tests/testthat/test-rast-ed-ses.R

In phyloraster: Evolutionary Diversity Metrics for Raster Data

test_that("check if the object class is correct", {

  # load data
  x <- terra::rast(system.file("extdata", "rast.presab.tif",
                               package="phyloraster"))
  tree <- ape::read.tree(system.file("extdata", "tree.nex",
                                     package="phyloraster"))

  # getting fewer cells to test all values
  x <- terra::crop(x, terra::ext(c(150.0157, 150.8157,
                                   -23.044, -22.8563)))

  require("SESraster")
  # tests
  expect_s4_class(rast.ed.ses(x, tree, aleats = 3),
                  "SpatRaster")

})

test_that("check if function corrects arguments with wrong names", {

  # load data
  x <- terra::rast(system.file("extdata", "rast.presab.tif",
                               package="phyloraster"))
  # getting fewer cells to test all values
  x <- terra::crop(x, terra::ext(c(150.0157, 150.8157,
                                   -23.044, -22.8563)))

  tree <- ape::read.tree(system.file("extdata", "tree.nex",
                                     package="phyloraster"))
  data <- phylo.pres(x, tree)
  # inv.R <- inv.range(data$x)
  branch.length <- data$branch.length
  n.descen <- data$n.descendants
  names(branch.length) <- sample(names(branch.length))
  names(n.descen) <- sample(names(n.descen))

  require("SESraster")
  # tests
  expect_s4_class(rast.ed.ses(x, tree, branch.length=branch.length,
                              n.descen=n.descen, aleats = 2), "SpatRaster")

})

test_that("error is returned when the raster does not have a longitude/latitude
          coordinate reference system (CRS)", {

            x <- terra::rast(system.file("extdata", "rast.presab.tif",
                                         package="phyloraster"))
            # getting fewer cells to test all values
            x <- terra::crop(x, terra::ext(c(150.0157, 150.8157,
                                             -23.044, -22.8563)))

            tree <- ape::read.tree(system.file("extdata", "tree.nex",
                                               package="phyloraster"))
            # data <- phylo.pres(x, tree)
            # area.branch <- inv.range(data$x, data$branch.length)
            w <- terra::project(x, "EPSG:2169")

            data <- phyloraster::phylo.pres(w, tree)
            branch.length <- data$branch.length
            n.descen <- data$n.descendants
            # area.branch <- phyloraster::inv.range(data$x)

            require("SESraster")
            # tests
            expect_error(rast.ed.ses(x = data$x,
                                     tree = data$tree,
                                     # FUN_args = list(range.BL=
                                     # area.branch$range.BL,
                                     # inv.R=area.branch$inv.R,
                                     # branch.length=data$branch.length,
                                     # n.descen = data$n.descendants),
                                     spat_alg = "bootspat_str",
                                     spat_alg_args = list(rprob = NULL,
                                                          rich = NULL,
                                                          fr_prob = NULL),
                                     aleats = 5))
          })

test_that("error is returned when only argument x is provided", {

  x <- terra::rast(system.file("extdata", "rast.presab.tif",
                               package="phyloraster"))
  # getting fewer cells to test all values
  x <- terra::crop(x, terra::ext(c(150.0157, 150.8157,
                                   -23.044, -22.8563)))

  require("SESraster")
  # tests
  expect_error(rast.ed.ses(
    x = x,
    # tree = data$tree,
    # FUN_args = list(range.BL=area.branch$range.BL,
    # inv.R=area.branch$inv.R,
    # branch.length=data$branch.length,
    # n.descen = data$n.descendants),
    spat_alg = "bootspat_str",
    spat_alg_args = list(rprob = NULL,
                         rich = NULL,
                         fr_prob = NULL),
    aleats = 5))
})

test_that("function compute branch lenght when tree is supplied", {

  x <- terra::rast(system.file("extdata", "rast.presab.tif",
                               package="phyloraster"))
  # getting fewer cells to test all values
  x <- terra::crop(x, terra::ext(c(150.0157, 150.8157, -23.044, -22.8563)))
  tree <- ape::read.tree(system.file("extdata", "tree.nex",
                                     package="phyloraster"))

  require("SESraster")
  # tests
  expect(rast.ed.ses(x = x, tree = tree,
                     spat_alg = "bootspat_str",
                     spat_alg_args = list(rprob = NULL,
                                          rich = NULL,
                                          fr_prob = NULL),
                     aleats = 5), ok = T)
})