tests/testthat/test_Contradiction_05-25-17.R

In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

test_that("contradiction distance tests work as expected", {

# test for hidden function testContradiction

library(paleotree)

test<-c(
  paleotree:::testContradiction(c("A","B"),c("A","B")), #should be FALSE (no contradiction)
  paleotree:::testContradiction(c("A","B"),c("C","D")), #should be FALSE
  paleotree:::testContradiction(c("A","B"),c("A","C")), #should be TRUE
  paleotree:::testContradiction(c("A","B"),c("B","C")), #should be TRUE
  paleotree:::testContradiction(c("A","B"),c("A","D")), #should be TRUE
  paleotree:::testContradiction(c("A","B"),c("B","D"))  #should be TRUE
)
expected<-c(FALSE,FALSE,TRUE,TRUE,TRUE,TRUE)

#if(!identical(test,expected)){
#	stop("testContradiction failed")
#	}

expect_identical(test,expected)

# test with three labels
test<-c(
  paleotree:::testContradiction(c("A","B","C"),c("A","B")), #should be FALSE
  paleotree:::testContradiction(c("A","B","C"),c("C","D")), #should be TRUE
  paleotree:::testContradiction(c("A","B","C"),c("A","C")), #should be FALSE
  paleotree:::testContradiction(c("A","B","C"),c("B","C")), #should be FALSE
  paleotree:::testContradiction(c("A","B","C"),c("A","D")), #should be TRUE
  paleotree:::testContradiction(c("A","B","C"),c("B","D"))  #should be TRUE
  )

expected<-c(FALSE,TRUE,FALSE,FALSE,TRUE,TRUE)

#if(!identical(test,expected)){
#	stop("testContradiction failed")
#	}

expect_identical(test, expected)

set.seed(1)
treeA<-ape::rtree(30,br=NULL)
treeB<-ape::rtree(30,br=NULL)
# let's simulate the worst resolved tree possible: a star tree
treeC<-ape::stree(30)

# Tree C (the star tree) has zero CD between it and trees A and B
test<-c(
	identical(treeContradiction(treeA,treeC),0),  # should be zero distance
	identical(treeContradiction(treeB,treeC),0),  # should be zero distance
	# two identical trees also have zero CD between them (as you'd hope) 
	identical(treeContradiction(treeA,treeA),0)  # should be zero distanceH
	)
	
#if(!all(test)){
#	stop("test of treeContradiction failed!")
#	}

expect_true(all(test))

})