/usr/share/doc/r-cran-phangorn/tests/testthat/test_splits.R is in r-cran-phangorn 2.4.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 | context("Test conversions")
## generate data
set.seed(1)
tree <- rtree(10, FALSE)
tree2spl <- as.splits(tree)
spl2tree <- as.phylo(tree2spl)
dm <- cophenetic(tree2spl)
mat <- as.matrix(tree2spl)
Mat <- as.Matrix(tree2spl)
trees <- nni(tree)
test_that("splits", {
## skip on CRAN
skip_on_cran()
## check classes
expect_is(as.splits(trees), "splits")
expect_is(tree2spl, "splits")
expect_is(spl2tree,"phylo")
expect_is(dm,"dist")
expect_is(mat, "matrix")
expect_is(Mat, "Matrix")
expect_equal(spl2tree , tree)
# test generics
c_spl <- c(tree2spl, tree2spl, tree2spl)
expect_equal(length(c_spl) , 3L*length(tree2spl))
expect_equal(length(unique(c_spl)) , length(tree2spl))
expect_equal(length(distinct.splits(c_spl)) , length(tree2spl))
spl <- allCircularSplits(6)
spl <- phangorn:::oneWise(spl, 6)
write.nexus.splits(spl, "tmp.nex")
spl2 <- read.nexus.splits("tmp.nex")
attr(spl2, "splitlabels") <- NULL
attr(spl2, "weights") <- NULL
class(spl2) <- "splits"
expect_equal(spl2 , spl)
unlink("tmp.nex")
})
test_that("networx ", {
net1 <- neighborNet(dm)
write.nexus.networx(net1, "tmp.nex")
net2 <- read.nexus.networx("tmp.nex")
net3 <- as.networx(tree)
# delete some additional attributes
net2$.plot <- net2$translate <- NULL
attr(net1, "order") <- NULL
expect_is(net1, "networx")
expect_is(net2, "networx")
expect_is(net3, "networx")
# expect_equal(net1, net2, tolerance=1e-6)
# expect_equal(net3, net2, tolerance=1e-6)
expect_equal(net1, net3)
unlink("tmp.nex")
cnet <- consensusNet(as.splits(trees))
expect_is(cnet, "networx")
net1$edge.length <- cnet$edge.length <- cnet$edge.labels <- NULL
attr(cnet, "order") <- NULL
expect_equal(cnet, net1)
expect_equal(nrow(cnet$edge), length(as.splits(cnet)))
cnet
})
|