, EXSEQ),
+    mode = "last",
+    by_vars = exprs(STUDYID, USUBJID)
+  ) %>%
+  ## Derive treatment end/start date TRTSDT/TRTEDT ----
+  derive_vars_dtm_to_dt(source_vars = exprs(TRTSDTM, TRTEDTM)) %>%
+  ## derive treatment duration (TRTDURD) ----
+  derive_var_trtdurd()
+
+# Variable labels ----
+attr(adsl_peds$TRTSDTM, "label") <- "Datetime of First Exposure to Treatment"
+attr(adsl_peds$TRTSTMF, "label") <- "Exposure Start Time Imputation Flag"
+attr(adsl_peds$TRTEDTM, "label") <- "Datetime of Last Exposure to Treatment"
+attr(adsl_peds$TRTETMF, "label") <- "Exposure End Time Imputation Flag"
+attr(adsl_peds$TRTSDT, "label") <- "Date of First Exposure to Treatment"
+attr(adsl_peds$TRTEDT, "label") <- "Date of Last Exposure to Treatment"
+attr(adsl_peds$TRTDURD, "label") <- "Total Treatment Duration (Days)"
+
+# Label dataset ----
+attr(adsl_peds, "label") <- "Subject Level Analysis Dataset"
+
+# Save dataset ----
+usethis::use_data(adsl_peds, overwrite = TRUE)

inst/WORDLIST

@@ -1,5 +1,6 @@
 ADaM
 ADaMs
+ADSL
 BMI
 Biologics
 CDISC