tests/testthat/test-as-phylo.R

In YuLab-SMU/treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

context("as.phylo")

## library(ggtree)

## in tree 1.3.4 and ggtree 1.11.4, converting tree to data.frame is deprecated.
## new treeio and ggtree supports tbl_tree object

## test_that("as.phylo for tbl_tree and ggtree", {
##     p <- ggtree(rtree(30))
##     x <- as.phylo(p) ## as.phylo.ggtree -> as.phylo.data.frame
##     msg <- capture.output(ape::checkValidPhylo(x))
##     expect_false(any(grepl("FATAL", msg)))
## })

test_that("as.phylo for tree igraph",{
  tr <- rtree(10)
  g <- ape::as.igraph.phylo(tr)
  tr2 <- as.phylo(g)
  expect_true(is(tr2, 'phylo'))
  expect_true(all(tr$tip.label %in% tr2$tip.label))
  expect_equal(tr$Nnode, tr2$Nnode)
})

test_that("as.phylo for tree igraph with weights",{
  set.seed(123)
  g <- igraph::sample_gnp(18, .3) %>%
        igraph::mst() %>%
        igraph::set_edge_attr(name='weight', value=abs(rnorm(length(igraph::E(.)))))
  tr <- as.phylo(g, branch.length = weight)
  expect_true(is(tr, 'phylo'))

  }
)