context("Testing phy_struct() function")
test_that("phy_struct works when species are missing from the partition", {
tree <- ape::rtree(n = 5)
tree$tip.label <- paste0("sp", seq_along(tree$tip.label))
partition <- cbind(a = c(1, 1, 1, 0, 0), b = c(0, 1, 0, 1, 1))
row.names(partition) <- tree$tip.label
# Remove species from partition
partition <- partition[-3, ]
partition <- partition / sum(partition)
# Calculate phy_struct
ps <- testthat::expect_warning(phy_struct(tree, partition))
})
test_that("phy_struct works when species are missing from the phylogeny", {
tree <- ape::rtree(n = 5)
tree$tip.label <- paste0("sp", seq_along(tree$tip.label))
partition <- cbind(a = c(1, 1, 1, 0, 0), b = c(0, 1, 0, 1, 1))
row.names(partition) <- tree$tip.label
# Remove species from partition
partition <- rbind(partition, sp9 = 1)
partition <- partition / sum(partition)
# Calculate phy_struct
ps <- testthat::expect_warning(phy_struct(tree, partition))
})
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