clinTrialData

clinTrialData is a community-grown library of clinical trial example datasets for R. The package ships with a core set of datasets and is designed to expand over time — anyone can contribute a new data source, and users can download any available study on demand without waiting for a new package release.

Data is stored in Parquet format and accessed through the connector package, giving a consistent API regardless of which study you are working with.

How the library grows

The core idea is simple: datasets live as assets on GitHub Releases, not inside the package itself. This means:

• Users can pull in any study with a single function call
• Contributors can add new datasets without a CRAN resubmission
• The library expands as the community adds more real-world clinical trial examples

# What's available to download from GitHub Releases?
list_available_studies()
#>                  source version size_mb cached
#> 1           cdisc_pilot  v0.1.0     3.7   TRUE
#> 2  cdisc_pilot_extended  v0.1.0     4.3  FALSE

# Inspect any study before downloading — fetches a tiny metadata file
dataset_info("cdisc_pilot_extended")
#> ──────────────────────────────────────────────────────────────────────────
#> cdisc_pilot_extended (v0.1.0)
#> ──────────────────────────────────────────────────────────────────────────
#> Enhanced CDISC Pilot 01 study with urinalysis data
#>
#> Domains & datasets:
#>   adam   (12): adsl, adae, adlb, adlbc, adlbh, adlbhy, adlburi, ...
#>   sdtm   (22): ae, cm, dm, ds, ex, lb, mh, qs, relrec, sc, ...
#>
#> Subjects:   254
#> Version:    v0.1.0
#> License:    CDISC Pilot — educational use
#> Source:     https://github.com/cdisc-org/sdtm-adam-pilot-project
#> ──────────────────────────────────────────────────────────────────────────

# Download once; cached locally from then on
download_study("cdisc_pilot_extended")

# Connect and analyse — same API for every study
db <- connect_clinical_data("cdisc_pilot_extended")
adsl <- db$adam$read_cnt("adsl")

Installation

# Install from CRAN
install.packages("clinTrialData")

# Or the development version from GitHub:
# install.packages("remotes")
remotes::install_github("Lovemore-Gakava/clinTrialData")

Quick Start

library(clinTrialData)

# What's already on your machine?
list_data_sources()

# What's available to download?
list_available_studies()

# Download a study (only needed once — cached locally after that)
download_study("cdisc_pilot")

# Connect and explore
db <- connect_clinical_data("cdisc_pilot")

db$adam$list_content_cnt()  # list ADaM datasets
db$sdtm$list_content_cnt()  # list SDTM datasets

adsl <- db$adam$read_cnt("adsl")
dm   <- db$sdtm$read_cnt("dm")

Available Data Sources

Bundled with the package

cdisc_pilot — Standard CDISC Pilot 01 study (11 ADaM, 22 SDTM datasets). Available immediately after installation, no download needed.

Available via GitHub Releases

cdisc_pilot_extended — Enhanced CDISC Pilot 01 study (11 ADaM, 24 SDTM datasets) with additional features:

• TRTDURY — Treatment duration in years
• ADLBURI — Urinalysis laboratory dataset
• ADLB — Combined labs including urinalysis

download_study("cdisc_pilot_extended")
connect_clinical_data("cdisc_pilot_extended")

Use list_data_sources() to see all locally available studies and list_available_studies() to see everything on GitHub Releases.

Contributing a New Data Source

Adding a new study to the library does not require a pull request or a CRAN submission. The data lives on GitHub Releases, not inside the package.

1. Prepare your data as Parquet files organised by domain (e.g. adam/, sdtm/):

your_study/
├── adam/
│   ├── adsl.parquet
│   └── adae.parquet
└── sdtm/
    ├── dm.parquet
    └── ae.parquet

2. Upload to a GitHub Release — open an issue on the repository to request a release slot, then use the helper script:

source("data-raw/upload_to_release.R")

# Upload the data zip
upload_study_to_release("your_study", tag = "v1.1.0")

# Generate and upload the metadata (enables dataset_info() for your study)
generate_and_upload_metadata(
  source      = "your_study",
  description = "Brief description of your study",
  version     = "v1.1.0",
  license     = "Your license here",
  source_url  = "https://link-to-original-data",
  tag         = "v1.1.0"
)

3. Users can inspect and access it immediately — no CRAN submission required:

dataset_info("your_study")      # inspect before downloading
download_study("your_study")    # download and cache
connect_clinical_data("your_study")

Data Protection

All datasets — whether bundled or downloaded — are automatically protected from accidental modification. Reading is always allowed; write and delete operations are blocked with a clear error message.

Data Attribution

The extended datasets are derived from the CDISC Pilot Study data.

Original Source: CDISC SDTM/ADaM Pilot Project

Modifications: This extended version includes additional derived variables (TRTDURY) and a simulated urinalysis dataset (ADLBURI) created for educational and development purposes.

Acknowledgments: We acknowledge and thank CDISC for making the original pilot data available. The extended datasets maintain the structure and quality of the original data while adding features to support additional analysis scenarios.

Documentation

# Browse all vignettes
vignette(package = "clinTrialData")

# Cache location
cache_dir()