tests/testthat/test-nleaves.R

In dendextend: Extending 'dendrogram' Functionality in R

# library(testthat)

context("Tree size")


test_that("Get a hclust number of leaves", {
  hc <- hclust(dist(USArrests[1:3, ]), "ave")

  expect_true(nleaves(hc) == 3L)
})


test_that("Get a dendrogram number of leaves", {
  hc <- hclust(dist(USArrests[1:3, ]), "ave")
  dend <- as.dendrogram(hc)

  expect_true(nleaves(dend) == 3L)
})


test_that("nleaves works the same for members and order", {
  dend <- as.dendrogram(hclust(dist(USArrests)))
  expect_identical(nleaves(dend, "order"), nleaves(dend, "members"))
})



test_that("Get a dendrogram number of nodes", {
  hc <- hclust(dist(USArrests[1:3, ]), "ave")
  dend <- as.dendrogram(hc)

  expect_true(nnodes(dend) == 5L)
  expect_true(nnodes(hc) == 5L)
  
  # no default for nnodes
  expect_error(
     nnodes.default()   
  )
  # if non-dend object passed in
  expect_warning(expect_error(
     nnodes.dendrogram(hc)
  ))
  # for phylo
  expect_identical(
     nnodes.phylo(as.phylo(hc)),
     5
  )
  
})


test_that("Can't get a tree size for an object which is not hclust, dendrogram or phylo", {
  x <- 1:4
  expect_error(nleaves(x))
  x <- letters[1:4]
  expect_error(nleaves(x))
  x <- list(1:4)
  expect_error(nleaves(x))
})



test_that("Get a dendrogram tree size with leaves having their branch of height 0", {
  hc <- hclust(dist(USArrests[1:3, ]), "ave")
  dend <- as.dendrogram(hc)

  ###
  # Trivial case
  #    count_terminal_nodes(dend) # 3 terminal nodes
  #    nleaves(dend) # 3 - the same number
  expect_true(count_terminal_nodes(dend) == nleaves(dend))

  ###
  # NON-Trivial case
  #    str(dend)
  attr(dend[[2]], "height") <- 0
  #    count_terminal_nodes(dend) # 2 terminal nodes, why? see this plot:
  #    plot(dend, main = "This is considered a tree \n with TWO terminal nodes only") # while we have 3 leaves, in practice we have only 2 terminal nodes (this is a feature, not a bug.)
  expect_false(count_terminal_nodes(dend) == nleaves(dend))
})


test_that("nleaves.dendlist works", {
   dend1 <- as.dendrogram(hclust(dist(USArrests[1:3, ])))
   dend2 <- as.dendrogram(hclust(dist(USArrests[4:5, ])))
   dend12 <- dendlist(dend1, dend2)
   
   expect_equal(
      nleaves.dendlist(dend12),
      c(3,2)
   )
   
})


test_that("unclass_dend works", {
   dend <- as.dendrogram(hclust(dist(USArrests[1:3, ])))
   
   result <- unclass_dend(dend)
   expect_identical(
      typeof(result),
      "list"
   )
   
})


test_that("head.dendrogram works", {
   hc <- hclust(dist(USArrests), "ave")
   dend <- as.dendrogram(hc)
   
   capture.output(expect_no_error(
      head(dend)
   ))
})