tests/testthat/test-package.R

In OHDSI/MethodEvaluation: Package for Evaluation of Estimation Methods

library(testthat)
library(dplyr)

test_that("Package results", {
  # packageOhdsiBenchmarkResults

  estimates <- readr::read_delim(col_names = TRUE, delim = ";", trim_ws = TRUE, file = "
    targetId ; outcomeId ; analysisId ; logRr ; seLogRr ; ci95Lb ; ci95Ub
    1 ; 3 ; 1; 0 ; 0 ; 0 ; 0")

  controlSummary <- readr::read_delim(col_names = TRUE, delim = ";", trim_ws = TRUE, file = "
    targetId ; comparatorId ; outcomeId ; nestingId; targetName ; comparatorName ; outcomeName ; nestingName ; type ; targetEffectSize ; trueEffectSize ; trueEffectSizeFirstExposure ; oldOutcomeId ; mdrrTarget ; mdrrComparator
      1 ; 2 ; 3 ; 1 ; name1 ; name2 ; name3 ; nest ; fun ; 1.25 ; 1 ; 1 ; 1 ; 1 ; 1")

  analysisRef <- data.frame(
    method = "CohortMethod",
    analysisId = 1,
    description = "1-on-1 matching",
    details = "",
    comparative = TRUE,
    nesting = FALSE,
    firstExposureOnly = TRUE
  )
  tempFolder <- tempfile()
  dir.create(tempFolder)

  packageOhdsiBenchmarkResults(
    estimates = estimates,
    controlSummary = controlSummary,
    analysisRef = analysisRef,
    databaseName = "test",
    exportFolder = tempFolder
  )
  result <- read.csv(file.path(tempFolder, "estimates_CohortMethod_test.csv"))
  expect_equal(result$analysisId[1], 1)

  expect_error(
    metrics <- computeOhdsiBenchmarkMetrics(exportFolder = tempFolder),
    "'response' must have two levels"
  )

  unlink(tempFolder, recursive = TRUE)
})