tests/testthat/test-phylo.R

In boydorr/RDiversity: Measurement and Partitioning of Similarity-Sensitive Biodiversity

context("Testing the phylogenetic diversity measures")

test_that("Answers match up with Leinster-Cobbold Appendix A", {
  # Ultrametric
  tree <- ape::read.tree(text = "(A:2,B:2)R:1;")
  partition <- c(0.6, 0.4)
  names(partition) <- tree$tip.label
  partition <- check_partition(partition)

  ps <- phy_struct(tree, partition)
  structure_matrix <- ps$structure
  T_bar <- ps$tbar
  similarity <- phy2branch(tree, partition)
  meta <- metacommunity(partition, similarity)

  expect_equivalent(sum(tree$edge.length) + tree$root.edge,
                    unlist(metadiv(raw_gamma(meta), 0)$diversity * T_bar))
  expect_equivalent(c(meta@type_abundance),
                    c(0.4, 0.2, (2 / 3) * 0.4, (1 / 3) * 0.4))
  expect_equivalent(meta@similarity,
                    rbind(c(1, 1, 0, 0), rep(1, 4), c(0, 0, 1, 1), rep(1, 4)))

  # Non-ultrametric
  tree <- ape::read.tree(text = "(A:1,B:2)R:1;")
  partition <- c(0.6, 0.4)
  names(partition) <- tree$tip.label
  partition <- check_partition(partition)
  #
  ps <- phy_struct(tree, partition)
  structure_matrix <- ps$structure
  T_bar <- ps$tbar
  similarity <- phy2branch(tree, partition)
  meta <- metacommunity(partition, similarity)

  expect_equivalent(sum(tree$edge.length) + tree$root.edge,
                    unlist(metadiv(raw_gamma(meta), 0)$diversity * T_bar))
  expect_equivalent(c(meta@type_abundance),
                    c(0.25, 0.25, (2 / 2.4) * 0.4, (1 / 2.4) * 0.4))
  expect_equivalent(meta@similarity,
                    rbind(c(1.2, 1.2, 0, 0), c(1.2, 1.2, 0.8, 0.8),
                          c(0, 0, 0.8, 0.8), c(1.2, 1.2, 0.8, 0.8)))
})


test_that("pmatrix is correct when tips belong to the same subcommunities", {
  # Using a specific example
  tree <- ape::read.tree(text="(A:2,B:2)R:1;")
  partition <- cbind(A = c(1, 1), B = c(1, 0))
  partition <- partition / sum(partition)
  row.names(partition) <- tree$tip.label
  similarity <- phy2branch(tree, partition)
  meta <- metacommunity(partition, similarity)

  expect_equivalent(meta@type_abundance,
                    cbind(A = c(2, 1, 2, 1), B = c(2, 1, 0, 0)) / 9)

  # Random example
  tree2 <- ape::rtree(10)
  partition2 <- cbind(A = sample(10), B = sample(10))
  partition2 <- partition2 / sum(partition2)
  row.names(partition2) <- tree2$tip.label
  similarity2 <- phy2branch(tree2, partition2)
  meta2 <- metacommunity(partition2, similarity2)

  expect_equivalent(sum(meta2@type_abundance), 1)
})