README.md

In rfhb/ctrdata: Retrieve and Analyze Clinical Trials in Public Registers

Main features • Installation • Overview • Databases • Data model • Example workflow • Analysis across trials • Tests • Acknowledgements • Future

ctrdata for aggregating and analysing clinical trials

The package ctrdata provides functions for retrieving (downloading) information on clinical trials from public registers, and for aggregating and analysing this information; it can be used for the

• EU Clinical Trials Register (“EUCTR”, https://www.clinicaltrialsregister.eu/)
• EU Clinical Trials Information System (“CTIS”, https://euclinicaltrials.eu/, see example)
• ClinicalTrials.gov (“CTGOV” classic and the 2023 “CTGOV2”, see example)
• ISRCTN Registry (https://www.isrctn.com/)

The motivation is to investigate and understand trends in design and conduct of trials, their availability for patients and to facilitate using their detailed results for research and meta-analyses. ctrdata is a package for the R system, but other systems and tools can be used with the databases created with the package. This README was reviewed on 2024-02-13 for version 1.17.1 (major improvement: removed external dependencies; refactored dbGetFieldsIntoDf()).

Main features

• Protocol- and results-related trial information is easily downloaded: Users define a query in a register’s web interface, then copy the URL and enter it into ctrdata which retrieves in one go all trials found. A script can automate copying the query URL from all registers. Personal annotations can be made when downloading trials. Also, trial documents available in registers on trials can be downloaded.
• Downloaded trial information is transformed and stored in a collection of a document-centric database, for fast and offline access. Information from different registers can be accumulated in a single collection. Uses DuckDB, PostgreSQL, RSQLite or MongoDB, via R package nodbi: see section Databases below. Easily re-run any previous query in a collection to retrieve and update trial records.
• For analyses, convenience functions in ctrdata allow find synonyms of an active substance, to identify unique (de-duplicated) trial records across all registers, to merge and recode fields as well as to easily access deeply-nested fields. Analysis can be done with R (see vignette) or other systems, using the JSON-structured information in the database.

Remember to respect the registers’ terms and conditions (see ctrOpenSearchPagesInBrowser(copyright = TRUE)). Please cite this package in any publication as follows: “Ralf Herold (2024). ctrdata: Retrieve and Analyze Clinical Trials in Public Registers. R package version 1.17.1, https://cran.r-project.org/package=ctrdata”.

rfhb/ctrdata documentation built on Feb. 28, 2024, 3:22 p.m.