# Copyright 2018 Observational Health Data Sciences and Informatics
#
# This file is part of PredictionNetworkStudySkeleton
#
# 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.
#' Package the results for sharing with OHDSI researchers
#'
#' @details
#' This function packages the results.
#'
#' @param outputFolder Name of local folder to place results; make sure to use forward slashes
#' (/)
#' @param minCellCount The minimum number of subjects contributing to a count before it can be included in the results.
#'
#' @export
packageResults <- function(outputFolder,
minCellCount = 5) {
if(missing(outputFolder)){
stop('Missing outputFolder...')
}
# for each analysis copy the requested files...
folders <- list.dirs(path = outputFolder, recursive = T, full.names = F)
folders <- folders[grep('Analysis_', folders)]
if(length(grep('inst/plp_models', folders))>0){
folders <- folders[-grep('inst/plp_models', folders)] #in case using package directory
}
if(length(folders)==0){
stop('No results to export...')
}
#create export subfolder in workFolder
exportFolder <- file.path(outputFolder, "export")
for(folder in folders){
#copy all plots across
if (!file.exists(file.path(exportFolder,folder))){
dir.create(file.path(exportFolder,folder), recursive = T)
}
# loads analysis results
if(file.exists(file.path(outputFolder,folder, 'validationResult.rds'))){
plpResult <- readRDS(file.path(outputFolder,folder, 'validationResult.rds'))
if(minCellCount==0){
minCellCount <- NULL
}
result <- PatientLevelPrediction::transportPlp(plpResult, save = T,
n=minCellCount,
includeEvaluationStatistics=T,
includeThresholdSummary=T,
includeDemographicSummary=T,
includeCalibrationSummary =T,
includePredictionDistribution=T,
includeCovariateSummary=T)
saveRDS(result, file.path(exportFolder,folder, 'validationResult.rds'))
}
}
### Add all to zip file ###
zipName <- paste0(outputFolder, '.zip')
OhdsiSharing::compressFolder(exportFolder, zipName)
# delete temp folder
unlink(exportFolder, recursive = T)
writeLines(paste("\nStudy results are compressed and ready for sharing at:", zipName))
return(zipName)
}
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