Insert a set of cohort definitions into package

insertCohortDefinitionSetInPackage(
  fileName = "inst/settings/CohortsToCreate.csv",
  baseUrl,
  jsonFolder = "inst/cohorts",
  sqlFolder = "inst/sql/sql_server",
  rFileName = "R/CreateCohorts.R",
  insertTableSql = TRUE,
  insertCohortCreationR = TRUE,
  generateStats = FALSE,
  packageName
)

Arguments

fileName: Name of a CSV file specifying the cohorts to insert. See details for the expected file format.
baseUrl: The base URL for the WebApi instance, for example: "http://server.org:80/WebAPI".
jsonFolder: Path to the folder where the JSON representations will be saved.
sqlFolder: Path to the folder where the SQL representations will be saved.
rFileName: Name of R file to generate when insertCohortCreationR = TRUE.
insertTableSql: Should the SQL for creating the cohort table be inserted into the package as well? This file will be called CreateCohortTable.sql.
insertCohortCreationR: Insert R code that will create the cohort table and instantiate the cohorts? This will create a file called R/CreateCohorts.R containing a function called .createCohorts.
generateStats: Should cohort inclusion rule statistics be created?
packageName: The name of the package (only needed when inserting the R code as well).

Details

The CSV file should have at least the following fields:

atlasId: The cohort ID in ATLAS.
cohortId: The cohort ID that will be used when instantiating the cohort (can be different from atlasId).
name: The name to be used for the cohort. This name will be used to generate file names, so please use letters and numbers only (no spaces).