Test new trees in sq_trees

tests/testthat/test-PartitionDistance.R

@@ -3,8 +3,8 @@ context("PartitionDistance.R")
 data('sq_trees')
 
 test_that("SplitStatus works", {
-  expect_equal(c(15, 8), dim(SplitStatus(sq_trees)))
-  expect_equal(c(15, 8), dim(SplitStatus(sq_trees, sq_trees$opposite_tree)))
+  expect_equal(c(length(sq_trees), 8), dim(SplitStatus(sq_trees)))
+  expect_equal(c(length(sq_trees), 8), dim(SplitStatus(sq_trees, sq_trees$opposite_tree)))
   expect_equal(SplitStatus(sq_trees, sq_trees$ref_tree), SplitStatus(sq_trees))
 })
 

tests/testthat/test-TernaryPoints.R

@@ -5,34 +5,35 @@ data('sq_trees')
 test_that("Splits comparisons are correct", {
 
 
-  expect_equal(c(15, 3), dim(BipartitionPoints(sq_trees)))
+  expect_equal(c(length(sq_trees), 3), dim(BipartitionPoints(sq_trees)))
   expect_identical(8, unique(rowSums(BipartitionPoints(sq_trees))))
-  expect_equal(c(15, 3), dim(BipartitionPoints(sq_trees, cf=sq_trees$collapse_some)))
+  expect_equal(c(length(sq_trees), 3), dim(BipartitionPoints(sq_trees, cf=sq_trees$collapse_some)))
   expect_equal(c(0,0,8, 0,1,7, 0,3,5, 0,4,4, 0,1,7, 0,2,6, 0,3,5,
-                 1,0,7, 5,0,3, 1,3,4, 3,3,2, 1,2,5, 5,0,3, 0,8,0, 0,8,0),
+                 1,0,7, 5,0,3, 1,3,4, 3,3,2, 1,2,5, 5,0,3, 0,8,0, 
+                 0,4,4, rep(c(0,8,0), 3)),
                as.integer(unlist(t(SplitPoints(sq_trees)))))
 
   splitsVsOne <- SplitPoints(sq_trees, cf=sq_trees$collapse_one)
   expect_equal(rownames(splitsVsOne), names(sq_trees))
   # Numbers lazily copied from output, rather than calculated;
   # independent verification could be valuable.
-  expect_equal(c(rep(0, 8),4,0,2,0,4,0,0), splitsVsOne$Unresolved)
-  expect_equal(c(0,1,3,4,1,2,3,0,0,3,3,2,0,7,7), splitsVsOne$Contradicted)
-  expect_equal(c(7,6,4,3,6,5,4,7,3,4,2,5,3,0,0), splitsVsOne$Consistent)
+  expect_equal(c(rep(0, 8),4,0,2,0,4,rep(0, 5)), splitsVsOne$Unresolved)
+  expect_equal(c(0,1,3,4,1,2,3,0,0,3,3,2,0,7,3,7,7,7), splitsVsOne$Contradicted)
+  expect_equal(c(7,6,4,3,6,5,4,7,3,4,2,5,3,0,4,0,0,0), splitsVsOne$Consistent)
   expect_equal(as.integer(data.frame(Unresolved=0, Contradicted=0, Consistent=3)),
                as.integer(SplitPoints(sq_trees$collapse_one, cf=sq_trees$collapse_some)))
 }
 )
 
 test_that("Quartet comparisons are correct", {
-  expect_equal(c(15, 3), dim(QuartetPoints(sq_trees)))
+  expect_equal(c(length(sq_trees), 3), dim(QuartetPoints(sq_trees)))
   expect_identical(330, unique(rowSums(QuartetPoints(sq_trees))))
   # Numbers lazily copied from output, rather than calculated;
   # independent verification could be valuable.
   cfCollapseOne <- QuartetPoints(sq_trees, cf=sq_trees$collapse_one)
-  expect_equal(c(rep(0, 8), 115, 0, 57, 0, 197, 0, 0), cfCollapseOne$Unresolved)
-  expect_equal(c(0, 8, 52, 76, 24, 78, 92, 0, 0, 52, 52, 78, 0, 237, 219), 
-               cfCollapseOne$Contradicted)
+  expect_equal(c(rep(0, 8), 115, 0, 57, 0, 197, rep(0, 5)), cfCollapseOne$Unresolved)
+  expect_equal(c(0, 8, 52, 76, 24, 78, 92, 0, 0, 52, 52, 78, 0, 237,
+                 84, 206, 240, 219), cfCollapseOne$Contradicted)
 })
 
 test_that("Line ends are correct", {

tests/testthat/test-ZZZ-Metrics.R

@@ -12,8 +12,10 @@ test_that("Quartets are counted correctly", {
   quartet_matches <- QuartetStatus(sq_trees)
 
   expected_identical <- c(330L, 322L, 278L, 254L, 306L, 252L, 238L, 
-                          322L, 207L, 270L, 213L, 244L, 125L, 86L, 104L)
-  expected_ambiguous <- c(rep(0L, 7), 8L, 123L, 8L, 65L, 8L, 205L, 0L, 0L)
+                          322L, 207L, 270L, 213L, 244L, 125L, 86L,
+                          244L, 122L, 85L, # Values for these three new trees copied without checking
+                          104L)
+  expected_ambiguous <- c(rep(0L, 7), 8L, 123L, 8L, 65L, 8L, 205L, rep(0L, 5L))
   names(expected_identical) <- names(expected_ambiguous) <- names(sq_trees)
 
   expect_identical(expected_identical, quartet_matches[, 's'])