From c6122d0e9eaf2ac392c0ece51eac32e65c300c03 Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Sun, 23 Mar 2025 23:45:13 -0400 Subject: [PATCH 1/8] Prepare for release --- DESCRIPTION | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6494104..26df2cc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,12 +1,13 @@ 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 + . License: MIT + file LICENSE Suggests: spelling, From 99ddb1bfb727dfa1594f7f981a1e39ba72ec015e Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Sun, 23 Mar 2025 23:47:54 -0400 Subject: [PATCH 2/8] Prepare for release --- .Rbuildignore | 1 + CRAN-SUBMISSION | 3 +++ NEWS.md | 3 +++ 3 files changed, 7 insertions(+) create mode 100644 CRAN-SUBMISSION create mode 100644 NEWS.md diff --git a/.Rbuildignore b/.Rbuildignore index 6a3d6fc..f49378c 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -7,3 +7,4 @@ ^_pkgdown\.yml$ ^docs$ ^pkgdown$ +^CRAN-SUBMISSION$ diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 0000000..753cb66 --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 0.0.1 +Date: 2025-03-24 03:47:28 UTC +SHA: c6122d0e9eaf2ac392c0ece51eac32e65c300c03 diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..1c4549f --- /dev/null +++ b/NEWS.md @@ -0,0 +1,3 @@ +# meddra.read 0.0.1 + +* Initial CRAN submission. From 554303920a31106a4cea58a4ff4b635660ebe74b Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Mon, 24 Mar 2025 12:54:08 -0400 Subject: [PATCH 3/8] Fix CRAN NOTES --- R/join_meddra.R | 16 +++++++--------- R/read_meddra.R | 4 ++-- 2 files changed, 9 insertions(+), 11 deletions(-) diff --git a/R/join_meddra.R b/R/join_meddra.R index cb81026..0f40197 100644 --- a/R/join_meddra.R +++ b/R/join_meddra.R @@ -6,14 +6,12 @@ #' "pt_soc_code", "llt_code", "llt_name", and "llt_currency" #' @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 } diff --git a/R/read_meddra.R b/R/read_meddra.R index 51f656c..18c6dff 100644 --- a/R/read_meddra.R +++ b/R/read_meddra.R @@ -21,7 +21,7 @@ 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 +121,7 @@ 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, From 5ec5c801fa99f459976eb20cfe5ada79dd3a1146 Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Mon, 24 Mar 2025 13:35:32 -0400 Subject: [PATCH 4/8] Notes for CRAN --- cran-comments.md | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 cran-comments.md diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 0000000..ee988e8 --- /dev/null +++ b/cran-comments.md @@ -0,0 +1,5 @@ +## R CMD check results + +0 errors | 0 warnings | 1 note + +* Resolved NOTEs from initial submission From e8af33ecd38f3f168f388267a504890a94612b83 Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Mon, 24 Mar 2025 13:36:47 -0400 Subject: [PATCH 5/8] As submitted --- CRAN-SUBMISSION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 753cb66..07f954a 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ Version: 0.0.1 -Date: 2025-03-24 03:47:28 UTC -SHA: c6122d0e9eaf2ac392c0ece51eac32e65c300c03 +Date: 2025-03-24 17:36:24 UTC +SHA: 5ec5c801fa99f459976eb20cfe5ada79dd3a1146 From 9a59597a383ee4162c57784a28717f4b4a165b17 Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Tue, 25 Mar 2025 12:19:53 -0400 Subject: [PATCH 6/8] Respond to CRAN comments --- DESCRIPTION | 10 +++++----- R/join_meddra.R | 4 ++++ R/read_meddra.R | 4 ++++ cran-comments.md | 11 ++++++++++- man/join_meddra.Rd | 4 ++++ man/read_meddra.Rd | 5 +++++ 6 files changed, 32 insertions(+), 6 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 26df2cc..74868c2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,14 +1,16 @@ Package: meddra.read -Title: Load and Use MedDRA Data for Clinical Trials +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. The package requires the data licensed from MedDRA + using this package. The package requires the data licensed from 'MedDRA' . License: MIT + file LICENSE +Imports: + dplyr Suggests: spelling, testthat (>= 3.0.0) @@ -16,7 +18,5 @@ 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 diff --git a/R/join_meddra.R b/R/join_meddra.R index 0f40197..9361c4f 100644 --- a/R/join_meddra.R +++ b/R/join_meddra.R @@ -4,6 +4,10 @@ #' @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" +#' \dontrun{ +#' meddra_raw <- read_meddra("/path/to/meddra/distribution") +#' meddra_df <- join_meddra(meddra_raw) +#' } #' @export join_meddra <- function(data) { ret <- dplyr::left_join(data$soc.asc, data$soc_hlgt.asc, by = "soc_code") diff --git a/R/read_meddra.R b/R/read_meddra.R index 18c6dff..a5328c9 100644 --- a/R/read_meddra.R +++ b/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) diff --git a/cran-comments.md b/cran-comments.md index ee988e8..c0702a1 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -2,4 +2,13 @@ 0 errors | 0 warnings | 1 note -* Resolved NOTEs from initial submission +* 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. diff --git a/man/join_meddra.Rd b/man/join_meddra.Rd index 3da0b0d..be4ed8c 100644 --- a/man/join_meddra.Rd +++ b/man/join_meddra.Rd @@ -13,6 +13,10 @@ join_meddra(data) 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" +\dontrun{ +meddra_raw <- read_meddra("/path/to/meddra/distribution") +meddra_df <- join_meddra(meddra_raw) +} } \description{ Combine together all of the MedDRA terms into a single data.frame diff --git a/man/read_meddra.Rd b/man/read_meddra.Rd index 526e128..8762313 100644 --- a/man/read_meddra.Rd +++ b/man/read_meddra.Rd @@ -16,3 +16,8 @@ A list of data.frames for each file in the MedDRA source distribution \description{ Read MedDRA datasets from the source MedDRA datasets } +\examples{ +\dontrun{ +read_meddra("/path/to/meddra/distribution") +} +} From 5604d351f4f9ba9555d221c81eb5c49da1654358 Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Tue, 25 Mar 2025 12:23:19 -0400 Subject: [PATCH 7/8] Fix doc issue --- R/join_meddra.R | 1 + man/join_meddra.Rd | 8 +++++--- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/R/join_meddra.R b/R/join_meddra.R index 9361c4f..6575c9a 100644 --- a/R/join_meddra.R +++ b/R/join_meddra.R @@ -4,6 +4,7 @@ #' @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) diff --git a/man/join_meddra.Rd b/man/join_meddra.Rd index be4ed8c..a4a6fb7 100644 --- a/man/join_meddra.Rd +++ b/man/join_meddra.Rd @@ -13,11 +13,13 @@ join_meddra(data) 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" +} +\description{ +Combine together all of the MedDRA terms into a single data.frame +} +\examples{ \dontrun{ meddra_raw <- read_meddra("/path/to/meddra/distribution") meddra_df <- join_meddra(meddra_raw) } } -\description{ -Combine together all of the MedDRA terms into a single data.frame -} From b25f60f64436f93e09f0411bd0ca21124e774c3a Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Tue, 25 Mar 2025 12:28:39 -0400 Subject: [PATCH 8/8] As submitted --- CRAN-SUBMISSION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 07f954a..54e3517 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ Version: 0.0.1 -Date: 2025-03-24 17:36:24 UTC -SHA: 5ec5c801fa99f459976eb20cfe5ada79dd3a1146 +Date: 2025-03-25 16:28:12 UTC +SHA: 5604d351f4f9ba9555d221c81eb5c49da1654358