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)) }) test_that("error is returned when the user choose a randomization method not available", { 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_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), random = "spatial", aleats = 5)) }) test_that("function runs ok with the method 'tip'", { 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(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), random = "tip", aleats = 3), ok = T) })