getCohortDefinitionSet: Get a cohort definition set

In CohortGenerator: Cohort Generation for the OMOP Common Data Model

Get a cohort definition set

Description

This function supports the legacy way of retrieving a cohort definition set from the file system or in a package. This function supports the legacy way of storing a cohort definition set in a package with a CSV file, JSON files, and SQL files in the 'inst' folder.

Usage

getCohortDefinitionSet(
  settingsFileName = "Cohorts.csv",
  jsonFolder = "cohorts",
  sqlFolder = "sql/sql_server",
  cohortFileNameFormat = "%s",
  cohortFileNameValue = c("cohortId"),
  subsetJsonFolder = "inst/cohort_subset_definitions/",
  packageName = NULL,
  warnOnMissingJson = TRUE,
  verbose = FALSE
)

Arguments

settingsFileName	The name of the CSV file that will hold the cohort information including the cohortId and cohortName
jsonFolder	The name of the folder that will hold the JSON representation of the cohort if it is available in the cohortDefinitionSet
sqlFolder	The name of the folder that will hold the SQL representation of the cohort.
cohortFileNameFormat	Defines the format string for naming the cohort JSON and SQL files. The format string follows the standard defined in the base sprintf function.
cohortFileNameValue	Defines the columns in the cohortDefinitionSet to use in conjunction with the cohortFileNameFormat parameter.
subsetJsonFolder	Defines the folder to store the subset JSON
packageName	The name of the package containing the cohort definitions.
warnOnMissingJson	Provide a warning if a .JSON file is not found for a cohort in the settings file
verbose	When TRUE, extra logging messages are emitted

Value

Returns a cohort set data.frame

CohortGenerator documentation built on Oct. 1, 2024, 1:09 a.m.