tests/testthat/test-phy_abundance.R

In rdiversity: Measurement and Partitioning of Similarity-Sensitive Biodiversity

context("Testing phy_abundance() function")

test_that("phy_abundance 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))

  # Calculate phy_abundance
  structure_matrix <- ps$structure
  pa <- testthat::expect_warning(phy_abundance(partition, structure_matrix))
})



test_that("phy_abundance 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))

  # Calculate phy_abundance
  structure_matrix <- ps$structure
  pa <- testthat::expect_warning(phy_abundance(partition, structure_matrix))
})