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Closes #221: Feature request - Provide CSV files #228

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Merged
Lina2689 merged 14 commits into from
Mar 4, 2026
Merged

Closes #221: Feature request - Provide CSV files #228

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9c12f0c
add CSV generation in create_sdtms_data.R (inst/extdata folder)
Gero1999 Jan 31, 2026
92ee61f
add in .Rbuildignore CSV files
Gero1999 Jan 31, 2026
52375b3
bump pkg dev version & add news in documentation
Gero1999 Feb 5, 2026
dec79f1
readme: add CSV info for data & how-to-update sections
Gero1999 Feb 17, 2026
d3d2aa6
Update NEWS.md
Gero1999 Feb 18, 2026
d9cd254
Update README.md
Gero1999 Feb 18, 2026
4e1dbc0
readme: change links to https paths
Gero1999 Feb 18, 2026
f1bc35e
rm interactive data exploration (change from different branch)
Gero1999 Feb 18, 2026
ea90f97
spelling: update wordlist
Gero1999 Feb 18, 2026
88f53a7
Apply suggestions from code review Lina2689
Gero1999 Feb 27, 2026
f2b7cc6
change NEWS.md: extdata/sdtm-csv/ > inst/extdata
Gero1999 Feb 27, 2026
a4b1c42
Merge accept incoming or both changes
Gero1999 Feb 27, 2026
e1cef5c
bump version to 1.4.0.9002
Gero1999 Feb 27, 2026
8164c8a
Return pkg version from 1.4.0.9002 to 1.4.0.9001
Gero1999 Mar 2, 2026
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1 change: 1 addition & 0 deletions .Rbuildignore
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Expand Up @@ -20,6 +20,7 @@
^vignettes/adxx\.Rmd$
^vignettes/pharmaversesdtm\.Rmd$
^data-raw$
^inst/extdata/.*\.csv$
^CRAN-SUBMISSION$
^cran-comments\.md$
^.devcontainer$
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1 change: 1 addition & 0 deletions NEWS.md
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Expand Up @@ -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)
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@manciniedoardo manciniedoardo Mar 2, 2026

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This news item is not in line with the issue that this PR is tackling - is this intended?

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@Gero1999 Gero1999 Mar 2, 2026

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this one comes from main but I am not sure if to you is appearing as a PR change... here is for me when I review files changed:

image

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@manciniedoardo manciniedoardo Mar 2, 2026

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ah ok np then!


# pharmaversesdtm 1.4.0
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15 changes: 11 additions & 4 deletions README.md
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Expand Up @@ -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)

Expand All @@ -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`).
Expand Down Expand Up @@ -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.
Expand All @@ -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`.
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5 changes: 4 additions & 1 deletion data-raw/create_sdtms_data.R
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Expand Up @@ -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$")]
Expand Down Expand Up @@ -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)
}

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3 changes: 1 addition & 2 deletions inst/WORDLIST
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Expand Up @@ -74,7 +74,6 @@ ISTEST
ISTESTCD
Immunogenicity
Intraocular
JSON
Kangjie
Kumari
LAMZ
Expand Down Expand Up @@ -141,7 +140,6 @@ RECIST
RENALCL
RSTEST
RSTESTCD
Recode
Retinopathy
Rohan
SCTEST
Expand Down Expand Up @@ -214,6 +212,7 @@ ae
anonymized
anthropometric
antidrug
extdata
flavoured
funder
iRECIST
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1,192 changes: 1,192 additions & 0 deletions inst/extdata/ae.csv
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1,192 changes: 1,192 additions & 0 deletions inst/extdata/ae_ophtha.csv
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69 changes: 69 additions & 0 deletions inst/extdata/ag_neuro.csv
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@@ -0,0 +1,69 @@
"STUDYID","DOMAIN","USUBJID","AGSEQ","AGTRT","AGCAT","AGDOSE","AGDOSEU","AGROUTE","AGLNKID","VISITNUM","VISIT","AGSTDTC"
"CDISCPILOT01","AG","01-701-1015",1,"18F-Florbetaben","AMYLOID TRACER","300","MBq","Intravenous",2,3,"BASELINE","2014-01-02"
"CDISCPILOT01","AG","01-701-1015",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2013-12-29"
"CDISCPILOT01","AG","01-701-1015",3,"18F-Florbetaben","AMYLOID TRACER","300","MBq","Intravenous",5,9,"WEEK 12","2014-03-26"
"CDISCPILOT01","AG","01-701-1015",4,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",6,9,"WEEK 12","2014-03-28"
"CDISCPILOT01","AG","01-701-1015",5,"18F-Florbetaben","AMYLOID TRACER","300","MBq","Intravenous",8,13,"WEEK 26","2014-07-02"
"CDISCPILOT01","AG","01-701-1015",6,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",9,13,"WEEK 26","2014-06-28"
"CDISCPILOT01","AG","01-701-1023",1,"18F-Florbetaben","AMYLOID TRACER","300","MBq","Intravenous",2,3,"BASELINE","2012-08-05"
"CDISCPILOT01","AG","01-701-1023",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2012-08-03"
"CDISCPILOT01","AG","01-701-1028",1,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",1,3,"BASELINE","2013-07-19"
"CDISCPILOT01","AG","01-701-1028",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2013-07-15"
"CDISCPILOT01","AG","01-701-1028",3,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",4,9,"WEEK 12","2013-10-09"
"CDISCPILOT01","AG","01-701-1028",4,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",6,9,"WEEK 12","2013-10-06"
"CDISCPILOT01","AG","01-701-1028",5,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",7,13,"WEEK 26","2014-01-14"
"CDISCPILOT01","AG","01-701-1028",6,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",9,13,"WEEK 26","2014-01-17"
"CDISCPILOT01","AG","01-701-1034",1,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",1,3,"BASELINE","2014-07-01"
"CDISCPILOT01","AG","01-701-1034",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2014-06-27"
"CDISCPILOT01","AG","01-701-1034",3,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",4,9,"WEEK 12","2014-09-25"
"CDISCPILOT01","AG","01-701-1034",4,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",6,9,"WEEK 12","2014-09-21"
"CDISCPILOT01","AG","01-701-1034",5,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",7,13,"WEEK 26","2014-12-30"
"CDISCPILOT01","AG","01-701-1034",6,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",9,13,"WEEK 26","2014-12-28"
"CDISCPILOT01","AG","01-701-1146",1,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",1,3,"BASELINE","2013-05-20"
"CDISCPILOT01","AG","01-701-1146",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2013-05-16"
"CDISCPILOT01","AG","01-701-1153",1,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",1,3,"BASELINE","2013-09-23"
"CDISCPILOT01","AG","01-701-1153",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2013-09-20"
"CDISCPILOT01","AG","01-701-1153",3,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",4,9,"WEEK 12","2013-12-16"
"CDISCPILOT01","AG","01-701-1153",4,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",6,9,"WEEK 12","2013-12-18"
"CDISCPILOT01","AG","01-701-1153",5,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",7,13,"WEEK 26","2014-04-01"
"CDISCPILOT01","AG","01-701-1153",6,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",9,13,"WEEK 26","2014-04-04"
"CDISCPILOT01","AG","01-701-1181",1,"18F-Florbetaben","AMYLOID TRACER","300","MBq","Intravenous",2,3,"BASELINE","2013-12-05"
"CDISCPILOT01","AG","01-701-1181",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2013-12-02"
"CDISCPILOT01","AG","01-701-1234",1,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",1,3,"BASELINE","2013-03-30"
"CDISCPILOT01","AG","01-701-1234",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2013-03-26"
"CDISCPILOT01","AG","01-701-1234",3,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",4,9,"WEEK 12","2013-07-07"
"CDISCPILOT01","AG","01-701-1234",4,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",6,9,"WEEK 12","2013-07-11"
"CDISCPILOT01","AG","01-701-1234",5,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",7,13,"WEEK 26","2013-09-22"
"CDISCPILOT01","AG","01-701-1234",6,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",9,13,"WEEK 26","2013-09-20"
"CDISCPILOT01","AG","01-701-1275",1,"18F-Florbetaben","AMYLOID TRACER","300","MBq","Intravenous",2,3,"BASELINE","2014-02-07"
"CDISCPILOT01","AG","01-701-1275",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2014-02-03"
"CDISCPILOT01","AG","01-701-1275",3,"18F-Florbetaben","AMYLOID TRACER","300","MBq","Intravenous",5,9,"WEEK 12","2014-05-03"
"CDISCPILOT01","AG","01-701-1275",4,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",6,9,"WEEK 12","2014-04-29"
"CDISCPILOT01","AG","01-701-1302",1,"18F-Florbetaben","AMYLOID TRACER","300","MBq","Intravenous",2,3,"BASELINE","2013-08-29"
"CDISCPILOT01","AG","01-701-1302",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2013-08-26"
"CDISCPILOT01","AG","01-701-1302",3,"18F-Florbetaben","AMYLOID TRACER","300","MBq","Intravenous",5,9,"WEEK 12","2013-11-05"
"CDISCPILOT01","AG","01-701-1302",4,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",6,9,"WEEK 12","2013-11-09"
"CDISCPILOT01","AG","01-701-1345",1,"18F-Florbetaben","AMYLOID TRACER","300","MBq","Intravenous",2,3,"BASELINE","2013-10-08"
"CDISCPILOT01","AG","01-701-1345",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2013-10-06"
"CDISCPILOT01","AG","01-701-1345",3,"18F-Florbetaben","AMYLOID TRACER","300","MBq","Intravenous",5,9,"WEEK 12","2013-12-31"
"CDISCPILOT01","AG","01-701-1345",4,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",6,9,"WEEK 12","2013-12-28"
"CDISCPILOT01","AG","01-701-1360",1,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",1,3,"BASELINE","2013-07-31"
"CDISCPILOT01","AG","01-701-1360",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2013-07-28"
"CDISCPILOT01","AG","01-701-1383",1,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",1,3,"BASELINE","2013-02-04"
"CDISCPILOT01","AG","01-701-1383",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2013-02-02"
"CDISCPILOT01","AG","01-701-1383",3,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",4,9,"WEEK 12","2013-04-30"
"CDISCPILOT01","AG","01-701-1383",4,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",6,9,"WEEK 12","2013-04-28"
"CDISCPILOT01","AG","01-701-1383",5,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",7,13,"WEEK 26","2013-08-06"
"CDISCPILOT01","AG","01-701-1383",6,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",9,13,"WEEK 26","2013-08-02"
"CDISCPILOT01","AG","01-701-1392",1,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",1,3,"BASELINE","2012-10-28"
"CDISCPILOT01","AG","01-701-1392",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2012-10-24"
"CDISCPILOT01","AG","01-701-1392",3,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",4,9,"WEEK 12","2013-01-20"
"CDISCPILOT01","AG","01-701-1392",4,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",6,9,"WEEK 12","2013-01-17"
"CDISCPILOT01","AG","01-701-1392",5,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",7,13,"WEEK 26","2013-04-28"
"CDISCPILOT01","AG","01-701-1392",6,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",9,13,"WEEK 26","2013-05-02"
"CDISCPILOT01","AG","01-714-1288",1,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",1,3,"BASELINE","2013-12-04"
"CDISCPILOT01","AG","01-714-1288",2,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",3,3,"BASELINE","2013-12-02"
"CDISCPILOT01","AG","01-714-1288",3,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",4,9,"WEEK 12","2014-03-02"
"CDISCPILOT01","AG","01-714-1288",4,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",6,9,"WEEK 12","2014-03-04"
"CDISCPILOT01","AG","01-714-1288",5,"18F-Florbetapir","AMYLOID TRACER","370","MBq","Intravenous",7,13,"WEEK 26","2014-06-17"
"CDISCPILOT01","AG","01-714-1288",6,"18F-Flortaucipir","TAU TRACER","370","MBq","Intravenous",9,13,"WEEK 26","2014-06-20"
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