tests/testthat/test-stratifyByConcept.R

In CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

test_that("multiplication works", {

  cdm <- mockVocabRef()
  cl <- omopgenerics::newCodelist(list(a = c(1,2,3),
                                       b = c(3,4,5)))

  cl_s1 <- stratifyByConcept(cl, cdm, keepOriginal = FALSE)
  expect_true(length(cl_s1) == 6)


  cl_s2 <- stratifyByConcept(cl, cdm, keepOriginal = TRUE)
  expect_true(length(cl_s2) == 8)
  expect_true(all(sort(names(cl)) == sort(setdiff(names(cl_s2), names(cl_s1)))))



  cl <- omopgenerics::newCodelistWithDetails(list(a = data.frame(concept_id = c(1,2,3),
                                                                 concept_name = c("a", "b", "c")),
                                                  b =  data.frame(concept_id = c(1,2,3),
                                                                  concept_name = c("c", "d", "e"))))

  cl_s1 <- stratifyByConcept(cl, cdm, keepOriginal = FALSE)
  expect_true(length(cl_s1) == 6)


  cl_s2 <- stratifyByConcept(cl, cdm, keepOriginal = TRUE)
  expect_true(length(cl_s2) == 8)
  expect_true(all(sort(names(cl)) == sort(setdiff(names(cl_s2), names(cl_s1)))))

  # if concepts are not in the cdm
  cdm <- mockVocabRef()
  cl <- omopgenerics::newCodelist(list(a = c(1,2,3),
                                       b = c(3,4,5,99999)))
  expect_warning(cl_s1 <- stratifyByConcept(cl, cdm, keepOriginal = FALSE))
  expect_true(length(cl_s1) == 6) # concept 99999 will have been dropped

  # if concepts are a list
  expect_no_error(cl_s2 <- stratifyByConcept(list("a" = c(1,2,3)), cdm, keepOriginal = FALSE))
})