ctrdata

<code>ctrdata</code> is a package for aggregating and analysing data on clinical
studies, and for obtaining documents, from public trial registers

package

A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Protocols, statistical analysis plans, informed consent sheets and other
documents in registers associated with trials can also be downloaded.
Other functions implement trial concepts canonically across registers,
identify deduplicated records, easily find and extract variables
(fields) of interest even from complex nested data as used by the
registers, merge variables and update queries.
The package can be used for monitoring, meta- and trend-analysis of
the design and conduct as well as of the results of clinical trials
across registers.

Ralf Herold

Retrieve and Analyze Clinical Trials Data from Public Registers

ctrdata function

Package <code>ctrdata</code> retrieves trial data and stores it in a database
collection. The connection is specified using <code>nodbi</code>, which allows to
use different database backends in an identical way.
A database connection object is specified once and then can be used as
parameter <code>con</code> in subsequent calls of <code>ctrdata</code> functions.
Specifying <code>collection = "&lt;my trial data collection's name&gt;"</code>
indicates the table in the database that package <code>ctrdata</code> should use.<table class="table">
<tr><td>Database</td><td>Connection object</td></tr>
<tr><td>SQLite</td><td><code>dbc &lt;- nodbi::src_sqlite(dbname = "my_db", collection = "my_coll")</code></td></tr>
<tr><td>DuckDB</td><td><code>dbc &lt;- nodbi::src_duckdb(dbname = "my_db", collection = "my_coll")</code></td></tr>
<tr><td>MongoDB</td><td><code>dbc &lt;- nodbi::src_mongo(db = "my_db", collection = "my_coll")</code></td></tr>
<tr><td>PostgreSQL</td><td><code>dbc &lt;- nodbi::src_postgres(dbname = "my_db"); dbc[["collection"]] &lt;- "my_coll"</code></td></tr>
</table>

1 - Define a database connection

ctrGenerateQueries (generate from simple user input specific queries
for registers EUCTR, CTIS, CTGOV2 and ISRCTN),
ctrOpenSearchPagesInBrowser (open queries in browser),
see <a href="https://raw.githubusercontent.com/rfhb/ctrdata/master/tools/ctrdataURLcopier.js">script</a>
(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).

2 - Load information from clinical trial registers

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).

3 - Use database with downloaded trial information

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).

4 - Operate on a trial data frame from dbGetFieldsIntoDf

Ralf Herold <a href="/link/ralf.herold%40mailbox.org?package=ctrdata&version=1.23.0" data-mini-rdoc="ctrdata::ralf.herold@mailbox.org">ralf.herold@mailbox.org</a>

Author

Getting started, database connection, function overview — ctrdata

Package <code>ctrdata</code> retrieves trial data and stores it in a database
collection. The connection is specified using <code>nodbi</code>, which allows to
use different database backends in an identical way.
A database connection object is specified once and then can be used as
parameter <code>con</code> in subsequent calls of <code>ctrdata</code> functions.
Specifying <code>collection = "&lt;my trial data collection's name&gt;"</code>
indicates the table in the database that package <code>ctrdata</code> should use.<table class='table'>
<tr><td>Database</td><td>Connection object</td></tr>
<tr><td>SQLite</td><td><code>dbc &lt;- nodbi::src_sqlite(dbname = "my_db", collection = "my_coll")</code></td></tr>
<tr><td>DuckDB</td><td><code>dbc &lt;- nodbi::src_duckdb(dbname = "my_db", collection = "my_coll")</code></td></tr>
<tr><td>MongoDB</td><td><code>dbc &lt;- nodbi::src_mongo(db = "my_db", collection = "my_coll")</code></td></tr>
<tr><td>PostgreSQL</td><td><code>dbc &lt;- nodbi::src_postgres(dbname = "my_db"); dbc[["collection"]] &lt;- "my_coll"</code></td></tr>
</table>

ctrGenerateQueries (generate from simple user input specific queries
for registers EUCTR, CTIS, CTGOV2 and ISRCTN),
ctrOpenSearchPagesInBrowser (open queries in browser),
see <a href='https://raw.githubusercontent.com/rfhb/ctrdata/master/tools/ctrdataURLcopier.js'>script</a>
(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).

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).

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).

Ralf Herold <a href='mailto:ralf.herold@mailbox.org'>ralf.herold@mailbox.org</a>

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

ctrdata: Getting started, database connection, function overview

Description

Arguments

1 - Define a database connection

2 - Load information from clinical trial registers

3 - Use database with downloaded trial information

4 - Operate on a trial data frame from dbGetFieldsIntoDf

Author

See Also