/usr/share/doc/r-cran-phangorn/tests/testthat/test_speciesTree.R is in r-cran-phangorn 2.4.0-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | context("speciesTree")
tr1 <- read.tree(text = "(((B:0.05,C:0.05):0.01,D:0.06):0.04,A:0.1);")
tr2 <- read.tree(text = "(((A:0.07,C:0.07):0.02,D:0.09):0.03,B:0.12);")
TR <- c(tr1, tr2)
start_tree <- read.tree(text = "(((B,C),D),A);")
x <- matrix(c("A", "B", "C", "D"), 4, 1)
rownames(x) <- c("A", "B", "C", "D")
X <- phyDat(x, type="USER", levels = c("A", "B", "C", "D"))
test_that("speciesTree", {
## check speciesTree
st1 <- coalSpeciesTree(TR)
st2 <- coalSpeciesTree(TR, X=X)
st3 <- coalSpeciesTree(TR, sTree = start_tree)
expect_equal(st1, st2)
expect_equal(st1, st3)
})
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