Merge branch 'main' into 2519_fix_param_tte

.Rbuildignore

@@ -28,7 +28,6 @@
 ^\.lycheeignore$
 ^staged_dependencies.yaml$
 ^inst/dev_dependencies.R$
-^\.devcontainer$
 ^vignettes/articles$
 ^inst/cheatsheet$
 ^data-raw$

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: admiral
 Title: ADaM in R Asset Library
-Version: 1.1.1.9012
+Version: 1.1.1.9018
 Authors@R: c(
     person("Ben", "Straub", , "ben.x.straub@gsk.com", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut",

NEWS.md

@@ -6,15 +6,24 @@
 `AVALCATx` & `AVALCAxN`. (#2480)
 - New function `derive_vars_crit_flag()` for deriving criterion flag variables
 (`CRITy`, `CRITyFL`, `CRITyFLN`). (#2468)
-
 - Replace use of `data("sdtm")` with `sdtm <- pharmaverse::sdtm` in templates and vignettes. (#2498)
 
+- Remove `dthcaus_source()` calls in `ADSL` template because they are deprecated. (#2517)
+
 ## Updates of Existing Functions
 
 - `derive_param_tte()` now provides a useful error message if in
 `event_conditions` or `censor_conditions` a dataset is referenced which is not
 specified in `source_datasets`. (#2519)
 
+- In `derive_vars_query()` the error message was improved for the cases that
+some of the requested query variables are already present in the input dataset
+or that the queries dataset contains duplicates. (#2543)
+
+- NCICTCAEv5 grading criteria fixed for `TERM = "INR Increased"`, criteria was
+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)
+
 ## Breaking Changes
 
 - The following function arguments are entering the next phase of the deprecation process: (#2487)
@@ -46,7 +55,9 @@ specified in `source_datasets`. (#2519)
 <details>
 <summary>Developer Notes</summary>
 
+- Created unit tests for developer internal function `restricted_imputed_dtc_dt()` (#2495)
 - Adopted `data-raw/data` R Package Convention (#2427)
+- Removed `.devcontainer` file (codespace) (#2524)
 
 </details>
 

R/data.R

@@ -24,15 +24,17 @@
 #' @keywords datasets
 #' @family datasets
 #' @source
-#' An example of standard query dataset to be used in deriving variables in ADAE and ADCM
+#' An example of standard query dataset to be used in deriving Standardized
+#' MedDRA Query variables in ADAE
 #'
 "queries"
 
 #' Queries MH Dataset
 #' @keywords datasets
 #' @family datasets
 #' @source
-#' An example of standard query MH dataset to be used in deriving variables in ADMH
+#' An example of standard query MH dataset to be used in deriving Standardized
+#' MedDRA Query variables in ADMH
 #'
 "queries_mh"
 

R/derive_vars_query.R

@@ -145,6 +145,14 @@ get_vars_query <- function(dataset, dataset_queries) { # nolint: cyclocomp_linte
     arrange(desc(order1), order2, order3) %>%
     pull(value)
 
+  existing_new_vars <- intersect(new_col_names, colnames(dataset))
+  if (length(existing_new_vars) > 0) {
+    cli_abort(paste(
+      "The following variable{?s} requested by {.arg dataset_queries} already",
+      "exist{?s/} in {.arg dataset}: {.var {existing_new_vars}}"
+    ))
+  }
+
   # queries restructured
   queries_wide <- dataset_queries %>%
     mutate(
@@ -316,7 +324,14 @@ derive_vars_query <- function(dataset, dataset_queries) { # nolint: cyclocomp_li
 #' @noRd
 assert_valid_queries <- function(queries, queries_name) {
   # check duplicate rows
-  signal_duplicate_records(queries, by_vars = exprs(!!!syms(colnames(queries))))
+  signal_duplicate_records(
+    queries,
+    msg = paste0(
+      "Queries dataset ({.var ", queries_name, "}) contains duplicate records ",
+      "with respect to {.var {replace_values_by_names(by_vars)}}"
+    ),
+    by_vars = exprs(!!!syms(colnames(queries)))
+  )
 
   # check illegal prefix category
   is_good_prefix <- grepl("^[a-zA-Z]{2,3}", queries$PREFIX)