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

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

## -----------------------------------------------------------------------------
# library(dplyr, warn.conflicts = FALSE)
# library(CohortConstructor)
# library(CohortCharacteristics)
# library(PatientProfiles)
# library(omock)
# library(clock)
# 
# cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
# 
# cdm$cohort <- demographicsCohort(cdm = cdm, name = "cohort", sex = "Female")

## -----------------------------------------------------------------------------
# cdm$cohort_observation_end <- cdm$cohort |>
#   exitAtObservationEnd(name = "cohort_observation_end")

## -----------------------------------------------------------------------------
# cdm$cohort_death <- cdm$cohort |>
#   exitAtDeath(requireDeath = TRUE, name = "cohort_death")

## -----------------------------------------------------------------------------
# # create cohort with of drugs diclofenac and acetaminophen
# cdm$medications <- conceptCohort(
#   cdm = cdm, name = "medications",
#   conceptSet = list("diclofenac" = 1124300, "acetaminophen" = 1127433)
# )
# 
# # add date first ocurrence of these drugs from index date
# cdm$cohort_dates <- cdm$cohort |>
#   addCohortIntersectDate(
#     targetCohortTable = "medications",
#     nameStyle = "{cohort_name}",
#     name = "cohort_dates"
#     )
# 
# # set cohort start at the first ocurrence of one of the drugs, or the end date
# cdm$cohort_entry_first <- cdm$cohort_dates |>
#   entryAtFirstDate(
#     dateColumns = c("diclofenac", "acetaminophen", "cohort_end_date"),
#     name = "cohort_entry_first"
#   )
# cdm$cohort_entry_first

## -----------------------------------------------------------------------------
# cdm$cohort_entry_last <- cdm$cohort_dates |>
#   entryAtLastDate(
#     dateColumns = c("diclofenac", "acetaminophen", "cohort_end_date"),
#     keepDateColumns = FALSE,
#     name = "cohort_entry_last"
#   )
# 
# cdm$cohort_entry_last

## -----------------------------------------------------------------------------
# cdm$cohort_exit_first <- cdm$cohort_dates |>
#   addFutureObservation(futureObservationType = "date", name = "cohort_exit_first") |>
#   exitAtFirstDate(
#     dateColumns = c("future_observation", "acetaminophen", "diclofenac"),
#     keepDateColumns = FALSE
#   )
# 
# cdm$cohort_exit_first

## -----------------------------------------------------------------------------
# cdm$cohort_exit_last <- cdm$cohort_dates |>
#   exitAtLastDate(
#     dateColumns = c("cohort_end_date", "acetaminophen", "diclofenac"),
#     returnReason = FALSE,
#     keepDateColumns = FALSE,
#     name = "cohort_exit_last"
#   )
# cdm$cohort_exit_last

## -----------------------------------------------------------------------------
# cdm$cohort_trim <- cdm$cohort |>
#   trimDemographics(ageRange = c(18, 65), name = "cohort_trim")

## -----------------------------------------------------------------------------
# # Trim cohort dates to be within the year 2000
# cdm$cohort_trim <- cdm$cohort_trim |>
#   trimToDateRange(dateRange = as.Date(c("2015-01-01", NA)))

## -----------------------------------------------------------------------------
# # Substract 50 days to cohort start
# cdm$cohort <- cdm$cohort |> padCohortStart(days = -50, collapse = FALSE)

## -----------------------------------------------------------------------------
# cdm$cohort_pad <- cdm$cohort |>
#   padCohortEnd(days = 1000, requireFullContribution = TRUE, name = "cohort_pad")

## -----------------------------------------------------------------------------
# cdm$cohort <- cdm$cohort |>
#   dplyr::mutate(days_to_add = date_count_between(start = cohort_start_date, end = cohort_end_date, precision = "day")) |>
#   padCohortEnd(days = "days_to_add", requireFullContribution = TRUE)

## -----------------------------------------------------------------------------
# cdm$cohort <- cdm$cohort |>
#   padCohortDate(days = 365, cohortDate = "cohort_end_date", indexDate = "cohort_start_date")

## -----------------------------------------------------------------------------
# cdm$medications <- cdm$medications |>
#   padCohortDate(days = 10, cohortId = "acetaminophen") |>
#   padCohortDate(days = 20, cohortId = "diclofenac")