context("Population Distance Tests")
test_that("dist.genpop matches distance", {
data(nancycats, package = "adegenet")
nanpop <- genind2genpop(nancycats, quiet = TRUE)
nei <- as.vector(nei.dist(nanpop))
edwards <- as.vector(edwards.dist(nanpop))
reynolds <- as.vector(reynolds.dist(nanpop))
rogers <- as.vector(rogers.dist(nanpop))
provesti <- as.vector(provesti.dist(nanpop))
expect_equivalent(as.vector(dist.genpop(nanpop, method = 1)), nei)
expect_equivalent(as.vector(dist.genpop(nanpop, method = 2)), edwards)
expect_equivalent(as.vector(dist.genpop(nanpop, method = 3)), reynolds)
expect_equivalent(as.vector(dist.genpop(nanpop, method = 4)), rogers)
expect_equivalent(as.vector(dist.genpop(nanpop, method = 5)), provesti)
})
test_that("aboot works with diss.dist", {
data(nancycats, package = "adegenet")
nan1 <- popsub(nancycats, 9)
expect_warning(ab <- aboot(nan1, dist = diss.dist, sample = 2, quiet = TRUE, showtree = FALSE))
expect_equal(class(ab), "phylo")
})
test_that("distances work with PA matrices", {
skip_on_cran()
data(Aeut)
Ath <- popsub(Aeut, "Athena")
expect_is(nei.dist(Ath), "dist")
expect_is(nei.dist(tab(Ath)), "dist")
expect_is(edwards.dist(Ath), "dist")
expect_is(edwards.dist(tab(Ath)), "dist")
expect_is(reynolds.dist(Ath), "dist")
expect_is(reynolds.dist(tab(Ath)), "dist")
expect_is(rogers.dist(Ath), "dist")
expect_is(rogers.dist(tab(Ath)), "dist")
expect_is(provesti.dist(Ath), "dist")
expect_is(provesti.dist(tab(Ath)), "dist")
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.