inst/tests/test-treedata.R

In arborworkflows/aRbor: An R package with useful functions for Arbor workflows

context("treedata works")
test_that("treedata can handle matrix/dataframe input", {
  require(testthat)
  data(anolis)
  norn <- anolis$dat[,-1]
  rownames(norn) <- anolis$dat[,1]
  td0 <- make.treedata(anolis$phy, norn)
  td1 <- make.treedata(anolis$phy, as.matrix(anolis$dat))
  td2 <- make.treedata(anolis$phy, anolis$dat, name_column=1)
  jacknife <- sample(1:nrow(anolis$dat), 50, replace=FALSE)
  td3 <- make.treedata(anolis$phy, anolis$dat[jacknife,], name_column=1)
  td4 <- make.treedata(anolis$phy, as.matrix(anolis$dat[jacknife,]), name_column=1)
  
  ##Tests
  expect_equal(td0$dat$SVL, td1$dat$SVL,  tolerance=0.000001)
  expect_equal(td1$dat$SVL, td2$dat$SVL,  tolerance=0.000001)
  expect_equal(td1$dat$island, td2$dat$island)
  expect_equal(td3$dat$SVL, td4$dat$SVL,  tolerance=0.000001)
  expect_equal(td3$phy$tip.label, rownames(td3$dat))
  expect_equal(td4$phy$tip.label, rownames(td4$dat))
  
})