tests/testthat/test-geophylo-ses.R

In phyloraster: Evolutionary Diversity Metrics for Raster Data

test_that("returned object class is correct", {

  x <- terra::rast(system.file("extdata", "rast.presab.tif",
                               package="phyloraster"))
  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)

  require("SESraster")
  # tests
  expect_s4_class(geo.phylo.ses(x = x,
                                tree = 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 = 3), "SpatRaster")
})

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

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

  require("SESraster")
  # tests
  expect_s4_class(geo.phylo.ses(ras, tree, inv.R=inv.R,
                                branch.length=branch.length, n.descen=n.descen,
                                aleats = 2), "SpatRaster")
  expect_s4_class(geo.phylo(ras, tree, inv.R=inv.R, branch.length=branch.length,
                            n.descen=n.descen), "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"))
            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$x,
            # data$branch.length, LR = T)

            require("SESraster")
            # tests
            expect_error(geo.phylo.ses(x = w,
                                       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"))

  require("SESraster")
  # tests
  expect_error(geo.phylo.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))
})