Closes #221: Feature request - Provide CSV files

.Rbuildignore

@@ -20,6 +20,7 @@
 ^vignettes/adxx\.Rmd$
 ^vignettes/pharmaversesdtm\.Rmd$
 ^data-raw$
+^inst/extdata/.*\.csv$
 ^CRAN-SUBMISSION$
 ^cran-comments\.md$
 ^.devcontainer$

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: pharmaversesdtm
 Title: SDTM Test Data for the 'Pharmaverse' Family of Packages
-Version: 1.4.0.9001
+Version: 1.4.0.9002
 Authors@R: c(
     person("Lina", "Patil", , "lina.patil@cytel.com", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut",

NEWS.md

@@ -2,6 +2,7 @@
 
 ## Documentation
 
+- Included CSV versions of all SDTM data under `inst/extdata` for ease of use of non R programmers. (#221)
 - Added a new vignette "Datasets Preview" to preview all datasets included in the package. (#146)
 
 # pharmaversesdtm 1.4.0

README.md

@@ -13,7 +13,7 @@ Test data (SDTM) for the pharmaverse family of packages
 
 -   [Purpose](#purpose)
 -   [Installation](#installation)
--   [Data Sources](#data-sources)
+-   [Data](#data)
 -   [Naming Conventions](#naming)
 -   [How To Update](#how-to-update)
 
@@ -33,10 +33,17 @@ if (!requireNamespace("remotes", quietly = TRUE)) {
 remotes::install_github("pharmaverse/pharmaversesdtm", ref = "main") # This command installs the latest development version directly from GitHub.
 ```
 
-## Data Sources {#data-sources}
+
+## Data {#data}
+
+### Data Sources
 
 Some test datasets have been sourced from the [CDISC pilot project](https://github.com/cdisc-org/sdtm-adam-pilot-project), while other datasets have been constructed ad-hoc by the {admiral} team. Please check the [Reference page](https://pharmaverse.github.io/pharmaversesdtm/reference/index.html) for detailed information regarding the source of specific datasets.
 
+### Data Formats
+
+Each dataset is provided in both RDA and CSV formats. The `.rda` files are used within the R package and saved in the [data](https://github.com/pharmaverse/pharmaversesdtm/tree/main/data) folder, while the `.csv` files are saved in the [inst/extdata/](https://github.com/pharmaverse/pharmaversesdtm/tree/main/inst/extdata) folder.
+
 ## Naming Conventions {#naming}
 
 -   Datasets that are TA-agnostic: same as SDTM domain name (e.g., `dm`, `rs`).
@@ -80,7 +87,7 @@ This metadata drives the automated documentation process, and the file is read b
 
 ### Adding New SDTM Datasets
 
--   Create a program in the `data-raw/` folder, named `<name>.R`, where `<name>` should follow the [naming convention](#naming), to generate the test data and output `<name>.rda` to the `data/` folder.
+-   Create a program in the `data-raw/` folder, named `<name>.R`, where `<name>` should follow the [naming convention](#naming), to generate the test data and output `<name>.rda` to the `data/` folder, and the `<name>.csv` to the `inst/extdata` folder.
     -   Use CDISC pilot data such as `dm` as input in this program in order to create realistic synthetic data that remains consistent with other domains (not mandatory).
     -   Note that **no personal data should be used** as part of this package, even if anonymized.
 -   Run the program.
@@ -99,7 +106,7 @@ This metadata drives the automated documentation process, and the file is read b
     -   Modifying the dataset purpose or structure.
     -   Updating the dataset therapeutic area.
     -   Removing a dataset (delete its entry from the JSON entirely).
--   Run the program, and output updated `<name>.rda` to the `data/` folder.
+-   Run the program, and output updated `<name>.rda` to the `data/` folder, and the `<name>.csv` to the `inst/extdata` folder. 
 -   Run `data-raw/create_sdtms_data.R` in order to update `NAMESPACE` and update the `.Rd` files in `man/`.
 -   Add your GitHub handle to `.github/CODEOWNERS`.
 -   Update `NEWS.md`.

data-raw/create_sdtms_data.R

@@ -146,6 +146,9 @@ for (dataset_name in datasets) {
   dataset <- get(dataset_name)
   metadata <- specs[specs$name == dataset_name, ]
 
+  # For each dataset, save a CSV version in inst/extdata/
+  write.csv(dataset, file = file.path("inst/extdata/", paste0(dataset_name, ".csv")), row.names = FALSE)
+
   # Add Test Codes and Test Names details in a table
   # Identify column names ending in TEST and TESTCD
   test_col <- names(dataset)[str_detect(string = names(dataset), pattern = "TEST$")]
@@ -201,7 +204,7 @@ for (dataset_name in datasets) {
     # Add Therapeutic area keyword to the dataset name
     dataset_keyword <- get_dataset_keyword(dataset_name, specs)
   }
-
+  # Write the R documentation
   write_doc(dataset, dataset_name, dataset_label, dataset_description, dataset_author, dataset_source, dataset_testnames, dataset_keyword)
 }
 

inst/WORDLIST

@@ -74,7 +74,6 @@ ISTEST
 ISTESTCD
 Immunogenicity
 Intraocular
-JSON
 Kangjie
 Kumari
 LAMZ
@@ -141,7 +140,6 @@ RECIST
 RENALCL
 RSTEST
 RSTESTCD
-Recode
 Retinopathy
 Rohan
 SCTEST
@@ -214,6 +212,7 @@ ae
 anonymized
 anthropometric
 antidrug
+extdata
 flavoured
 funder
 iRECIST