inst/shiny/ResultsExplorer/SaveRDS.R

In DrugExposureDiagnostics: Diagnostics for OMOP Common Data Model Drug Records

#### PACKAGES -----
library(shiny)
library(bslib)
library(here)
library(readr)
library(dplyr)
library(stringr)
library(checkmate)
library(DT)
library(shinycssloaders)
library(shinyWidgets)
library(glue)
library(ggplot2)
library(plotly)
library(shinyjs)
source("dataPlotPanel.R")
source("metaDataPanel.R")
source("utils.R")
source("plots.R")

# input directory: this directory should have 1 or more zip files
if (exists("shinySettings") && !is.null(shinySettings$dataFolder)) {
  DATA_DIRECTORY <- shinySettings$dataFolder
} else {
  DATA_DIRECTORY <- "data"
}

if (!dir.exists(DATA_DIRECTORY)) {
  stop(glue("Please make sure the '{DATA_DIRECTORY}' directory exists."))
}

# Check for zip files
zipFiles <- list.files(DATA_DIRECTORY, pattern = ".zip", full.names = TRUE)
if (length(zipFiles) == 0) {
  stop(glue("Please make sure the '{DATA_DIRECTORY}' contains 1 or more zip files from drug exposure diagnostics."))
}

# Process zip files
for (i in 1:length(zipFiles)) {
  writeLines(paste("Processing", zipFiles[i]))
  tempFolder <- tempfile()
  dir.create(tempFolder)
  unzip(zipFiles[i], exdir = tempFolder, junkpaths = TRUE)

  csvFiles <- list.files(tempFolder, pattern = ".csv")
  lapply(csvFiles, loadFile, folder = tempFolder, overwrite = (i == 1), i)

  unlink(tempFolder, recursive = TRUE)
}

commonInputsInitValue <- c("INIT")

ingredientConcepts <- formatResult(conceptsummary)

# data overall and by concept
drugRoutes <- drugRoutesByConcept <- data.frame()
if (exists("drugroutesoverall")) {
  drugRoutes <- formatResult(drugroutesoverall)
  drugRoutesByConcept <- formatResult(drugroutesbyconcept)
}

drugVariablesMissing <- drugVariablesMissingByConcept <- data.frame()
if (exists("missingvaluesoverall")) {
  drugVariablesMissing <- formatResult(missingvaluesoverall)
  drugVariablesMissingByConcept <- formatResult(missingvaluesbyconcept)
}

drugTypes <- drugTypesByConcept <- data.frame()
if (exists("drugtypesoverall")) {
  drugTypes <- formatResult(drugtypesoverall)
  drugTypesByConcept <- formatResult(drugtypesbyconcept)
}

drugExposureDuration <- drugExposureDurationByConcept <- data.frame()
if (exists("drugexposuredurationoverall")) {
  drugExposureDuration <- formatResult(drugexposuredurationoverall)
  drugExposureDurationByConcept <- formatResult(drugexposuredurationbyconcept)
}

drugSourceConcepts <- data.frame()
if (exists("drugsourceconceptsoverall")) {
  drugSourceConcepts <- formatResult(drugsourceconceptsoverall)
}

drugDaysSupply <- drugDaysSupplyByConcept <- data.frame()
if (exists("drugdayssupply")) {
  drugDaysSupply <- formatResult(drugdayssupply)
  drugDaysSupplyByConcept <- formatResult(drugdayssupplybyconcept)
}

drugQuantity <- drugQuantityByConcept <- data.frame()
if (exists("drugquantity")) {
  drugQuantity <- formatResult(drugquantity)
  drugQuantityByConcept <- formatResult(drugquantitybyconcept)
}

drugSig <- drugSigByConcept <- data.frame()
if (exists("drugsig")) {
  drugSig <- formatResult(drugsig)
  drugSigByConcept <- formatResult(drugsigbyconcept)
}

drugVerbatimEndDate <- drugVerbatimEndDateByConcept <- data.frame()
if (exists("drugverbatimenddate")) {
  drugVerbatimEndDate <- formatResult(drugverbatimenddate)
  drugVerbatimEndDateByConcept <- formatResult(drugverbatimenddatebyconcept)
}

drugDailyDose <- data.frame()
if (exists("drugdose") && nrow(ingredientConcepts) > 0) {
  drugDailyDose <- formatResult(drugdose) %>%
    dplyr::filter(!is.na(strata_level)) %>%
    dplyr::mutate(result_id = as.integer(result_id))
}

metaData <- data.frame()
if (exists("metadata")) {
  metaData <- metadata
}

result <- list("conceptSummary" = ingredientConcepts,
               "drugRoutesOverall" = drugRoutes,
               "drugRoutesByConcept" = drugRoutesByConcept,
               "drugTypesOverall" = drugTypes,
               "drugTypesByConcept" = drugTypesByConcept,
               "drugExposureDurationOverall" = drugExposureDuration,
               "drugExposureDurationByConcept" = drugExposureDurationByConcept,
               "missingValuesOverall" = drugVariablesMissing,
               "missingValuesByConcept" = drugVariablesMissingByConcept,
               "drugSourceConceptsOverall" = drugSourceConcepts,
               "drugDaysSupply" = drugDaysSupply,
               "drugDaysSupplyByConcept" = drugDaysSupplyByConcept,
               "drugQuantity" = drugQuantity,
               "drugQuantityByConcept" = drugQuantityByConcept,
               "drugSig" = drugSig,
               "drugSigByConcept" = drugSigByConcept,
               "drugVerbatimEndDate" = drugVerbatimEndDate,
               "drugVerbatimEndDateByConcept" = drugVerbatimEndDateByConcept,
               "drugDose" = drugDailyDose,
               "metadata" = metaData)

saveRDS(result, "ded.rds")