tests/testthat/test-xpert_result_fixer.R

In JayAchar/tbcleanr: tbcleanr: tools for cleaning TB datade

context("test-xpert_result_fixer")

groz_raw <- system.file("testdata", "xpert_grozny.rds", package = "tbcleanr") %>% 
  readRDS() 

groz <- suppressWarnings(xpert_result_fixer(groz_raw, rm_orig = FALSE))
groz_narrow <- suppressWarnings(xpert_result_fixer(groz_raw, rm_orig = TRUE))

test_that("grozny correct", {
  expect_equal(ncol(groz_raw) + 2, ncol(groz))
  expect_equal(nrow(groz_raw), nrow(groz))
  expect_equal(ncol(groz_narrow), 3)
  expect_true(groz$xpert1err %>% unique() %in% c(0, 1) %>% all())
  expect_true(groz$xpert2err %>% unique() %in% c(0, 1) %>% all())
  expect_true(groz$xpert1res %>% unique() %in% c(0, 1, NA_integer_) %>% all())
  expect_true(groz$xpert2res %>% unique() %in% c(0, 1, NA_integer_) %>% all())
  expect_true(groz$xpert1rif %>% unique() %in% c(0, 1, NA_integer_) %>% all())
  expect_true(groz$xpert2rif %>% unique() %in% c(0, 1, NA_integer_) %>% all())
  expect_true(groz$xpert_res %>% unique() %in% c("Negative", "Positive", NA_character_) %>% all())
  expect_true(groz$xpert_rif %>% unique() %in% c("Not detected", "Detected", NA_character_) %>% all())
  
  # no rif results when Xpert negative = warning
  expect_warning(xpert_result_fixer(groz_raw), "Xpert rif result available when Xpert MTB not detected")
  expect_warning(xpert_result_fixer(groz_raw), "Xpert rif result available when Xpert MTB not available")
})


epiinfo_raw <- system.file("testdata", "xpert_epiinfo.rds", package = "tbcleanr") %>% 
  readRDS() 

epiinfo <- xpert_result_fixer(epiinfo_raw, rm_orig = FALSE)

test_that("epiinfo correct", {
  expect_equal(ncol(epiinfo_raw) + 2, ncol(epiinfo))
  expect_equal(nrow(epiinfo_raw), nrow(epiinfo))
  expect_true(epiinfo$xpert_res %>% unique() %in% c("Negative", "Positive", NA_character_) %>% all())
  expect_true(epiinfo$xpert_rif %>% unique() %in% c("Not detected", "Detected", NA_character_) %>% all())
  
  
  # no rif results when Xpert negative
  expect_equal(sum(epiinfo$xpert_res == "Negative" &
                     epiinfo$xpert_rif %in% c("Not detected", "Detected"), na.rm = T), 0)
  
})