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ctrdata on an R systemThe R Project website (https://www.r-project.org/) provides installers for the R system. It can be used with software products and graphical user interfaces such as R Studio, or from Visual Studio Code.
General information on the ctrdata package is available
here: https://rfhb.github.io/ctrdata/.
In R, execute:
For using the development version of package ctrdata,
install from GitHub:
# install package under development
install.packages(c("remotes"))
remotes::install_github("rfhb/ctrdata", dependencies = TRUE, build_vignettes = TRUE)Either of the above should install package ctrdata into
the user’s library.
At this time, a PostgreSQL, DuckDB, an SQLite or a MongoDB (local or
remote) database can be used with the package ctrdata. A
full SQLite database is provided in the R package RSQLite. Suggested
installation instructions for PostgreSQL are here and for a local
MongoDB server are here;
a remote MongoDB database server is accessible here. See here for a speed
comparison of the databases; recommended: DuckDB, PostgreSQL or MongoDB
local server.
| Purpose | Function call |
|---|---|
| Create SQLite database connection | dbc <- nodbi::src_sqlite(dbname = "name_of_my_database", collection = "name_of_my_collection") |
| Create DuckDB database connection | dbc <- nodbi::src_duckdb(dbname = "name_of_my_database", collection = "name_of_my_collection") |
| Create MongoDB database connection | dbc <- nodbi::src_mongo(db = "name_of_my_database", collection = "name_of_my_collection") |
| Create PostgreSQL database connection | dbc <- nodbi::src_postgres(dbname = "name_of_my_database"); dbc[["collection"]] <- "name_of_my_collection" |
Use connection with ctrdata functions |
ctrdata::{ctrLoadQueryIntoDb, dbQueryHistory, dbFindIdsUniqueTrials, dbFindFields, dbGetFieldsIntoDf}(con = dbc, ...) |
ctrdataAfter completing the installation, attach the package from the user’s library:
Remember to respect the registers’ terms and conditions (see
ctrOpenSearchPagesInBrowser(copyright = TRUE)).
ctrdataIn any publication, please cite this package as follows:
Herold R (2025). “Aggregating and analysing clinical trials data from
multiple public registers using R package ctrdata.” Research
Synthesis Methods, 1–33. doi:10.1017/rsm.2025.10061 https://doi.org/10.1017/rsm.2025.10061. or
Herold R
(2025). ctrdata: Retrieve and Analyze Clinical Trials Data from
Public Registers. R package version 1.25.1, https://cran.r-project.org/package=ctrdata.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.