## ----include = FALSE----------------------------------------------------------
NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true")

knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
eval = NOT_CRAN
)

## ----include = FALSE----------------------------------------------------------
# knitr::opts_chunk$set(
#   collapse = TRUE,
#   comment = "#>"
# )

## ----message=FALSE, warning=FALSE, eval=FALSE---------------------------------
# library(CohortConstructor)
# library(PhenotypeR)
# library(dplyr)
# library(readr)
# library(here)
# library(omock)
# 
# cdm <- mockCdmFromDataset(datasetName = "synpuf-1k_5.3",
#                           source = "duckdb")
# 
# # Create a code lists
# codes <- list("user_of_warfarin" = c(1310149L, 40163554L),
#               "user_of_acetaminophen" = c(1125315L, 1127078L, 1127433L, 40229134L,
#                                           40231925L, 40162522L, 19133768L),
#               "user_of_morphine" = c(1110410L, 35605858L, 40169988L),
#               "measurements_cohort" = c(40660437L, 2617206L, 4034850L,  2617239L,
#                                         4098179L))
# 
# # Instantiate cohorts with CohortConstructor
# cdm$my_cohort <- conceptCohort(cdm = cdm,
#                                conceptSet = codes,
#                                exit = "event_end_date",
#                                overlap = "merge",
#                                name = "my_cohort")
# 
# # Run PhenotypeDiagnostics including all diagnostics
# result <- phenotypeDiagnostics(cdm$my_cohort)
# 
# # Generate expectations (see the vignette for more details)
# chat <- chat("google_gemini")
# expectations <- getCohortExpectations(chat = chat,
#                       phenotypes = result)
# 
# expectationsDir <- here()
# write_csv(expectations,
#           file = here("expectations.csv"))
# 
# # Create database descriptions (see the vignette for more details)
# databaseDescriptionDir <- here("database_descriptions")
# downloadDatabaseDescriptionTemplate(directory = databaseDescriptionDir,
#                                     name = "synpuf-1k")
# 
# # Create clinical descriptions (see the vignette for more details)
# clinicalDescriptionDir <- here("cinical_descriptions")
# downloadClinicalDescriptionTemplate(directory = clinicalDescriptionDir, name = "user_of_warfarin")
# downloadClinicalDescriptionTemplate(directory = clinicalDescriptionDir, name = "user_of_acetaminophen")
# downloadClinicalDescriptionTemplate(directory = clinicalDescriptionDir, name = "user_of_morphine")
# downloadClinicalDescriptionTemplate(directory = clinicalDescriptionDir, name = "measurements_cohort")
# 
# # Create the shiny app based on PhenotypeDiagnostics results, suppressing all
# # cell counts smaller than 2, saved in a temporary directory, with the
# # expectations created using "gemini" and the database and clinical descriptions:
# shinyDiagnostics(result = result,
#                  minCellCount = 2,
#                  directory = tempdir(),
#                  expectationsDir = expectationsDir,
#                  databaseDescriptionsDir = databaseDescriptionDir,
#                  clinicalDescriptionsDir = clinicalDescriptionDir)

## ----echo=FALSE, out.width='90%'----------------------------------------------
# knitr::include_graphics(here::here("vignettes/ShinyDiagnosticsFigures/figure1.png"))

## ----echo=FALSE, out.width='90%'----------------------------------------------
# knitr::include_graphics(here::here("vignettes/ShinyDiagnosticsFigures/figure2.png"))

## ----echo=FALSE, out.width='90%'----------------------------------------------
# knitr::include_graphics(here::here("vignettes/ShinyDiagnosticsFigures/figure3.png"))

## ----echo=FALSE, out.width='90%'----------------------------------------------
# knitr::include_graphics(here::here("vignettes/ShinyDiagnosticsFigures/figure4.png"))

## ----echo=FALSE, out.width='90%'----------------------------------------------
# knitr::include_graphics(here::here("vignettes/ShinyDiagnosticsFigures/figure5.png"))

## ----echo=FALSE, out.width='90%'----------------------------------------------
# knitr::include_graphics(here::here("vignettes/ShinyDiagnosticsFigures/figure6.png"))

## ----echo=FALSE, out.width='90%'----------------------------------------------
# knitr::include_graphics(here::here("vignettes/ShinyDiagnosticsFigures/figure7.png"))

## ----echo=FALSE, out.width='90%'----------------------------------------------
# knitr::include_graphics(here::here("vignettes/ShinyDiagnosticsFigures/figure8.png"))

## ----echo=FALSE, out.width='90%'----------------------------------------------
# knitr::include_graphics(here::here("vignettes/ShinyDiagnosticsFigures/figure9.png"))

## ----echo=FALSE, out.width='90%'----------------------------------------------
# knitr::include_graphics(here::here("vignettes/ShinyDiagnosticsFigures/figure10.png"))

## ----echo=FALSE, out.width='90%'----------------------------------------------
# knitr::include_graphics(here::here("vignettes/ShinyDiagnosticsFigures/figure11.png"))

## ----echo=FALSE, out.width='90%'----------------------------------------------
# knitr::include_graphics(here::here("vignettes/ShinyDiagnosticsFigures/figure12.png"))