ctrdata is a package for aggregating and analysing data on clinical
studies, and for obtaining documents, from public trial registers
1 - Database connection
Package ctrdata retrieves trial data and stores it in a database
collection. A database connection object has to be specified in
parameter con for several ctrdata functions.
The connection object is built using nodbi which allows to use
different database backends in an identical way.
Specifying a parameter collection = "<my collection's name>" is
necessary for package ctrdata.
| Database | Connection object |
| MongoDB | dbc <- nodbi::src_mongo(db = "my_db", collection = "my_coll") |
| DuckDB | dbc <- nodbi::src_duckdb(dbname = "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" |
2 - Operate on trial registers
ctrGenerateQueries (generate from simple user input specific queries for registers EUCTR, CTIS, CTGOV2 and ISRCTN), ctrOpenSearchPagesInBrowser (open queries in browser), see script (automatically copy user search in any register to clipboard), see ctrdata-registers for details on registers and how to search, ctrLoadQueryIntoDb (load trial records found with query into database collection).
3 - Get data frame from collection
ctrShowOneTrial (show widget to explore structure, fields and data of a trial), dbFindFields (find names of fields of interest in trial records in a collection), dbGetFieldsIntoDf (create a data frame with fields of interest and calculated trial concepts from collection), ctrdata-trial-concepts (calculate pre-defined trial concepts for every register), dbFindIdsUniqueTrials (get de-duplicated identifiers of clinical trials' records to subset a data frame).
4 - Operate on a trial data frame
dfTrials2Long (convert fields with nested elements into long format), dfName2Value (get values for variable(s) of interest), ctrdata-trial-concepts (calculate pre-defined trial concepts for every register).
Author
Ralf Herold ralf.herold@mailbox.org