data("sq_trees")
test_that("Distances are calculated from strings", {
set.seed(0)
trees <- structure(lapply(rep(15, 5), ape::rtree, br = NULL),
class = "multiPhylo")
strs <- write.tree(trees)
fileName <- TQFile(trees)
on.exit(file.remove(fileName))
expect_equal(AllPairsQuartetDistance(fileName),
TQDist(trees))
expect_equal(AllPairsQuartetAgreement(fileName),
TQAE(trees))
expect_equal(ManyToManyQuartetAgreement(trees)[1, , ],
SingleTreeQuartetAgreement(trees, trees[[1]])[, ])
})
test_that("Splits are compared", {
trees <- TreeTools::UnshiftTree(
ape::drop.tip(sq_trees$move_one_near, 10),
ape::drop.tip(sq_trees$ref_tree, 11))
expect_equal(c(N = 252L, Q = 126L, s = 120L, d = 6L, r1 = 0L, r2 = 0L, u = 0L),
SharedQuartetStatus(trees)[2, ])
})
test_that("PlotQuartet() works", {
skip_if_not_installed("vdiffr")
vdiffr::expect_doppelganger("PlotQuartet", function() {
data("sq_trees")
par(mfrow = c(3, 2), mar = rep(0.5, 4), cex = 1.1)
PlotQuartet(sq_trees[c(1, 9, 13:16)], c(2, 5, 3, 8), overwritePar = FALSE)
})
vdiffr::expect_doppelganger("PlotQuartet-one-star", function() {
PlotQuartet(StarTree(4), 1:4, caption = FALSE)
})
vdiffr::expect_doppelganger("PlotQuartet-gain", function() {
par(mfrow = c(3, 2), mar = rep(0.5, 4), cex = 1.1)
PlotQuartet(c(StarTree(4), BalancedTree(4)), 1:4, overwritePar = TRUE)
})
})
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