# Copyright 2018 Observational Health Data Sciences and Informatics
#
# This file is part of Legend
#
# 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 outcome cohorts
#'
#' @details
#' This function will create the 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 tablePrefix A prefix to be used for all table names created for this study.
#' @param indicationId A string denoting the indicationId for which the exposure cohorts
#' should be created.
#' @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
createOutcomeCohorts <- function(connectionDetails,
cdmDatabaseSchema,
cohortDatabaseSchema,
tablePrefix = "legend",
indicationId = "Depression",
oracleTempSchema,
outputFolder) {
ParallelLogger::logInfo("Creating outcome cohorts for indicationId: ", indicationId)
indicationFolder <- file.path(outputFolder, indicationId)
outcomeCohortTable <- paste(tablePrefix, tolower(indicationId), "out_cohort", sep = "_")
if (!file.exists(indicationFolder)) {
dir.create(indicationFolder, recursive = TRUE)
}
conn <- DatabaseConnector::connect(connectionDetails)
on.exit(DatabaseConnector::disconnect(conn))
# Creating outcome of interest cohorts ------------------------------
ParallelLogger::logInfo("- Creating outcome of interest cohorts")
.createCohorts(connection = conn,
cdmDatabaseSchema = cdmDatabaseSchema,
cohortDatabaseSchema = cohortDatabaseSchema,
cohortTable = outcomeCohortTable,
oracleTempSchema = oracleTempSchema,
outputFolder = indicationFolder,
indicationId = indicationId)
# Creating negative control outcome cohorts -------------------
ParallelLogger::logInfo("- Creating negative control outcome cohorts")
pathToCsv <- system.file("settings", "NegativeControls.csv", package = "Legend")
negativeControls <- read.csv(pathToCsv)
negativeControls <- negativeControls[negativeControls$indicationId == indicationId, ]
data <- negativeControls[, c("conceptId", "cohortId")]
colnames(data) <- SqlRender::camelCaseToSnakeCase(colnames(data))
DatabaseConnector::insertTable(connection = conn,
tableName = "#negative_controls",
data = data,
dropTableIfExists = TRUE,
createTable = TRUE,
tempTable = TRUE,
oracleTempSchema = oracleTempSchema)
sql <- SqlRender::loadRenderTranslateSql("NegativeControls.sql",
"Legend",
dbms = connectionDetails$dbms,
oracleTempSchema = oracleTempSchema,
cdm_database_schema = cdmDatabaseSchema,
target_database_schema = cohortDatabaseSchema,
target_cohort_table = outcomeCohortTable)
DatabaseConnector::executeSql(conn, sql)
sql <- "TRUNCATE TABLE #negative_controls; DROP TABLE #negative_controls;"
sql <- SqlRender::translateSql(sql = sql,
targetDialect = connectionDetails$dbms,
oracleTempSchema = oracleTempSchema)$sql
DatabaseConnector::executeSql(conn, sql, progressBar = FALSE, reportOverallTime = FALSE)
# Count cohorts --------------------------------------------------------------------------------
ParallelLogger::logInfo("Counting outcome cohorts")
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 = outcomeCohortTable)$sql
sql <- SqlRender::translateSql(sql, targetDialect = connectionDetails$dbms)$sql
counts <- DatabaseConnector::querySql(conn, sql)
names(counts) <- SqlRender::snakeCaseToCamelCase(names(counts))
pathToCsv <- system.file("settings", "OutcomesOfInterest.csv", package = "Legend")
outcomesOfInterest <- read.csv(pathToCsv)
countsOutcomesOfInterest <- merge(counts,
data.frame(cohortDefinitionId = outcomesOfInterest$cohortId,
cohortName = outcomesOfInterest$name))
countsNegativeControls <- merge(counts, data.frame(cohortDefinitionId = negativeControls$cohortId,
cohortName = negativeControls$name))
counts <- rbind(countsOutcomesOfInterest, countsNegativeControls)
counts <- unique(counts)
write.csv(counts, file.path(indicationFolder, "outcomeCohortCounts.csv"), row.names = FALSE)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.