saveCohortDefinitionSet: Save the cohort definition set to the file system

In CohortGenerator: Cohort Generation for the OMOP Common Data Model

Save the cohort definition set to the file system

Description

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.

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