## ---- include = FALSE---------------------------------------------------------
options(rmarkdown.html_vignette.check_title = FALSE)
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>")

## ----setup,message= FALSE, warning=FALSE--------------------------------------
library(DrugExposureDiagnostics)
library(CDMConnector)
library(dplyr)
library(DT)

## -----------------------------------------------------------------------------
cdm <- mockDrugExposure()

## ----executeChecks------------------------------------------------------------
all_checks <- executeChecks(cdm,
                            ingredients = c(1125315),
                            subsetToConceptId = NULL,
                            checks = c("missing", "exposureDuration", "type", "route", "sourceConcept", "daysSupply", 
                                       "verbatimEndDate", "dose", "sig", "quantity", "diagnosticsSummary"), 
                            minCellCount = 5,
                            sample = 10000,
                            tablePrefix = NULL,
                            earliestStartDate = "2010-01-01",
                            verbose = FALSE,
                            byConcept = TRUE)

## -----------------------------------------------------------------------------
names(all_checks)

## ----  message=FALSE, warning=FALSE-------------------------------------------
datatable(all_checks$conceptSummary,
  rownames = FALSE
)

## ----eval=FALSE---------------------------------------------------------------
#  writeResultToDisk(all_checks,
#                    databaseId = "your_database",
#                    outputFolder = "output_folder")

## ----eval=FALSE---------------------------------------------------------------
#  viewResults(dataFolder = file.path(getwd(), "output_folder"),
#              makePublishable = TRUE,
#              publishDir = file.path(getwd(), "MyStudyResultsExplorer"),
#              overwritePublishDir = TRUE
#  )

## ---- echo=FALSE--------------------------------------------------------------
  DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)