test_SH.R
In phangorn: Phylogenetic Reconstruction and Analysis

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")

# SH-test
tmp <- SH.test(fits[[1]], fits[[2]])
expect_true(tmp[1,"p-value"] > 0)
expect_true(tmp[2,"p-value"] <= 0.05)
tmp <- SH.test(X, weight=weight)
expect_true(tmp[1,"p-value"] > 0)
expect_true(tmp[2,"p-value"] <= 0.05)
tmp <- SH.test(fits)
expect_true(tmp[1,"p-value"] > 0)
expect_true(tmp[2,"p-value"] <= 0.05)
expect_true(tmp[3,"p-value"] <= 0.05)