Prepare for release

.Rbuildignore

@@ -7,3 +7,4 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^CRAN-SUBMISSION$

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.0.1
+Date: 2025-03-25 16:28:12 UTC
+SHA: 5604d351f4f9ba9555d221c81eb5c49da1654358

DESCRIPTION

@@ -1,21 +1,22 @@
 Package: meddra.read
-Title: Load and Merge MedDRA Data for Clinical Trials
-Version: 0.0.0.9000
+Title: Load and Use 'MedDRA' Data for Clinical Trials
+Version: 0.0.1
 Authors@R: 
     person("Bill", "Denney", email="wdenney@humanpredictions.com", role=c("aut", "cre"), comment=c(ORCID="0000-0002-5759-428X"))
 Description:
-    MedDRA data is used for defining adverse events in clinical studies.  You
+    'MedDRA' data is used for defining adverse events in clinical studies. You
     can load and merge the data for use in categorizing the adverse events
-    using this package.
+    using this package. The package requires the data licensed from 'MedDRA'
+    <https://www.meddra.org/>.
 License: MIT + file LICENSE
+Imports: 
+    dplyr
 Suggests: 
     spelling,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-Imports: 
-    dplyr
 URL: https://humanpred.github.io/meddra.read/
 Language: en-US

NEWS.md

@@ -0,0 +1,3 @@
+# meddra.read 0.0.1
+
+* Initial CRAN submission.

R/join_meddra.R

@@ -4,16 +4,19 @@
 #' @return A data.frame with the "soc_code", "soc_name", "soc_abbrev",
 #'   "hlgt_code", "hlgt_name", "hlt_code", "hlt_name", "pt_code", "pt_name",
 #'   "pt_soc_code", "llt_code", "llt_name", and "llt_currency"
+#' @examples
+#' \dontrun{
+#' meddra_raw <- read_meddra("/path/to/meddra/distribution")
+#' meddra_df <- join_meddra(meddra_raw)
+#' }
 #' @export
 join_meddra <- function(data) {
-  ret <-
-    data$soc.asc |>
-    dplyr::left_join(data$soc_hlgt.asc, by = "soc_code") |>
-    dplyr::left_join(data$hlgt.asc, by = "hlgt_code") |>
-    dplyr::left_join(data$hlgt_hlt.asc, by = "hlgt_code") |>
-    dplyr::left_join(data$hlt.asc, by = "hlt_code") |>
-    dplyr::left_join(data$hlt_pt.asc, by = "hlt_code") |>
-    dplyr::left_join(data$pt.asc, by = "pt_code") |>
-    dplyr::left_join(data$llt.asc, by = "pt_code")
+  ret <- dplyr::left_join(data$soc.asc, data$soc_hlgt.asc, by = "soc_code")
+  ret <- dplyr::left_join(ret, data$hlgt.asc, by = "hlgt_code")
+  ret <- dplyr::left_join(ret, data$hlgt_hlt.asc, by = "hlgt_code")
+  ret <- dplyr::left_join(ret, data$hlt.asc, by = "hlt_code")
+  ret <- dplyr::left_join(ret, data$hlt_pt.asc, by = "hlt_code")
+  ret <- dplyr::left_join(ret, data$pt.asc, by = "pt_code")
+  ret <- dplyr::left_join(ret, data$llt.asc, by = "pt_code")
   ret
 }

R/read_meddra.R

@@ -3,6 +3,10 @@
 #' @param directory the directory containing the MedAscii and SeqAscii
 #'   directories
 #' @return A list of data.frames for each file in the MedDRA source distribution
+#' @examples
+#' \dontrun{
+#' read_meddra("/path/to/meddra/distribution")
+#' }
 #' @export
 read_meddra <- function(directory) {
   dirs_available <- list.dirs(path = directory, full.names = FALSE)
@@ -21,7 +25,7 @@ read_meddra <- function(directory) {
 read_meddra_dir <- function(directory, extension) {
   files <- list.files(directory, full.names = TRUE, pattern = sprintf("\\.%s$", extension))
   stopifnot(length(files) > 0)
-  files <- setNames(files, tolower(basename(files)))[order(tolower(basename(files)))]
+  files <- stats::setNames(files, tolower(basename(files)))[order(tolower(basename(files)))]
   lapply(X = files, FUN = read_meddra_file)
 }
 
@@ -121,7 +125,7 @@ read_meddra_file <- function(filename) {
       ))
   } else {
     ret <-
-      read.delim(
+      utils::read.delim(
         # Some files (at least meddra_release.asc in version 28.0) are missing
         # newlines at the end, this suppresses a warning about that.
         text = file_text,

cran-comments.md

@@ -0,0 +1,14 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* From initial review: "Ideally, add small executable examples in your Rd-files
+  to illustrate the use of the exported function but also enable automatic
+  testing."
+    * Due to 'MedDRA' licensing restrictions, I cannot include any actual data
+      in the package or read it from a remote source. I have added "dontrun"
+      examples which I know are not preferred.
+    * For clarity, there are example files intended to test some of the oddities
+      of loading 'MedDRA' data, but they are not real data. And, I would prefer
+      not to point users to those files so that they are not confusing to the
+      user.