/usr/share/doc/r-cran-phangorn/tests/testthat/test_treeRearrangement.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 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 | context("tree_rearrangement")
set.seed(42)
tree_u <- rtree(100, rooted=FALSE)
tree_r <- rtree(100)
test_that("nni", {
nni_trees_u <- nni(tree_u)
nni_trees_r <- nni(tree_r)
## nni
expect_is(nni(tree_u), "multiPhylo")
expect_true(all(RF.dist(nni_trees_u, tree_u)>0))
expect_true(length(nni_trees_u) == 194L)
expect_true(length(nni_trees_r) == 196L)
expect_true(all( RF.dist(tree_u, nni_trees_u) == 2))
expect_true(median( RF.dist(tree_r, nni_trees_r) ) == 2)
})
r_nni <- rNNI(tree_u, 3, 100)
test_that("rNNI", {
expect_true(length(r_nni) == 100L)
expect_true(median( RF.dist(tree_u, r_nni) ) == 6)
expect_true(median( RF.dist(r_nni[[1]], r_nni) ) == 12)
})
r_spr <- rSPR(tree_u, 3, 100)
test_that("allTrees", {
expect_true(length(r_spr) == 100L)
expect_true(median( SPR.dist(tree_u, r_spr) ) == 3)
expect_true(median( SPR.dist(r_spr[[1]], r_spr) ) == 6)
})
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