# Copyright 2019 Observational Health Data Sciences and Informatics
#
# This file is part of RASBlockerInCovid
#
# 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.
#' Execute the Study
#'
#' @details
#' This function executes the RASBlockerInCovid Study.
#'
#' The \code{createCohorts}, \code{synthesizePositiveControls}, \code{runAnalyses}, and \code{runDiagnostics} arguments
#' are intended to be used to run parts of the full study at a time, but none of the parts are considerd to be optional.
#'
#' @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
#' (/). Do not use a folder on a network drive since this greatly impacts
#' performance.
#' @param databaseId A short string for identifying the database (e.g.
#' 'Synpuf').
#' @param databaseName The full name of the database (e.g. 'Medicare Claims
#' Synthetic Public Use Files (SynPUFs)').
#' @param databaseDescription A short description (several sentences) of the database.
#' @param createCohorts Create the cohortTable table with the exposure and outcome cohorts?
#' @param synthesizePositiveControls Should positive controls be synthesized?
#' @param runAnalyses Perform the cohort method analyses?
#' @param runDiagnostics Compute study diagnostics?
#' @param packageResults Should results be packaged for later sharing?
#' @param maxCores How many parallel cores should be used? If more cores are made available
#' this can speed up the analyses.
#' @param minCellCount The minimum number of subjects contributing to a count before it can be included
#' in packaged results.
#'
#' @examples
#' \dontrun{
#' connectionDetails <- createConnectionDetails(dbms = "postgresql",
#' user = "joe",
#' password = "secret",
#' server = "myserver")
#'
#' execute(connectionDetails,
#' cdmDatabaseSchema = "cdm_data",
#' cohortDatabaseSchema = "study_results",
#' cohortTable = "cohort",
#' oracleTempSchema = NULL,
#' outputFolder = "c:/temp/study_results",
#' maxCores = 4)
#' }
#'
#' @export
execute <- function(connectionDetails,
cdmDatabaseSchema,
cohortDatabaseSchema = cdmDatabaseSchema,
cohortTable = "cohort",
oracleTempSchema = cohortDatabaseSchema,
outputFolder,
databaseId = "Unknown",
databaseName = "Unknown",
databaseDescription = "Unknown",
createCohorts = TRUE,
synthesizePositiveControls = TRUE,
runAnalyses = TRUE,
runDiagnostics = TRUE,
packageResults = TRUE,
maxCores = 4,
minCellCount= 5) {
if (!file.exists(outputFolder))
dir.create(outputFolder, recursive = TRUE)
if (!is.null(getOption("fftempdir")) && !file.exists(getOption("fftempdir"))) {
warning("fftempdir '", getOption("fftempdir"), "' not found. Attempting to create folder")
dir.create(getOption("fftempdir"), recursive = TRUE)
}
ParallelLogger::addDefaultFileLogger(file.path(outputFolder, "log.txt"))
if (createCohorts) {
ParallelLogger::logInfo("Creating exposure and outcome cohorts")
createCohorts(connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
cohortDatabaseSchema = cohortDatabaseSchema,
cohortTable = cohortTable,
oracleTempSchema = oracleTempSchema,
outputFolder = outputFolder)
}
# Set doPositiveControlSynthesis to FALSE if you don't want to use synthetic positive controls:
doPositiveControlSynthesis = FALSE
if (doPositiveControlSynthesis) {
if (synthesizePositiveControls) {
ParallelLogger::logInfo("Synthesizing positive controls")
synthesizePositiveControls(connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
cohortDatabaseSchema = cohortDatabaseSchema,
cohortTable = cohortTable,
oracleTempSchema = oracleTempSchema,
outputFolder = outputFolder,
maxCores = maxCores)
}
}
if (runAnalyses) {
ParallelLogger::logInfo("Running CohortMethod analyses")
runCohortMethod(connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
cohortDatabaseSchema = cohortDatabaseSchema,
cohortTable = cohortTable,
oracleTempSchema = oracleTempSchema,
outputFolder = outputFolder,
maxCores = maxCores)
}
if (runDiagnostics) {
ParallelLogger::logInfo("Running diagnostics")
generateDiagnostics(outputFolder = outputFolder,
maxCores = maxCores)
}
if (packageResults) {
ParallelLogger::logInfo("Packaging results")
exportResults(outputFolder = outputFolder,
databaseId = databaseId,
databaseName = databaseName,
databaseDescription = databaseDescription,
minCellCount = minCellCount,
maxCores = maxCores)
}
invisible(NULL)
}
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