Read cohort from JSON

Read cohort from JSON

Usage

cohortFromJSON(pathToJSON, cdm, cohortId = NULL)

Arguments

pathToJSON

Path to the cohort data JSON file

cdm

Connection to the database (package CDMConnector)

cohortId

The id for cohort in cohorts' table, if NULL whole table will be imported

Value

a tbl object for further CohortContrast usage

Examples

if (requireNamespace("CDMConnector", quietly = TRUE) &&
    requireNamespace("DBI", quietly = TRUE) &&
    requireNamespace("duckdb", quietly = TRUE) &&
    nzchar(Sys.getenv("EUNOMIA_DATA_FOLDER")) &&
    isTRUE(tryCatch(
      CDMConnector::eunomiaIsAvailable("GiBleed"),
      error = function(...) FALSE
    ))) {
  pathToJSON <- system.file(
    "example", "example_json", "diclofenac",
    package = "CohortContrast"
  )
  con <- DBI::dbConnect(
    duckdb::duckdb(),
    dbdir = CDMConnector::eunomiaDir("GiBleed")
  )
  cdm <- CDMConnector::cdmFromCon(
    con = con,
    cdmName = "eunomia",
    cdmSchema = "main",
    writeSchema = "main"
  )

  targetTable <- cohortFromJSON(pathToJSON = pathToJSON, cdm = cdm)
  targetTable

  DBI::dbDisconnect(con, shutdown = TRUE)
}