tests/testthat/test-spatiotemp_pseudoabs.R

In dynamicSDM: Species Distribution and Abundance Modelling at High Spatio-Temporal Resolution

data("sample_explan_data")
data("sample_extent_data")
sample_explan_data <- sample_explan_data[1:3, ]
test_that("stops if no occcurence data provided and method buffer chosen", {
  expect_error(
    spatiotemp_pseudoabs(
      n.pseudoabs = 1000,
      spatial.method = "buffer",
      temporal.method = "random",
      spatial.buffer = c(100, 1000),
      temporal.ext = c('2020-6-16', '2022-6-16')
    )
  )
})

test_that("stops if no spatial.method provided", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 1000,
      temporal.method = "random",
      spatial.ext = c(0, 20, 0, 20),
      temporal.ext = c('2020-6-16', '2022-6-16')
    )
  )
})

test_that("stops if no temporal.method provided", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 1000,
      spatial.method = "random",
      spatial.ext = c(0, 20, 0, 20),
      temporal.ext = c('2020-6-16', '2022-6-16')
    )
  )
})

test_that("stops if n.pseudoabs is not numeric", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = "onethousands",
      temporal.method = "random",
      spatial.method = "random",
      spatial.ext = c(0, 20, 0, 20),
      temporal.ext = c('2020-6-16', '2022-6-16')
    )
  )
})

test_that("stops if temporal.method specified not accepted", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 100,
      temporal.method = "static",
      spatial.method = "random",
      spatial.ext = c(0, 20, 0, 20),
      temporal.ext = c('2020-6-16', '2022-6-16')
    )
  )
})

test_that("stops if spatial.method specified not accepted", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 100,
      temporal.method = "random",
      spatial.method = "static",
      spatial.ext = c(0, 20, 0, 20),
      temporal.ext = c('2020-6-16', '2022-6-16')
    )
  )
})

test_that("stops if temporal.method buffer but no buffer given", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 100,
      temporal.method = "buffer",
      spatial.method = "random",
      spatial.ext = c(0, 20, 0, 20)
    )
  )
})

test_that("stops if temporal.method buffer but incorrect class", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 100,
      temporal.method = "buffer",
      spatial.method = "random",
      spatial.ext = c(0, 20, 0, 20),
      temporal.buffer = "five days"
    )
  )
})

test_that("stops if temporal.method buffer but buffer incorrect length", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 100,
      temporal.method = "buffer",
      spatial.method = "random",
      spatial.ext = c(0, 20, 0, 20),
      temporal.buffer = c(5, 8, 9, 9, 9, 9)
    )
  )
})

test_that("stops if temporal.method buffer but buffer first further away than second",
          {
            expect_error(
              spatiotemp_pseudoabs(
                occ.data = sample_explan_data,
                n.pseudoabs = 100,
                temporal.method = "buffer",
                spatial.method = "random",
                spatial.ext = c(0, 20, 0, 20),
                temporal.buffer = c(30, 5)
              )
            )
          })

test_that("stops if temporal.method random but no temporal.ext given", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 100,
      temporal.method = "random",
      spatial.method = "random",
      spatial.ext = c(0, 20, 0, 20)
    )
  )
})

test_that("stops if temporal.method random but temporal.ext given wrong class",
          {
            expect_error(
              spatiotemp_pseudoabs(
                occ.data = sample_explan_data,
                n.pseudoabs = 100,
                temporal.method = "random",
                spatial.method = "random",
                spatial.ext = c(0, 20, 0, 20),
                temporal.ext = 4
              )
            )
          })

test_that("stops if temporal.method random but two dates not given in temporal.ext",
          {
            expect_error(
              spatiotemp_pseudoabs(
                occ.data = sample_explan_data,
                n.pseudoabs = 100,
                temporal.method = "random",
                spatial.method = "random",
                spatial.ext = c(0, 20, 0, 20),
                temporal.ext = "2000-04-05"
              )
            )
          })

test_that("stops if temporal.method random and temporal.ext contains invalid date",
          {
            expect_error(
              spatiotemp_pseudoabs(
                occ.data = sample_explan_data,
                n.pseudoabs = 100,
                temporal.method = "random",
                spatial.method = "random",
                spatial.ext = c(0, 20, 0, 20),
                temporal.ext = c("2004-15-01", "2000-04-05")
              )
            )
          })

test_that("stops if temporal.method random and temporal.ext not in date order",
          {
            expect_error(
              spatiotemp_pseudoabs(
                occ.data = sample_explan_data,
                n.pseudoabs = 100,
                temporal.method = "random",
                spatial.method = "random",
                spatial.ext = c(0, 20, 0, 20),
                temporal.ext = c("2004-01-01", "2000-04-05")
              )
            )
          })

test_that("stops if spatial.method buffer but no buffer given", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 100,
      temporal.method = "random",
      spatial.method = "buffer",
      temporal.ext = c("2000-12-01", "2004-04-05")
    )
  )
})

test_that("stops if spatial.method buffer but incorrect class", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 100,
      temporal.method = "random",
      spatial.method = "buffer",
      spatial.buffer = c("300m") ,
      temporal.ext = c("2000-12-01", "2004-04-05")
    )
  )
})

test_that("stops if spatial.method buffer but buffer incorrect length", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 100,
      temporal.method = "random",
      spatial.method = "buffer",
      spatial.buffer = c(2, 3, 4, 5, 6),
      temporal.ext = c("2000-12-01", "2004-04-05")
    )
  )
})

test_that("stops if spatial.method buffer but buffer first further away than second",
          {
            expect_error(
              spatiotemp_pseudoabs(
                occ.data = sample_explan_data,
                n.pseudoabs = 100,
                temporal.method = "random",
                spatial.method = "buffer",
                spatial.buffer = c(300, 10),
                temporal.ext = c("2000-12-01", "2004-04-05")
              )
            )
          })

test_that("stops if spatial.method random but no spatial.ext given", {
  expect_error(
    spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 100,
      temporal.method = "random",
      spatial.method = "random",
      temporal.ext = c("2000-12-01", "2004-04-05")
    )
  )
})

test_that("stops if temporal.method random but spatial.ext given wrong class",
          {
            expect_error(
              spatiotemp_pseudoabs(
                occ.data = sample_explan_data,
                n.pseudoabs = 10,
                temporal.method = "random",
                spatial.method = "random",
                spatial.ext = "faraway",
                temporal.ext = c("2000-12-01", "2004-04-05")
              )
            )
          })

test_that("Success if temporal buffer and spatial buffer method", {
  results <- spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 10,
      temporal.method = "buffer",
      spatial.method = "buffer",
      spatial.buffer = c(100, 1000),
      temporal.buffer = c(14, 30)
    )
  expect_equal(class(results), "data.frame")
})

test_that("Success if temporal buffer and spatial buffer method", {
  results <- spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 10,
      temporal.method = "buffer",
      spatial.method = "buffer",
      spatial.buffer = c(100, 1000),
      temporal.buffer = c(14, 30)
    )
  expect_equal(nrow(results), 10)
})

test_that("Success if temporal buffer and spatial buffer method, and n.pseudoabs default",
          {
            results <- spatiotemp_pseudoabs(
                occ.data = sample_explan_data,
                temporal.method = "buffer",
                spatial.method = "buffer",
                spatial.buffer = c(100, 1000),
                temporal.buffer = c(14, 30)
              )
            expect_equal(nrow(results), 100)
          })

test_that("Success if spatial extent numeric", {
  numeric <- c(20, 36, -35, -12)
  results <- spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 10,
      temporal.method = "buffer",
      spatial.method = "random",
      spatial.ext = numeric,
      temporal.buffer = c(14, 30)
    )
  expect_equal(class(results), "data.frame")
})

test_that("Success if spatial extent sf multipol", {
  results <- spatiotemp_pseudoabs(
    occ.data = sample_explan_data,
    n.pseudoabs = 10,
    temporal.method = "buffer",
    spatial.method = "random",
    spatial.ext = sample_extent_data$geometry,
    temporal.buffer = c(14, 30)
  )
  expect_equal(class(results), "data.frame")
})

test_that("Success if spatial extent extent", {
  Extent <- terra::ext(c(20, 36, -35, -12))
  results <- spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 10,
      temporal.method = "buffer",
      spatial.method = "random",
      spatial.ext = Extent,
      temporal.buffer = c(14, 30)
    )
  expect_equal(class(results), "data.frame")
})

test_that("Success if spatial extent raster", {
  raster <- terra::rast(terra::ext(c(20, 36, -35, -12)))
  results <- spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 10,
      temporal.method = "buffer",
      spatial.method = "random",
      spatial.ext = raster,
      temporal.buffer = c(14, 30)
    )
  expect_equal(class(results), "data.frame")
})

test_that("Success if spatial extent polygon", {
  polygon <-  sf::st_polygon(list(cbind(c(20, 12, 36, 36,20), c(-35, -12, -35, -12,-35))))
  results <-spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 10,
      temporal.method = "buffer",
      spatial.method = "random",
      spatial.ext = polygon,
      temporal.buffer = c(14, 30)
    )
  expect_equal(class(results), "data.frame")
})

data("sample_extent_data")
test_that("Success if sf extent", {
  results <- spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 10,
      temporal.method = "buffer",
      spatial.method = "random",
      spatial.ext = sample_extent_data,
      temporal.buffer = c(14, 30)
    )
  expect_equal(class(results), "data.frame")
})

test_that("Success if temporal method random and spatial buffer", {
  results <- spatiotemp_pseudoabs(
      occ.data = sample_explan_data,
      n.pseudoabs = 10,
      temporal.method = "random",
      spatial.method = "buffer",
      spatial.buffer = c(100, 1000),
      temporal.ext = c("2005-01-01", "2020-01-01")
    )
  expect_equal(class(results), "data.frame")
})

test_that("Success if temporal method random and spatial random, n.pseudoabs default",
          {
            results <- spatiotemp_pseudoabs(
                occ.data = sample_explan_data,
                n.pseudoabs = 10,
                temporal.method = "random",
                spatial.method = "buffer",
                spatial.buffer = c(100, 1000),
                temporal.ext = c("2005-01-01", "2020-01-01")
              )
            expect_equal(class(results), "data.frame")
          })