## ----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(CDMConnector)
library(dplyr, warn.conflicts = FALSE)

if (Sys.getenv("EUNOMIA_DATA_FOLDER") == ""){
  Sys.setenv("EUNOMIA_DATA_FOLDER" = file.path(tempdir(), "eunomia"))}
if (!dir.exists(Sys.getenv("EUNOMIA_DATA_FOLDER"))){ dir.create(Sys.getenv("EUNOMIA_DATA_FOLDER"))
  downloadEunomiaData()  
}

## ----setup--------------------------------------------------------------------
# library(CohortConstructor)
# library(CohortCharacteristics)
# library(ggplot2)

## -----------------------------------------------------------------------------
# con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomiaDir())
# cdm <- cdmFromCon(con, cdmSchema = "main",
#                     writeSchema = c(prefix = "my_study_", schema = "main"))

## -----------------------------------------------------------------------------
# cdm$medications <- conceptCohort(cdm = cdm,
#                                  conceptSet = list("diclofenac" = 1124300,
#                                                    "acetaminophen" = 1127433),
#                                  name = "medications")
# cohortCount(cdm$medications)

## -----------------------------------------------------------------------------
# cdm$medintersect <- CohortConstructor::intersectCohorts(
#   cohort = cdm$medications,
#   name = "medintersect"
# )
# 
# cohortCount(cdm$medintersect)

## ----include=FALSE, warning=FALSE---------------------------------------------
# con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomiaDir())
# cdm <- CDMConnector::cdmFromCon(con, cdmSchema = "main",
#                     writeSchema = "main", writePrefix = "my_study_")
# cdm$medications <- conceptCohort(cdm = cdm,
#                                  conceptSet = list("diclofenac" = 1124300,
#                                                    "acetaminophen" = 1127433),
#                                  name = "medications")

## -----------------------------------------------------------------------------
# cdm$medintersect <- CohortConstructor::intersectCohorts(
#   cohort = cdm$medications,
#   gap = 365,
#   name = "medintersect"
# )
# 
# cohortCount(cdm$medintersect)

## -----------------------------------------------------------------------------
# cdm$medunion <- CohortConstructor::unionCohorts(
#   cohort = cdm$medications,
#   name = "medunion"
# )
# 
# cohortCount(cdm$medunion)

## ----include=FALSE, warning=FALSE---------------------------------------------
# con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomiaDir())
# cdm <- cdmFromCon(con, cdmSchema = "main",
#                     writeSchema = c(prefix = "my_study_", schema = "main"))
# cdm$medications <- conceptCohort(cdm = cdm,
#                                  conceptSet = list("diclofenac" = 1124300,
#                                                    "acetaminophen" = 1127433),
#                                  name = "medications")

## -----------------------------------------------------------------------------
# cdm$medunion <- CohortConstructor::unionCohorts(
#   cohort = cdm$medications,
#   name = "medunion",
#   keepOriginalCohorts = TRUE
# )
# 
# cohortCount(cdm$medunion)

## ----include=FALSE, warning=FALSE---------------------------------------------
# con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomiaDir())
# cdm <- cdmFromCon(con, cdmSchema = "main",
#                     writeSchema = c(prefix = "my_study_", schema = "main"))
# cdm$medications <- conceptCohort(cdm = cdm,
#                                  conceptSet = list("diclofenac" = 1124300,
#                                                    "acetaminophen" = 1127433),
#                                  name = "medications")

## -----------------------------------------------------------------------------
# cdm$medunion <- CohortConstructor::unionCohorts(
#   cohort = cdm$medications,
#   name = "medunion",
#   gap = 365,
#   keepOriginalCohorts = TRUE
# )
# 
# cohortCount(cdm$medunion)