inst/template/Package/extras/getIncidenceRateDataUsingCohortDiagnostics.R

In gowthamrao/StudyManagement: An OHDSI R package to conduct reproducible research.

z <- 0
incidenceRate <- list()
# get incidence rate data using Cohort Diagnostics package
for (i in (1:length(cohortIds))) {
  for (j in (1:length(cdmSources$cdmDatabaseSchema))) {

    cdmDatabaseSchema <- cdmSources$cdmDatabaseSchema[[j]]
    resultsDatabaseSchema <- cdmSources$resultsDatabaseSchema[[j]]
    cohortId <- cohortIds[[i]]
    cohortTable <- 'cohort'

    connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,
                                                                    server = server,
                                                                    port = port,
                                                                    schema = cdmDatabaseSchema)


    result <-
      CohortDiagnostics::getIncidenceRate(
        connectionDetails = connectionDetails,
        connection = DatabaseConnector::connect(connectionDetails),
        cohortDatabaseSchema = resultsDatabaseSchema,
        cohortTable = cohortTable,
        cdmDatabaseSchema = cdmDatabaseSchema,
        oracleTempSchema = NULL,
        firstOccurrenceOnly = TRUE,
        washoutPeriod = 365,
        cohortId = cohortId
      ) %>%
      tibble::as_tibble() %>%
      dplyr::mutate(cohortId = cohortId,
                    cdmDatabase = cdmDatabaseSchema)

    z <-  z + 1
    incidenceRate[[z]] <- result
  }
}
incidenceRates <- dplyr::bind_rows(incidenceRate)
saveRDS(incidenceRates, file = paste0(rstudioapi::getActiveProject(), '/data/incidenceRates.rds'))
incidenceRates <- readRDS(file = paste0(rstudioapi::getActiveProject(), '/data/incidenceRates.rds'))