Nothing
test_that("returned object classes are correct", {
# 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 <- phyloraster::phylo.pres(x, tree)
# branch.length <- data$branch.length
# n.descen <- data$n.descendants
inv.R <- phyloraster::inv.range(data$x)
t <- geo.phylo(data$x, inv.R = inv.R, edge.path = data$edge.path,
branch.length = data$branch.length,
n.descen = data$n.descendants)
# tests
expect_s4_class(t, "SpatRaster")
})
test_that("Are the returned values correct?", {
# load data
x <- terra::rast(system.file("extdata", "rast.presab.tif",
package="phyloraster"))
tree <- ape::read.tree(system.file("extdata", "tree.nex",
package="phyloraster"))
# getting fewer cells to test all values
xcrop <- terra::crop(x, terra::ext(c(150.0157, 150.8157,
-23.044, -22.8563)))
# matching phylogenetic tree and the raster
data <- phylo.pres(xcrop, tree, full_tree_metr = T)
branch.length <- data$branch.length
n.descen <- data$n.descendants
inv.R <- phyloraster::inv.range(data$x)
# metric SE
t <- phyloraster::geo.phylo(data$x, inv.R = inv.R, edge.path = data$edge.path,
branch.length = data$branch.length,
n.descen = data$n.descendants)
se.observed <- terra::values(t$SR)
se.expect <- matrix(data = c(12, 12, 12, 13, 14,
14, 14, 14, 12, 12,
11, 12, 13, 14, 14, 14),
ncol = 1, byrow = F)
expect_equivalent(terra::values(t$SR), se.expect)
# metric PE
pe.obs <- round(terra::values(t$PE),7)
pe.expect <- c(0.3807860, 0.3807860, 0.3807860,
0.4651102, 0.4776858, 0.4776858,
0.4776858, 0.4776858, 0.3805112,
0.3805112, 0.3496615, 0.3805112,
0.3930776, 0.4773410, 0.4773410,
0.4773410)
expect_equivalent(pe.obs, pe.expect)
# metric WE
# metric PE
we.obs <- round(terra::values(t$WE),7)
we.expect <- c(0.7544373, 0.7544373, 0.7544373,
0.8794712, 1.0045163, 1.0045163,
1.0045163, 1.0045163, 0.7538928,
0.7538928, 0.6872518, 0.7538928,
0.8788477,
1.0037913, 1.0037913, 1.0037913)
expect_equivalent(we.obs, we.expect)
# metric PD
pd.obs <- terra::values(t$PD)
pd.expect <- matrix(data = c(6.583520, 6.583520, 6.583520,
6.705980, 7.704928,
7.704928, 7.704928, 7.704928,
6.583520, 6.583520,
5.994505, 6.583520, 7.582468,
7.704928, 7.704928,
7.704928),
ncol = 1, byrow = F)
expect_equivalent(pd.obs, pd.expect)
# metric ED
ed.obs <- round(terra::values(t$ED), 7)
ed.expect <- c(0.4002847, 0.4002847, 0.4002847, 0.3789135,
0.3554159, 0.3554159, 0.3554159, 0.3554159,
0.4002847, 0.4002847, 0.4099008,
0.4002847, 0.3733356, 0.3554159, 0.3554159, 0.3554159)
expect_equivalent(ed.obs, ed.expect)
})
test_that("error is returned when an argument is missing", {
# 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 <- phyloraster::inv.range(data$x)
# tests
expect_error(geo.phylo(data$x,
inv.R = inv.R,
branch.length = data$branch.length))
expect_error(geo.phylo(data$x,
inv.R = inv.R,
n.descen = data$n.descendants))
})
test_that("arguments are calculated when is missing and the
tree is provided", {
# load data
x <- terra::rast(system.file("extdata", "rast.presab.tif",
package="phyloraster"))
# getting fewer cells to test all values
x <- terra::crop(x, terra::ext(c(150.0157, 150.8157,
-23.044, -22.8563)))
tree <- ape::read.tree(system.file("extdata", "tree.nex",
package="phyloraster"))
data <- phylo.pres(x, tree)
# area.branch <- phyloraster::inv.range(data$x)
# tests
expect(geo.phylo(data$x, tree), ok = T)
})
test_that("names are reordened in the function geo.phylo", {
# load data
x <- terra::rast(system.file("extdata", "rast.presab.tif",
package="phyloraster"))
# getting fewer cells to test all values
x <- terra::crop(x, terra::ext(c(150.0157, 150.8157,
-23.044, -22.8563)))
tree <- ape::read.tree(system.file("extdata", "tree.nex",
package="phyloraster"))
data <- phylo.pres(x, tree)
inv.R <- phyloraster::inv.range(data$x)
# tests
expect(geo.phylo(data$x, tree, #range.BL = area.branch$range.BL,
inv.R = inv.R,
edge.path = data$edge.path[sample(1:nrow(data$edge.path)),],
branch.length = data$branch.length,
n.descen = data$n.descendants), ok = T)
})
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"))
# getting fewer cells to test all values
x <- terra::crop(x, terra::ext(c(150.0157, 150.8157,
-23.044, -22.8563)))
w <- terra::project(x, "EPSG:2169")
data <- phyloraster::phylo.pres(w, tree)
# branch.length <- data$branch.length
# n.descen <- data$n.descendants
# inv.R <- phyloraster::inv.range(data$x)
# tests
expect_error(geo.phylo(data$x,
data$n.descendants))
})
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