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.
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