Check source codes used in a cohort definition

Source: R/CohortSourceCodeCheck.R

This function first extracts all concept sets used in a cohort definition. Then, for each concept set the concept found in the CDM database the contributing source codes are identified. OVerall and per month counts are computed and shown for all concept sets, concepts, and source codes in a HTML table.

This function requires the rmarkdown package as well as PanDoc.

checkCohortSourceCodes(connectionDetails, cdmDatabaseSchema,
  oracleTempSchema = NULL, cohortJson, cohortSql, outputFile)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package.
cdmDatabaseSchema

Schema name where your patient-level data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
oracleTempSchema

Should be used in Oracle to specify a schema where the user has write priviliges for storing temporary tables.
cohortJson

A characteric string containing the JSON of a cohort definition.
cohortSql

The OHDSI SQL representation of the same cohort definition.
outputFile

The name of the HTML file to create.