Save the cohort definition set to the file system

This function saves a cohortDefinitionSet to the file system and provides options for specifying where to write the individual elements: the settings file will contain the cohort information as a CSV specified by the settingsFileName, the cohort JSON is written to the jsonFolder and the SQL is written to the sqlFolder. We also provide a way to specify the json/sql file name format using the cohortFileNameFormat and cohortFileNameValue parameters.

Usage

saveCohortDefinitionSet(
  cohortDefinitionSet,
  settingsFileName = "inst/Cohorts.csv",
  jsonFolder = "inst/cohorts",
  sqlFolder = "inst/sql/sql_server",
  cohortFileNameFormat = "%s",
  cohortFileNameValue = c("cohortId"),
  subsetJsonFolder = "inst/cohort_subset_definitions/",
  verbose = FALSE
)

Arguments

cohortDefinitionSet

The cohortDefinitionSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

sql

The OHDSI-SQL used to generate the cohort

Optionally, this data frame may contain:

json

The Circe JSON representation of the cohort

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

verbose

When TRUE, logging messages are emitted to indicate export progress.