Replace base messages with rlang and cli

NAMESPACE

@@ -1,7 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(ctl_new_rowid_pillar,cnd_df)
-S3method(mutate,cnd_df)
 S3method(print,iso8601)
 S3method(tbl_sum,cnd_df)
 export("%.>%")

R/cnd_df.R

@@ -340,7 +340,7 @@ condition_add <- function(dat, ..., .na = NA, .dat2 = rlang::env()) {
 #'
 #' @inheritParams dplyr::mutate
 #' @importFrom dplyr mutate
-#' @export
+#' @keywords internal
 mutate.cnd_df <- function(.data,
                           ...,
                           .by = NULL,

R/ct.R

@@ -278,7 +278,7 @@ ct_map <-
 #' read_ct_spec(file = path)
 #'
 #' @export
-read_ct_spec <- function(file = stop("`file` must be specified")) {
+read_ct_spec <- function(file = rlang::abort("`file` must be specified")) {
   ct_spec <- utils::read.csv(file = file, na.strings = c("NA", ""), colClasses = "character") |>
     tibble::as_tibble()
   assert_ct_spec(ct_spec)
@@ -327,12 +327,7 @@ ct_spec_example <- function(example) {
   local_path <- system.file(path, package = "sdtm.oak")
 
   if (identical(local_path, "")) {
-    stop(
-      stringr::str_glue(
-        "'{example}' does not match any ct spec files. Run `ct_spec_example()` for options."
-      ),
-      call. = FALSE
-    )
+    cli::cli_abort("'{example}' does not match any ct spec files. Run `ct_spec_example()` for options.", call = NULL)
   } else {
     local_path <-
       system.file(path, package = "sdtm.oak", mustWork = TRUE)

R/derive_blfl.R

@@ -345,7 +345,7 @@ derive_blfl <- function(sdtm_in,
     ))
 
   if (nrow(ds_mod) == 0L) {
-    stop(paste0(
+    rlang::abort(paste0(
       "No rows for which both --ORRES is not missing\n  and --STAT not equals to NOT DONE.\n",
       "  Not able to derive Baseline Flag or Last Observation Before Exposure Flag"
     ))
@@ -428,7 +428,7 @@ derive_blfl <- function(sdtm_in,
   ds_base <- dplyr::arrange_at(ds_base, c("USUBJID", con_col))
 
   if (nrow(ds_base) == 0L) {
-    message(paste0("There are no baseline records."))
+    rlang::inform("There are no baseline records.")
   }
 
   # Group by USUBJID and --TESTCD and filter on the rows that have max value
@@ -466,12 +466,10 @@ derive_blfl <- function(sdtm_in,
 
   # Assert that merged data frame has same number of rows as input data frame
   if (nrow(ds_out) != nrow(sdtm_in)) {
-    stop(sprintf(
+    cli::cli_abort(
       "Internal error: The processed dataset was expected to have the same
-      number of rows (%d) as the input dataset (sdtm_in), but it actually has %d rows.",
-      nrow(sdtm_in),
-      nrow(ds_out)
-    ))
+      number of rows ({nrow(sdtm_in)}) as the input dataset (sdtm_in), but it actually has {nrow(ds_out)} rows."
+    )
   }
 
   return(ds_out)

R/derive_study_day.R

@@ -62,9 +62,11 @@ derive_study_day <- function(sdtm_in,
   assertthat::assert_that(is.character(study_day_var))
   # check tgdt and study_day_var matching, for example, CMSTDTC matches CMSTDY
   if (gsub("DTC", "", tgdt, fixed = TRUE) != gsub("DY", "", study_day_var, fixed = TRUE)) {
-    warning(
-      "Target date and the returned study day doesn't match. ",
-      "Expecting matching date and study day, for example, CMENDTC and CMENDY"
+    rlang::warn(
+      paste(
+        "Target date and the returned study day doesn't match.",
+        "Expecting matching date and study day, for example, CMENDTC and CMENDY"
+      )
     )
   }
 
@@ -77,10 +79,12 @@ derive_study_day <- function(sdtm_in,
       dplyr::group_by(dplyr::pick({{ merge_key }})) |>
       dplyr::filter(dplyr::n() > 1L)
     if (nrow(check_refdt_uniqueness) > 0L) {
-      warning(
-        "Reference date is not unique for each patient! ",
-        "Patient without unique reference date will be ingored. ",
-        "NA will be returned for such records."
+      rlang::warn(
+        paste(
+          "Reference date is not unique for each patient!",
+          "Patient without unique reference date will be ingored.",
+          "NA will be returned for such records."
+        )
       )
       dm_domain <- dm_domain[
         !dm_domain[[merge_key]] %in% check_refdt_uniqueness[[merge_key]],
@@ -102,23 +106,27 @@ derive_study_day <- function(sdtm_in,
   sdtm_in[[refdt]] <- tryCatch(
     as.Date(sdtm_in[[refdt]], "%Y-%m-%d"),
     error = function(e) {
-      warning(
-        "Encountered errors when converting refdt to dates. ",
-        "The warning message is ",
-        e$message,
-        call. = FALSE
+      rlang::warn(
+        paste(
+          "Encountered errors when converting refdt to dates.",
+          "The warning message is",
+          e$message
+        ),
+        call = NULL
       )
       sdtm_in[[refdt]]
     }
   )
   sdtm_in[[tgdt]] <- tryCatch(
     as.Date(sdtm_in[[tgdt]], "%Y-%m-%d"),
     error = function(e) {
-      warning(
-        "Encountered errors when converting tgdt to dates. ",
-        "The warning message is ",
-        e$message,
-        call. = FALSE
+      rlang::warn(
+        paste(
+          "Encountered errors when converting tgdt to dates.",
+          "The warning message is",
+          e$message
+        ),
+        call = NULL
       )
       sdtm_in[[tgdt]]
     }

R/domain_example.R

@@ -79,11 +79,9 @@ domain_example <- function(example) {
   local_path <- system.file(path, package = "sdtm.oak")
 
   if (identical(local_path, "")) {
-    stop(
-      stringr::str_glue(
-        "'{example}' does not match any domain example files. Run `domain_example()` for options."
-      ),
-      call. = FALSE
+    cli::cli_abort(
+      "'{example}' does not match any domain example files. Run `domain_example()` for options.",
+      call = NULL
     )
   } else {
     local_path <-

vignettes/articles/cnd_df.Rmd → vignettes/cnd_df.Rmd

@@ -1,5 +1,11 @@
 ---
 title: "Conditioned Data Frames"
+output: 
+  rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Conditioned Data Frames}
+  %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
 ---
 
 ```{r setup, include=FALSE}

vignettes/articles/iso_8601.Rmd → vignettes/iso_8601.Rmd

@@ -1,5 +1,11 @@
 ---
 title: "Converting dates, times or date-times to ISO 8601"
+output: 
+  rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Converting dates, times or date-times to ISO 8601}
+  %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
 ---
 
 ```{r, include = FALSE}