R: ctrdata: get started, database connection, function overview

ctrdata {ctrdata}

R Documentation

ctrdata: get started, database connection, function overview

Description

A package for aggregating and analysing information on clinical studies, and for obtaining documents, from public registers

1 - Database connection

Package ctrdata retrieves trial information and stores it in a database collection, which has to be given as a connection object to parameter con for several ctrdata functions; this connection object is created in almost identical ways for these supported backends:

Database	Connection object
MongoDB	`dbc <- nodbi::src_mongo(db = "my_db", collection = "my_coll")`
SQLite	`dbc <- nodbi::src_sqlite(dbname = "my_db", collection = "my_coll")`
PostgreSQL	`dbc <- nodbi::src_postgres(dbname = "my_db"); dbc[["collection"]] <- "my_coll"`
DuckDB	`dbc <- nodbi::src_duckdb(dbname = "my_db", collection = "my_coll")`

Use a connection object with a ctrdata function, for example dbQueryHistory, or other packages, for example mongolite::mongo or nodbi::docdb_query. Use a demo database: dbc <- nodbi::src_sqlite(dbname = system.file("extdata", "demo.sqlite", package = "ctrdata"), collection = "my_trials")

2 - Operate on a clinical trial register

ctrOpenSearchPagesInBrowser, ctrLoadQueryIntoDb (load trial records into database collection); see ctrdata-registers for details on registers and how to search.

3 - Get a data frame from the database collection

dbFindFields (find names of fields of interest in trial records in a collection), dbGetFieldsIntoDf (create a data frame with fields of interest from collection), dbFindIdsUniqueTrials (get de-duplicated identifiers of clinical trials' records that can be used to subset a data frame).

4 - Operate on a data frame with trial information

dfTrials2Long (convert fields with nested elements into long format), dfName2Value (get values for variable(s) of interest).

Author(s)

Ralf Herold ralf.herold@mailbox.org