R/CreateAllCohorts.R

In schuemie/DistributedRegressionEval:

# Copyright 2018 Observational Health Data Sciences and Informatics
#
# This file is part of DistributedRegressionEval
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

#' Create the exposure and outcome cohorts
#'
#' @details
#' This function will create the exposure and outcome cohorts following the definitions included in
#' this package.
#'
#' @param connectionDetails    An object of type \code{connectionDetails} as created using the
#'                             \code{\link[DatabaseConnector]{createConnectionDetails}} function in the
#'                             DatabaseConnector package.
#' @param cdmDatabaseSchema    Schema name where your patient-level data in OMOP CDM format resides.
#'                             Note that for SQL Server, this should include both the database and
#'                             schema name, for example 'cdm_data.dbo'.
#' @param cohortDatabaseSchema Schema name where intermediate data can be stored. You will need to have
#'                             write priviliges in this schema. Note that for SQL Server, this should
#'                             include both the database and schema name, for example 'cdm_data.dbo'.
#' @param cohortTable          The name of the table that will be created in the work database schema.
#'                             This table will hold the exposure and outcome cohorts used in this
#'                             study.
#' @param oracleTempSchema     Should be used in Oracle to specify a schema where the user has write
#'                             priviliges for storing temporary tables.
#' @param outputFolder         Name of local folder to place results; make sure to use forward slashes
#'                             (/)
#'
#' @export
createCohorts <- function(connectionDetails,
                          cdmDatabaseSchema,
                          cohortDatabaseSchema,
                          cohortTable = "cohort",
                          oracleTempSchema,
                          outputFolder) {
  if (!file.exists(outputFolder))
    dir.create(outputFolder, recursive = TRUE)

  conn <- DatabaseConnector::connect(connectionDetails)

  .createCohorts(connection = conn,
                 cdmDatabaseSchema = cdmDatabaseSchema,
                 cohortDatabaseSchema = cohortDatabaseSchema,
                 cohortTable = cohortTable,
                 oracleTempSchema = oracleTempSchema,
                 outputFolder = outputFolder)

  sql <- SqlRender::loadRenderTranslateSql(sqlFilename = "SampleTarget.sql",
                                           packageName = "DistributedRegressionEval",
                                           dbms = conn@dbms,
                                           oracleTempSchema = oracleTempSchema,
                                           cohort_database_schema = cohortDatabaseSchema,
                                           cohort_table = cohortTable,
                                           cohort_id = 2,
                                           sample_size = 100000,
                                           new_cohort_id = 102)
  DatabaseConnector::executeSql(conn, sql, progressBar = FALSE, reportOverallTime = FALSE)


  sql <- "SELECT cohort_definition_id, COUNT(*) AS count FROM @cohort_database_schema.@cohort_table GROUP BY cohort_definition_id"
  sql <- SqlRender::renderSql(sql,
                              cohort_database_schema = cohortDatabaseSchema,
                              cohort_table = cohortTable)$sql
  sql <- SqlRender::translateSql(sql, targetDialect = conn@dbms)$sql
  counts <- DatabaseConnector::querySql(conn, sql)
  names(counts) <- SqlRender::snakeCaseToCamelCase(names(counts))
  write.csv(counts, file.path(outputFolder, "CohortCounts.csv"))

  DatabaseConnector::disconnect(conn)
}