Merge pull request #127 from Merck/126-release-metaliteae-011

address cran comments

.Rbuildignore

@@ -26,3 +26,4 @@
 ^metalite.ae\.Rcheck$
 ^metalite.ae.*\.tar\.gz$
 ^metalite.ae.*\.tgz$
+^cran-comments\.md$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metalite.ae
 Title: Adverse Events Analysis Using 'metalite'
-Version: 0.1.0
+Version: 0.1.1
 Authors@R: c(
     person("Yilong", "Zhang", role = c("aut")),
     person("Yujie", "Zhao", email = "[email protected]", role = c("aut", "cre")),
@@ -19,7 +19,7 @@ Description: Analyzes adverse events in clinical trials using the 'metalite'
     production-ready tables, listings, and figures discussed in the
     adverse events analysis chapters of
     "R for Clinical Study Reports and Submission"
-    (Zhang et al., 2022, <https://r4csr.org/>).
+    by Zhang et al. (2022) <https://r4csr.org/>.
 License: GPL-3
 URL: https://merck.github.io/metalite.ae/, https://github.com/Merck/metalite.ae
 BugReports: https://github.com/Merck/metalite.ae/issues

NEWS.md

@@ -1,3 +1,8 @@
+# metalite.ae 0.1.1
+
+- Updated the `DESCRIPTION` file to reformat the reference.
+- Uncommented the previously commented code example.
+
 # metalite.ae 0.1.0
 
 - Initial submission to CRAN.

R/meta_ae_example.R

@@ -111,7 +111,7 @@ meta_ae_example <- function() {
   )
 
   # Assign label
-  adae <- assign_label(adae,
+  adae <- metalite::assign_label(adae,
     var = c("related", "outcome", "duration", "AESEV", "AESER", "AEDECOD", "action_taken"),
     label = c("Related", "Outcome", "Duration", "Intensity", "Serious", "Adverse Event", "Action Taken")
   )

R/n_subject.R

@@ -77,12 +77,11 @@ n_subject <- function(id, group, par = NULL, use_na = c("ifany", "no", "always")
 #' @noRd
 #'
 #' @examples
-#' # library(r2rtf)
-#' #
-#' # r2rtf_adae$TRTA <- factor(r2rtf_adae$TRTA)
-#' #
-#' # metalite.ae:::avg_event(r2rtf_adae$USUBJID, r2rtf_adae$TRTA)
-#' # metalite.ae:::avg_event(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$AEDECOD)
+#' library(r2rtf)
+#'
+#' r2rtf_adae$TRTA <- factor(r2rtf_adae$TRTA)
+#' metalite.ae:::avg_event(r2rtf_adae$USUBJID, r2rtf_adae$TRTA)
+#' metalite.ae:::avg_event(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$AEDECOD)
 avg_event <- function(id, group, par = NULL) {
   if ("factor" %in% class(group)) {
     u_group <- as.character(levels(group))

R/prepare_ae_specific_subgroup.R

@@ -30,14 +30,15 @@
 #' @export
 #'
 #' @examples
-#' # meta <- meta_ae_example()
-#' # prepare_ae_specific_subgroup(
-#' #   meta,
-#' #   population = "apat",
-#' #   observation = "wk12",
-#' #   parameter = "rel",
-#' #   subgroup_var = "RACE"
-#' # )$data
+#' meta <- meta_ae_example()
+#'
+#' prepare_ae_specific_subgroup(
+#'   meta,
+#'   population = "apat",
+#'   observation = "wk12",
+#'   parameter = "rel",
+#'   subgroup_var = "RACE"
+#' )
 prepare_ae_specific_subgroup <- function(meta,
                                          population,
                                          observation,
@@ -47,7 +48,8 @@ prepare_ae_specific_subgroup <- function(meta,
                                          components = c("soc", "par"),
                                          display_total = TRUE,
                                          display_subgroup_total = TRUE) {
-  stop("This function is still under development.", call. = FALSE)
+  message("This function is still under development.")
+  return(invisible(NULL))
 
   if (!subgroup_header %in% c(1, 2)) {
     stop("`subgroup_header` can only have value 1 or 2.", call. = FALSE)

cran-comments.md

@@ -0,0 +1,6 @@
+## Resubmission
+
+This is a resubmission. In this version, I have fixed the issues identified in v0.1.0:
+
+* Uncommented the previously commented code example in `prepare_ae_specific_subgroup.Rd`.
+* Updated DESCRIPTION to format the reference as authors (year) <https:...>.