tests/testthat/test-multipleCohortTables.R

In TreatmentPatterns: Analyzes Real-World Treatment Patterns of a Study Population of Interest

library(dplyr)
library(TreatmentPatterns)
library(testthat)

test_that("multiple cohort_tables", {
  skip_on_cran()
  skip_if_not(ableToRun()$CDMC)
  con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomiaDir())

  cohorts <- data.frame(
    cohortId = c(1, 2, 3),
    cohortName = c("X", "A", "B"),
    type = c("target", "event", "event")
  )

  cohort_table_target <- dplyr::tribble(
    ~cohort_definition_id, ~subject_id, ~cohort_start_date, ~cohort_end_date,
    1L, 5L, as.Date("2014-01-01"), as.Date("2015-01-01")
  )

  cohort_table_event <- dplyr::tribble(
    ~cohort_definition_id, ~subject_id, ~cohort_start_date, ~cohort_end_date,
    2L, 5L, as.Date("2014-01-10"), as.Date("2014-03-10")
  )

  cdm <- cdmFromCon(
    con = con,
    cdmSchema = "main",
    writeSchema = "main"
  )

  cdm <- CDMConnector::insertTable(
    cdm = cdm,
    name = "cohort_table_event",
    table = cohort_table_event,
    overwrite = TRUE
  )

  cdm <- CDMConnector::insertTable(
    cdm = cdm,
    name = "cohort_table_target",
    table = cohort_table_target,
    overwrite = TRUE
  )

  andromeda <- TreatmentPatterns::computePathways(
    cohorts = cohorts,
    cohortTableName = c("cohort_table_target", "cohort_table_event"),
    cdm = cdm,
    minEraDuration = 0,
    eraCollapseSize = 5,
    combinationWindow = 30,
    minPostCombinationDuration = 30,
    filterTreatments = "All",
    maxPathLength = 5
  )

  result <- TreatmentPatterns::export(andromeda, minCellCount = 1)

  expect_identical(result$treatment_pathways$pathway, "A")

  DBI::dbDisconnect(con, shutdown = TRUE)
})

test_that("multiple cohort_tables", {
  skip("Eunomia [2.0.0] bug")
  skip_on_cran()
  skip_if_not(ableToRun()$CG)

  cohorts <- data.frame(
    cohortId = c(1, 2, 3),
    cohortName = c("X", "A", "B"),
    type = c("target", "event", "event")
  )

  cohort_table_target <- dplyr::tribble(
    ~cohort_definition_id, ~subject_id, ~cohort_start_date,    ~cohort_end_date,
    1,                     5,           as.Date("2014-01-01"), as.Date("2015-01-01")
  )

  cohort_table_event <- dplyr::tribble(
    ~cohort_definition_id, ~subject_id, ~cohort_start_date,    ~cohort_end_date,
    2,                     5,           as.Date("2014-01-10"), as.Date("2014-03-10")
  )

  conDet <- Eunomia::getEunomiaConnectionDetails()
  con <- DatabaseConnector::connect(conDet)

  DatabaseConnector::dbWriteTable(conn = con, name = "cohort_table_target", value = cohort_table_target)
  DatabaseConnector::dbWriteTable(conn = con, name = "cohort_table_event", value = cohort_table_event)

  DatabaseConnector::disconnect(con)

  andromeda <- TreatmentPatterns::computePathways(
    cohorts = cohorts,
    cohortTableName = c("cohort_table_target", "cohort_table_event"),
    connectionDetails = conDet,
    cdmSchema = "main",
    resultSchema = "main",
    tempEmulationSchema = NULL,
    minEraDuration = 0,
    eraCollapseSize = 5,
    combinationWindow = 30,
    minPostCombinationDuration = 30,
    filterTreatments = "All",
    maxPathLength = 5
  )

  result <- TreatmentPatterns::export(andromeda, minCellCount = 1)

  expect_identical(result$treatment_pathways$pathway, "A")
})