tests/testthat/test_branch_matrix.R

In oppr: Optimal Project Prioritization

context("branch matrix")

test_that("phylo input", {
  # create data
  phy <- structure(list(edge = structure(c(6L, 7L, 8L, 8L, 7L, 6L, 9L,
          9L, 7L, 8L, 1L, 2L, 3L, 9L, 4L, 5L), .Dim = c(8L, 2L)),
          tip.label = c("t1",  "t5", "t4", "t2", "t3"),
          edge.length = c(0.357997308950871, 0.279826242243871,
          0.22146653640084, 0.357243377715349, 0.00875525642186403,
          0.967695261584595,
          0.723838896490633, 0.0858941006008536), Nnode = 4L, .Names = c("edge",
          "tip.label", "edge.length", "Nnode", "tip.labels")),
          class = "phylo", order = "cladewise")
  # make branch matrix
  m <- branch_matrix(phy)
  # create correct branch matrix
  s <- matrix(0, ncol = nrow(phy$edge), nrow = length(phy$tip.label))
  s[1, c(3, 2, 1)] <- 1
  s[2, c(4, 2, 1)] <- 1
  s[3, c(5, 1)] <- 1
  s[4, c(7, 6)] <- 1
  s[5, c(8, 6)] <- 1
  s <- as_Matrix(s, "dgCMatrix")
  # tests
  expect_is(m, "dgCMatrix")
  expect_true(all(m == s))
})

test_that("invalid arguments", {
  tr <- ape::rtree(3)
  tr$edge[1] <- 0
  expect_error(branch_matrix(tr))
  expect_error(branch_matrix("a"))
})