tests/testthat/test_na_handling.R

In IsoriX: Isoscape Computation and Inference of Spatial Origins using Mixed Models

## preparation step:
GNIPDataDEagg <- prepsources(data = GNIPDataDE)

## tests:
test_that("isofit() can handle NA", {
  GNIPDataDEagg[1, "n_source_value"] <- NA

  expect_error(GermanFit <<- isofit(
    data = GNIPDataDEagg,
    mean_model_fix = list(elev = FALSE, lat_abs = FALSE),
    mean_model_rand = list(uncorr = FALSE, spatial = TRUE),
    disp_model_rand = list(uncorr = FALSE, spatial = FALSE)
  ), regexp = NA)
})

test_that("isoscape() can handle NA", {
  ElevRasterDE[50, 50] <- NA
  GermanFit2 <- isofit(
    data = GNIPDataDEagg,
    mean_model_fix = list(elev = TRUE, lat_abs = FALSE), ## Elev is TRUE for NA to have an effect
    mean_model_rand = list(uncorr = FALSE, spatial = TRUE),
    disp_model_rand = list(uncorr = FALSE, spatial = FALSE)
  )
  expect_error(GermanScape <<- isoscape(raster = ElevRasterDE, isofit = GermanFit2), regexp = NA)
})

test_that("plot.ISOSCAPE() can handle NA", {
  expect_error(plot(GermanScape), regexp = NA)
})

test_that("calibfit() can handle NA", {
  CalibDataAlien[1, "sample_value"] <- NA
  expect_error(CalibAlien <<- calibfit(
    data = CalibDataAlien,
    isofit = GermanFit,
    control_optim = list(maxit = 15)
  ), regexp = NA)
})

test_that("plot.CALIBFIT can handle NA", {
  expect_error(plot(CalibAlien), regexp = NA)
})

test_that("isofind() can handle NA", {
  AssignDataAlien[1, "sample_value"] <- NA

  expect_error(AssignmentDry <<- isofind(
    data = AssignDataAlien,
    isoscape = GermanScape,
    calibfit = CalibAlien
  ), regexp = NA)

  expect_false(all(is.na(terra::values(AssignmentDry$group$pv$lyr.1))))
})

test_that("plot.ISOFIND() can handle NA", {
  expect_warning(plot(AssignmentDry, who = 2)) # "The assignment test occurred at location(s) with unknown isoscape value(s); p-values set to 0 for such (a) location(s)."
  expect_warning(plot(AssignmentDry, who = "group")) # "The assignment test occurred at location(s) with unknown isoscape value(s); p-values set to 0 for such (a) location(s)."
})