## ----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,
#   fig.width = 7
# )
# 
# library(CDMConnector)
# if (Sys.getenv("EUNOMIA_DATA_FOLDER") == "") Sys.setenv("EUNOMIA_DATA_FOLDER" = tempdir())
# if (!dir.exists(Sys.getenv("EUNOMIA_DATA_FOLDER"))) dir.create(Sys.getenv("EUNOMIA_DATA_FOLDER"))
# if (!eunomiaIsAvailable()) downloadEunomiaData(datasetName = "synpuf-1k")

## -----------------------------------------------------------------------------
# library(CDMConnector)
# library(CohortConstructor)
# library(CodelistGenerator)
# library(PhenotypeR)
# library(MeasurementDiagnostics)
# library(dplyr)
# library(ggplot2)
# 
# con <- DBI::dbConnect(duckdb::duckdb(),
#                       CDMConnector::eunomiaDir("synpuf-1k", "5.3"))
# cdm <- CDMConnector::cdmFromCon(con = con,
#                                 cdmName = "Eunomia Synpuf",
#                                 cdmSchema   = "main",
#                                 writeSchema = "main",
#                                 achillesSchema = "main")
# 
# cdm$injuries <- conceptCohort(cdm = cdm,
#   conceptSet = list(
#     "ankle_sprain" = 81151,
#     "ankle_fracture" = 4059173,
#     "forearm_fracture" = 4278672,
#     "hip_fracture" = 4230399,
#     "measurements_cohort" = c(40660437L, 2617206L, 4034850L,  2617239L, 4098179L)
#   ),
#   name = "injuries")
# cdm$injuries |>
#   glimpse()

## -----------------------------------------------------------------------------
# code_diag <- codelistDiagnostics(cdm$injuries)

## -----------------------------------------------------------------------------
# cohortCodelist(cdm$injuries, cohortId = 1)
# cdm$injuries <- cdm$injuries |>
#   addCodelistAttribute(codelist = list(new_codelist = c(1L, 2L)), cohortName = "ankle_fracture")
# cohortCodelist(cdm$injuries, cohortId = 1)

## -----------------------------------------------------------------------------
# tableAchillesCodeUse(code_diag)

## -----------------------------------------------------------------------------
# tableOrphanCodes(code_diag)

## -----------------------------------------------------------------------------
# tableCohortCodeUse(code_diag)

## -----------------------------------------------------------------------------
# tableMeasurementSummary(code_diag)

## -----------------------------------------------------------------------------
# plotMeasurementSummary(code_diag)

## -----------------------------------------------------------------------------
# tableMeasurementValueAsConcept(code_diag)

## -----------------------------------------------------------------------------
# plotMeasurementValueAsConcept(code_diag)

## -----------------------------------------------------------------------------
# tableMeasurementValueAsNumber(code_diag)

## -----------------------------------------------------------------------------
# plotMeasurementValueAsNumber(code_diag)