cdmCommentContents: Insert Patient CDM Contents as Aligned Comments in RStudio

In CDMConnector: Connect to an OMOP Common Data Model

Insert Patient CDM Contents as Aligned Comments in RStudio

Description

This function retrieves the longitudinal event table for one or more persons in a CDM object and inserts it as a nicely formatted, R-style comment block directly into your active RStudio document. This is particularly useful for documenting reproducible test cases or examples by showing relevant CDM contents inline in test scripts or analysis code.

Usage

cdmCommentContents(cdm, personIds = NULL)

Arguments

cdm	A CDMConnector cdm_reference object.
personIds	Optional numeric vector of person IDs to filter the rows to include. If NULL (default), includes all persons in the cdm.

Details

Each row of patient data will be aligned in columns as a commented table, making it easy to copy, review, and maintain sample data expectations in documentation or test suites.

Requires an interactive RStudio session with the rstudioapi package available. The function utilizes CDMConnector::cdmFlatten() to extract a longitudinal view, and writes the commented results directly below the cursor in the active RStudio document.

This workflow is especially helpful when documenting expected patient timelines for use in testthat or other test scripts, or when sharing reproducible CDM content for instructional examples.

See Also

cdmFlatten

Examples

## Not run: 
library(CDMConnector)
con <- DBI::dbConnect(duckdb::duckdb(), eunomiaDir())
cdm <- cdmFromCon(con, "main", "main")
cdmCommentContents(cdm, personIds = 6)
# person_id | observation_concept_id | start_date | end_date   | type_concept_id...
# 6         | 40213296               | 2006-01-10 | 2006-01-10 | 581452         ...
# 6         | 40213227               | 2006-01-10 | 2006-01-10 | 581452         ...
# 6         | 1118084                | 2005-07-13 | 2005-07-13 | 38000177       ...
# 6         | 80180                  | 2005-07-13 | NA         | 32020          ...
cdmDisconnect(cdm)

## End(Not run)

CDMConnector documentation built on April 3, 2026, 9:09 a.m.