/usr/share/doc/r-cran-phangorn/tests/testthat/test_SH.R is in r-cran-phangorn 2.4.0-1.
This file is owned by root:root, with mode 0o644.
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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 | context("SH-test")
tree <- read.tree(text="(t1:0.1,t2:0.1,(t3:0.1,(t4:0.1,t5:0.1):0.1):0.1);")
set.seed(42)
dat <- simSeq(tree, l=500)
trees <- c(tree, nni(tree))
fits <- lapply(trees, pml, data=dat)
X <- sapply(fits, function(x)x$siteLik)
weight <- attr(dat, "weight")
test_that("SH-test works properly", {
skip_on_cran()
tmp <- SH.test(fits[[1]], fits[[2]])
expect_gt(tmp[1,"p-value"], 0)
expect_lt(tmp[2,"p-value"], 0.05)
tmp <- SH.test(X, weight=weight)
expect_gt(tmp[1,"p-value"], 0)
expect_lt(tmp[2,"p-value"], 0.05)
tmp <- SH.test(fits)
expect_gt(tmp[1,"p-value"], 0)
expect_lt(tmp[2,"p-value"], 0.05)
expect_lt(tmp[3,"p-value"], 0.05)
})
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