Merge branch 'main' into propagation-march-2024

insightsengineering · Apr 18, 2024 · 2017f55 · 2017f55
2 parents 9306a1c + b174c12
commit 2017f55
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.0
+    rev: v0.4.2
     hooks:
       - id: style-files
         name: Style code with `styler`

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: random.cdisc.data
 Title: Create Random ADaM Datasets
-Version: 0.3.15.9000
-Date: 2024-03-28
+Version: 0.3.15.9002
+Date: 2024-04-16
 Authors@R: c(
     person("Pawel", "Rucki", , "[email protected]", role = "aut"),
     person("Nick", "Paszty", , "[email protected]", role = "aut"),
@@ -19,6 +19,10 @@ Description: A set of functions to create random Analysis Data Model
     described by the Clinical Data Interchange Standards Consortium
     (CDISC) Analysis Data Model Team.
 License: Apache License 2.0
+URL: https://insightsengineering.github.io/random.cdisc.data/,
+    https://github.com/insightsengineering/random.cdisc.data/
+BugReports: 
+    https://github.com/insightsengineering/random.cdisc.data/issues
 Depends:
     R (>= 3.6)
 Imports:

diff --git a/NAMESPACE b/NAMESPACE
@@ -28,7 +28,6 @@ export(replace_na)
 export(rtexp)
 export(rtpois)
 export(sample_fct)
-export(var_relabel)
 export(visit_schedule)
 import(dplyr)
 importFrom(lifecycle,badge)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,8 @@
-# random.cdisc.data 0.3.15.9000
+# random.cdisc.data 0.3.15.9002
+
+### Miscellaneous
+* Renamed `var_relabel` into `rcd_var_relabel` and copied new functionalities to avoid namespace conflict with `formatters` package.
+* Made `rcd_var_relabel` internal as it was intended for developers use only.
 
 # random.cdisc.data 0.3.15
 

diff --git a/R/radae.R b/R/radae.R
@@ -134,7 +134,7 @@ radae <- function(adsl,
       AETOXGR %in% c(4, 5) ~ "SEVERE"
     ))
 
-  adae <- var_relabel(
+  adae <- rcd_var_relabel(
     adae,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/radaette.R b/R/radaette.R
@@ -223,12 +223,12 @@ radaette <- function(adsl,
       dplyr::bind_rows(patient_data, ae_data)
     }) %>%
     Reduce(rbind, .) %>%
-    var_relabel(
+    rcd_var_relabel(
       STUDYID = "Study Identifier",
       USUBJID = "Unique Subject Identifier"
     )
 
-  adaette <- var_relabel(
+  adaette <- rcd_var_relabel(
     adaette,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/radcm.R b/R/radcm.R
@@ -82,7 +82,7 @@ radcm <- function(adsl,
     `[`(c(4, 5, 1, 2, 3)) %>%
     dplyr::mutate(CMCAT = CMCLAS)
 
-  adcm <- var_relabel(
+  adcm <- rcd_var_relabel(
     adcm,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/raddv.R b/R/raddv.R
@@ -101,7 +101,7 @@ raddv <- function(adsl,
     Reduce(rbind, .) %>%
     dplyr::mutate(DVSCAT = DVCAT)
 
-  addv <- var_relabel(
+  addv <- rcd_var_relabel(
     addv,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/radeg.R b/R/radeg.R
@@ -167,16 +167,12 @@ radeg <- function(adsl,
     dplyr::mutate(BNRIND = ANRIND[ABLFL == "Y"]) %>%
     dplyr::ungroup() %>%
     dplyr::mutate(ATPTN = 1) %>%
-    dplyr::mutate(DTYPE = NA) %>%
-    var_relabel(
-      STUDYID = attr(adeg$STUDYID, "label"),
-      USUBJID = attr(adeg$USUBJID, "label")
-    )
+    dplyr::mutate(DTYPE = NA)
 
   adeg$ANRIND <- factor(adeg$ANRIND, levels = c("LOW", "NORMAL", "HIGH"))
   adeg$BNRIND <- factor(adeg$BNRIND, levels = c("LOW", "NORMAL", "HIGH"))
 
-  adeg <- var_relabel(
+  adeg <- rcd_var_relabel(
     adeg,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/radex.R b/R/radex.R
@@ -213,7 +213,7 @@ radex <- function(adsl,
       AVAL
     ))
 
-  adex <- var_relabel(
+  adex <- rcd_var_relabel(
     adex,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/radhy.R b/R/radhy.R
@@ -168,7 +168,7 @@ radhy <- function(adsl,
     dplyr::ungroup()
 
   adhy <- adhy %>%
-    var_relabel(
+    rcd_var_relabel(
       STUDYID = attr(adsl$STUDYID, "label"),
       USUBJID = attr(adsl$USUBJID, "label")
     )

diff --git a/R/radlb.R b/R/radlb.R
@@ -260,7 +260,7 @@ radlb <- function(adsl,
       ATOXGR == "-3" ~ "<Missing>",
       ATOXGR == "-4" ~ "<Missing>",
     ))) %>%
-    var_relabel(
+    rcd_var_relabel(
       STUDYID = attr(adsl$STUDYID, "label"),
       USUBJID = attr(adsl$USUBJID, "label")
     )
@@ -294,7 +294,7 @@ radlb <- function(adsl,
   # merge grade_lookup onto adlb
   adlb <- dplyr::left_join(adlb, grade_lookup, by = "PARAMCD")
 
-  adlb <- var_relabel(
+  adlb <- rcd_var_relabel(
     adlb,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/radmh.R b/R/radmh.R
@@ -81,7 +81,7 @@ radmh <- function(adsl,
     `[`(c(4, 5, 1, 2, 3)) %>%
     dplyr::mutate(MHTERM = MHDECOD)
 
-  admh <- var_relabel(
+  admh <- rcd_var_relabel(
     admh,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/radqlqc.R b/R/radqlqc.R
@@ -111,14 +111,14 @@ radqlqc <- function(adsl,
     dplyr::mutate(PCHG2 = 100 * (CHG2 / BASE2)) %>%
     dplyr::mutate(CHG = AVAL - BASE) %>%
     dplyr::mutate(PCHG = 100 * (CHG / BASE)) %>%
-    var_relabel(
+    rcd_var_relabel(
       STUDYID = attr(adsl$STUDYID, "label"),
       USUBJID = attr(adsl$USUBJID, "label")
     )
   # derive CHGCAT1 ----------------------------------------------------------
   adqlqc_tmp <- derv_chgcat1(dataset = adqlqc_tmp)
 
-  adqlqc_tmp <- var_relabel(
+  adqlqc_tmp <- rcd_var_relabel(
     adqlqc_tmp,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/radqs.R b/R/radqs.R
@@ -128,12 +128,12 @@ radqs <- function(adsl,
     dplyr::mutate(PCHG2 = 100 * (CHG2 / BASE2)) %>%
     dplyr::mutate(CHG = AVAL - BASE) %>%
     dplyr::mutate(PCHG = 100 * (CHG / BASE)) %>%
-    var_relabel(
+    rcd_var_relabel(
       STUDYID = attr(adsl$STUDYID, "label"),
       USUBJID = attr(adsl$USUBJID, "label")
     )
 
-  adqs <- var_relabel(
+  adqs <- rcd_var_relabel(
     adqs,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/radrs.R b/R/radrs.R
@@ -145,12 +145,12 @@ radrs <- function(adsl,
     }) %>%
     Reduce(rbind, .) %>%
     dplyr::mutate(AVALC = factor(AVALC, levels = names(param_codes))) %>%
-    var_relabel(
+    rcd_var_relabel(
       STUDYID = "Study Identifier",
       USUBJID = "Unique Subject Identifier"
     )
 
-  adrs <- var_relabel(
+  adrs <- rcd_var_relabel(
     adrs,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/radsub.R b/R/radsub.R
@@ -143,7 +143,7 @@ radsub <- function(adsl,
 
   adsub <- adsub[order(adsub$STUDYID, adsub$USUBJID, adsub$PARAMCD), ]
 
-  adsub <- var_relabel(
+  adsub <- rcd_var_relabel(
     adsub,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/radtte.R b/R/radtte.R
@@ -105,7 +105,7 @@ radtte <- function(adsl,
         dplyr::select(-"LAMBDA", -"CNSR_P")
     }) %>%
     Reduce(rbind, .) %>%
-    var_relabel(
+    rcd_var_relabel(
       STUDYID = "Study Identifier",
       USUBJID = "Unique Subject Identifier" # )
     )
@@ -202,7 +202,7 @@ radtte <- function(adsl,
   adtte <- do.call("rbind", adtte_lst)
   rownames(adtte) <- NULL
 
-  adtte <- var_relabel(
+  adtte <- rcd_var_relabel(
     adtte,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/radvs.R b/R/radvs.R
@@ -184,12 +184,12 @@ radvs <- function(adsl,
     dplyr::ungroup() %>%
     dplyr::mutate(ATPTN = 1) %>%
     dplyr::mutate(DTYPE = NA) %>%
-    var_relabel(
+    rcd_var_relabel(
       USUBJID = attr(adsl$USUBJID, "label"),
       STUDYID = attr(adsl$STUDYID, "label")
     )
 
-  advs <- var_relabel(
+  advs <- rcd_var_relabel(
     advs,
     STUDYID = "Study Identifier",
     USUBJID = "Unique Subject Identifier"

diff --git a/R/utils.R b/R/utils.R
@@ -180,28 +180,32 @@ retain <- function(df, value_var, event, outside = NA) {
 
 #' Primary Keys: Labels
 #'
-#' Relabel a subset of variables in a data set.
+#' @description Shallow copy of `formatters::var_relabel()`. Used mainly internally to
+#'   relabel a subset of variables in a data set.
 #'
 #' @param x (`data.frame`)\cr Data frame containing variables to which labels are applied.
 #' @param ... (`named character`)\cr Name-Value pairs, where name corresponds to a variable
-#' name in `x` and the value to the new variable label.
+#'   name in `x` and the value to the new variable label.
 #' @return x (`data.frame`)\cr Data frame with labels applied.
 #'
-#' @export
-#'
-#' @examples
-#' adsl <- radsl()
-#' var_relabel(adsl,
-#'   STUDYID = "Study Identifier",
-#'   USUBJID = "Unique Subject Identifier"
-#' )
-var_relabel <- function(x, ...) {
+#' @keywords internal
+rcd_var_relabel <- function(x, ...) {
+  stopifnot(is.data.frame(x))
+  if (missing(...)) {
+    return(x)
+  }
   dots <- list(...)
   varnames <- names(dots)
   if (is.null(varnames)) {
     stop("missing variable declarations")
   }
-  map_varnames <- match(varnames, names(x))
+  map_varnames <- match(varnames, colnames(x))
+  if (any(is.na(map_varnames))) {
+    stop("variables: ", paste(varnames[is.na(map_varnames)], collapse = ", "), " not found")
+  }
+  if (any(vapply(dots, Negate(is.character), logical(1)))) {
+    stop("all variable labels must be of type character")
+  }
   for (i in seq_along(map_varnames)) {
     attr(x[[map_varnames[[i]]]], "label") <- dots[[i]]
   }

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -96,5 +96,5 @@ reference:
       - rtexp
       - rtpois
       - sample_fct
-      - var_relabel
+      - rcd_var_relabel
       - visit_schedule
diff --git a/man/random.cdisc.data-package.Rd b/man/random.cdisc.data-package.Rd
diff --git a/man/var_relabel.Rd → man/rcd_var_relabel.Rd b/man/var_relabel.Rd → man/rcd_var_relabel.Rd
diff --git a/random.cdisc.data.Rproj b/random.cdisc.data.Rproj
@@ -16,5 +16,6 @@ AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 
 BuildType: Package
+PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageRoxygenize: rd,collate,namespace
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
@@ -79,17 +79,17 @@ test_that("retain works as expected", {
   expect_equal(result, expected)
 })
 
-test_that("var_relabel works as expected", {
-  result <- random.cdisc.data:::var_relabel(
+test_that("rcd_var_relabel works as expected", {
+  result <- rcd_var_relabel(
     data.frame(letters = letters[1:5]),
     letters = "Letter Variable"
   )
   expect_identical(attr(result$letters, "label"), "Letter Variable")
 })
 
-test_that("var_relabel returns correct error message", {
+test_that("rcd_var_relabel returns correct error message", {
   expect_error(
-    random.cdisc.data:::var_relabel(
+    rcd_var_relabel(
       data.frame(letters = letters[1:5]),
       "Letter Variable"
     ), "missing variable declarations"