Nothing
context("simmap")
## Make a simmap tree
test_that("we can coerce an ape::phylo tree with a
phytools:simmap extension into nexml", {
skip_if_not_installed("phytools")
require("phytools")
set.seed(10)
tree <- rbdtree(b = log(50), d = 0, Tmax = .5)
Q <- matrix(c(-2, 1, 1, 1, -2 ,1 ,1, 1, -2), 3, 3)
rownames(Q) <- colnames(Q) <- c("A", "B", "C")
## Note that state symbols must be integers! factors will be converted
mtree <- sim.history(tree, Q)
cols <- c("red", "blue", "green")
names(cols) <- rownames(Q)
nex <- simmap_to_nexml(mtree)
expect_is(nex, "nexml")
phy <- nexml_to_simmap(nex)
orig <- plotSimmap(mtree,cols,ftype="off")
roundtrip <- plotSimmap(phy,cols,ftype="off")
# checks that the edge mappings are correct
expect_equal(mtree$maps, phy$maps)
orig <- as.integer(as.factor(mtree$states[sort(names(mtree$states))]))
converted <- as.integer(phy$states[sort(names(phy$states))])
# checks that we got the states slot correct
expect_equal(converted, orig)
})
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