tests/testthat/test-calculate_properties.R

In move2: Processing and Analysing Animal Trajectories

test_that("all have units", {
  expect_s3_class(x <- mt_sim_brownian_motion(), "move2")
  expect_identical(st_crs(x), st_crs(NA))
  expect_false(inherits(mt_distance(x), "units"))
  expect_type(mt_distance(x), "double")
  expect_false(inherits(mt_time_lags(x), "units"))
  expect_type(mt_time_lags(x), "integer")
  expect_false(inherits(mt_speed(x), "units"))
  expect_type(mt_speed(x), "double")
  expect_identical(
    mt_sim_brownian_motion() |>
      mutate(time = as.POSIXct(time, origin = "1970-1-1")) |> mt_speed() |> units()
      |> as.character(),
    "1/s"
  )
  expect_identical(
    mt_sim_brownian_motion() |> sf::st_set_crs(3857L) |>
      mutate(time = set_units(time, "h")) |> mt_speed() |> units()
      |> as.character(),
    "m/h"
  )
})
test_that("all movebank downloaded data has units", {
  testthat::skip_if_not_installed("lwgeom")
  skip_if_offline()
  skip_on_cran()
  skip_if_no_mbpwd()
  withr::with_envvar(
    list("movebank:move2_user" = Sys.getenv("MBPWD")),
    withr::with_options(list(keyring_backend = "env"), {
      expect_s3_class(x <- movebank_download_study(2911040L,
        attributes = NULL,
        timestamp_end = as.POSIXct("2008-06-6 06:00:00")
      ), "move2")
      expect_s3_class(x <- filter(x, !st_is_empty(x)), "move2")
      expect_s3_class(mt_distance(x), "units")
      # prevent message on loading s2
      suppressMessages(expect_s3_class(mt_azimuth(x), "units"))
      expect_s3_class(mt_turnangle(x), "units")
      expect_s3_class(mt_speed(x), "units")
      expect_s3_class(mt_time_lags(x), "units")
    })
  )
})
test_that("all have correct length", {
  expect_s3_class(x <- mt_sim_brownian_motion(t = list(1L, 1L:2L, 1L:3L, 1L:4L, 1L:10L), tracks = 5L), "move2")
  expect_length(mt_distance(x), 20L)
  expect_length(mt_time_lags(x), 20L)
  expect_length(mt_time(x), 20L)
  expect_length(mt_speed(x), 20L)
  expect_length(x |> sf::st_set_crs(4326) |> mt_azimuth(), 20L)
  expect_length(x |> sf::st_set_crs(4326) |> mt_turnangle(), 20L)
})
test_that("all have na in correct locations", {
  expect_s3_class(x <- mt_sim_brownian_motion(t = list(1, 1:2, 1:3, 1:4, 1:10), tracks = 5L), "move2")
  expect_equal(which(is.na(mt_distance(x))), c(1L, 3L, 6L, 10L, 20L), ignore_attr = TRUE)
  expect_identical(which(is.na(mt_time_lags(x))), c(1L, 3L, 6L, 10L, 20L))
  expect_false(anyNA(mt_time(x)))
  expect_equal(which(is.na(mt_speed(x))),
    c(1L, 3L, 6L, 10L, 20L),
    ignore_attr = TRUE
  )
  expect_identical(x |>
    sf::st_set_crs(4326L) |>
    mt_azimuth() |>
    is.na() |>
    which(), c(1L, 3L, 6L, 10L, 20L))
  expect_identical(
    x |>
      sf::st_set_crs(4326L) |>
      mt_turnangle() |>
      is.na() |>
      which(),
    c(1L, 2L, 3L, 4L, 6L, 7L, 10L, 11L, 20L)
  )
})
test_that("has correct value", {
  n <- 10
  d <- data.frame(
    x = c(0, 0, 1, 0, 1, 0, -1, -2, -3, -3), y = c(1:4, 4, 5, 6, 6, 5, 4),
    timestamp = 1:n, track = gl(1, n)
  )
  m <- mt_as_move2(st_as_sf(d, coords = 1L:2L, crs = 3857L),
    track_id_column = "track", time_column = "timestamp"
  ) |>
    st_transform(4326)
  expect_identical(
    units::set_units(mt_azimuth(m), "degrees") |> round(),
    set_units(c(0, 45, -45, 90, -45, -45, -90, -135, 180, NA), "degrees")
  )
  expect_identical(
    units::set_units(mt_turnangle(m), "degrees") |> round(),
    set_units(c(NA, 45, -90, 135, -135, 0, -45, -45, -45, NA), "degrees")
  )
  m <- mt_as_move2(st_as_sf(d, coords = 1:2), track_id_column = "track", time_column = "timestamp")
  expect_identical(
    units::set_units(mt_azimuth(m), "degrees"),
    set_units(c(0, 45, -45, 90, -45, -45, -90, -135, 180, NA), "degrees")
  )
  expect_equal(
    units::set_units(mt_turnangle(m), "degrees"),
    set_units(c(NA, 45, -90, 135, -135, 0, -45, -45, -45, NA), "degrees"),
    tolerance = 1e-10
  )
})
test_that("turn angles in -180 180 range", {
  d <- data.frame(x = c(0L, 0L, 1L, 0L, 1L), y = -c(1L:5L), timestamp = 1L:5L, track = gl(1L, 5L), timestamp2 = c(0, 1, 3, 6, 10))
  expect_identical(
    mt_as_move2(st_as_sf(d, coords = 1L:2L), track_id_column = "track", time_column = "timestamp") |>
      mt_azimuth() |> set_units("degrees"),
    set_units(c(180L, 135L, -135L, 135L, NA), "degrees")
  )
  expect_identical(
    mt_as_move2(st_as_sf(d, coords = 1L:2L), track_id_column = "track", time_column = "timestamp") |>
      mt_turnangle() |> set_units("degrees"),
    set_units(c(NA, -45L, 90L, -90L, NA), "degrees")
  )
  expect_identical(
    mt_as_move2(st_as_sf(d, coords = 2L:1L), track_id_column = "track", time_column = "timestamp") |>
      mt_turnangle() |> set_units("degrees"),
    set_units(c(NA, 45L, -90L, 90L, NA), "degrees")
  )
  d[["y"]] <- -d[["y"]]
  expect_identical(
    mt_as_move2(st_as_sf(d, coords = 1L:2L), track_id_column = "track", time_column = "timestamp") |>
      mt_turnangle() |> set_units("degrees"),
    set_units(c(NA, 45L, -90L, 90L, NA), "degrees")
  )
  expect_identical(
    mt_as_move2(st_as_sf(d, coords = 2L:1L), track_id_column = "track", time_column = "timestamp") |>
      mt_turnangle() |> set_units("degrees"),
    set_units(c(NA, -45L, 90L, -90L, NA), "degrees")
  )
  expect_equal(mt_as_move2(st_as_sf(d, coords = 2L:1L), track_id_column = "track", time_column = "timestamp") |>
    mt_distance(), c(1.0, sqrt(2.0), sqrt(2.0), sqrt(2.0), NA), ignore_attr = TRUE)
  expect_equal(mt_as_move2(st_as_sf(d, coords = 2L:1L), track_id_column = "track", time_column = "timestamp") |>
    mt_speed(), c(1.0, sqrt(2.0), sqrt(2.0), sqrt(2.0), NA), ignore_attr = TRUE)
  expect_equal(mt_as_move2(st_as_sf(d, coords = 2L:1L), track_id_column = "track", time_column = "timestamp2") |>
    mt_speed(), c(1.0, sqrt(2.0) / 2.0, sqrt(2.0) / 3.0, sqrt(2.0) / 4.0, NA), ignore_attr = TRUE)
  expect_equal(mt_as_move2(st_as_sf(d, coords = 2L:1L), track_id_column = "track", time_column = "timestamp2") |>
    mt_distance(), c(1.0, sqrt(2.0), sqrt(2.0), sqrt(2.0), NA), ignore_attr = TRUE)
  expect_equal(mt_as_move2(st_as_sf(d, coords = 1L:2L), track_id_column = "track", time_column = "timestamp") |>
    mt_distance(), c(1, sqrt(2), sqrt(2), sqrt(2), NA), ignore_attr = TRUE)
  expect_equal(mt_as_move2(st_as_sf(d, coords = 1L:2L), track_id_column = "track", time_column = "timestamp") |>
    mt_speed(), c(1, sqrt(2), sqrt(2), sqrt(2), NA), ignore_attr = TRUE)
  expect_equal(mt_as_move2(st_as_sf(d, coords = 1L:2L), track_id_column = "track", time_column = "timestamp2") |>
    mt_speed(), c(1, sqrt(2) / 2, sqrt(2) / 3, sqrt(2) / 4, NA), ignore_attr = TRUE)
  expect_equal(mt_as_move2(st_as_sf(d, coords = 1L:2L), track_id_column = "track", time_column = "timestamp2") |>
    mt_distance(), c(1.0, sqrt(2.0), sqrt(2.0), sqrt(2.0), NA), ignore_attr = TRUE)
})

test_that("Failures correct", {
  expect_s3_class(m <- mt_sim_brownian_motion(tracks = 1L, t = 1L:3L), "move2")
  expect_error(m[c(1, 3, 2), ] |> mt_distance(), "Not all timestamps in `x` are ordered within track.")
  expect_error(m[c(1, 3, 2), ] |> mt_time_lags(), "Not all timestamps in `x` are ordered within track.")
  expect_error(
    m |> sf::st_set_crs(4326L) |> st_transform(3857L) |> mt_azimuth(),
    "Currently the calculation of azimuths is not implemented for this projectio"
  )
  expect_error(
    m |> sf::st_set_crs(4326L) |> st_transform(3857L) |> mt_turnangle(),
    "Currently the calculation of azimuths is not implemented for this projectio"
  )

  expect_error(
    {
      m$geometry[2L] <- st_point()
      m
    } |> mt_distance(),
    "Not all locations are non empty points."
  )
})

test_that("mt_azimuth with different types of track ids", {
  a <- mt_sim_brownian_motion()
  expect_identical(mt_azimuth(a), mt_azimuth(mt_set_track_id(a, as.character(mt_track_id(a)))))
  expect_identical(mt_azimuth(a), mt_azimuth(mt_set_track_id(a, factor(mt_track_id(a)))))
})



test_that("sim data no units", {
  a <- mt_sim_brownian_motion()
  expect_false(inherits(mt_speed(a), "units"))
  expect_false(inherits(mt_distance(a), "units"))
  expect_s3_class(mt_turnangle(a), "units")
  expect_s3_class(mt_azimuth(a), "units")
  expect_false(inherits(mt_time_lags(a), "units"))
  expect_false(inherits(mt_speed(a, "m/s"), "units"))
  expect_false(inherits(mt_distance(a, "km"), "units"))
  expect_s3_class(mt_turnangle(a, "degree"), "units")
  expect_s3_class(mt_azimuth(a, "degree"), "units")
  expect_false(inherits(mt_time_lags(a, "s"), "units"))
  expect_identical(units(mt_turnangle(a, "degree")), units(as_units("degree")))
  expect_identical(units(mt_azimuth(a, "degree")), units(as_units("degree")))
})
test_that("units handling spatial dat", {
  a <- mt_read(mt_example())[1L:100L, ]
  a <- a[!st_is_empty(a), ]
  expect_s3_class(mt_speed(a), "units")
  expect_s3_class(mt_distance(a), "units")
  expect_s3_class(mt_turnangle(a), "units")
  expect_s3_class(mt_azimuth(a), "units")
  expect_s3_class(mt_time_lags(a), "units")
  expect_identical(units(mt_speed(a, "km/ms")), units(as_units("km/ms")))
  expect_identical(units(mt_distance(a, "hm")), units(as_units("hm")))
  expect_identical(units(mt_time_lags(a, "ms")), units(as_units("ms")))
  expect_identical(units(mt_turnangle(a, "degree")), units(as_units("degree")))
  expect_identical(units(mt_azimuth(a, "degree")), units(as_units("degree")))
  expect_error(mt_speed(a, "km"))
  expect_error(mt_distance(a, "hm/s"))
  expect_error(mt_time_lags(a, "ms^2"))
  expect_error(mt_turnangle(a, "degree/s"))
  expect_error(mt_azimuth(a, "degree/s"))
})