Merge branch 'master' into no-phangorn

ms609 · Jun 27, 2024 · 24d2eeb · 24d2eeb
2 parents ffef11e + ed1423a
commit 24d2eeb
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Showing 4 changed files with 22 additions and 10 deletions.
diff --git a/R/cluster_stats.R b/R/cluster_stats.R
@@ -226,7 +226,7 @@ MeanMSTEdge.dist <- function(x, cluster = 1) {
   d <- as.matrix(x)
   diag(d) <- NA_real_
   vapply(seq_along(unique(cluster)),
-         function(i) .MeanNN.dist(d[cluster == i, cluster == i, drop = FALSE]),
+         function(i) .MeanMSTEdge.dist(d[cluster == i, cluster == i, drop = FALSE]),
          numeric(1))
 }
 

diff --git a/R/tree_distance_kendall-colijn.R b/R/tree_distance_kendall-colijn.R
@@ -219,7 +219,7 @@ KCDiameter.numeric <- function(tree) {
 
 #' @export
 KCDiameter.list <- function(tree) {
-  lapply(tree, KCDiameter)
+  vapply(tree, KCDiameter, double(1))
 }
 
 #' @export

diff --git a/tests/testthat/test-information.R b/tests/testthat/test-information.R
@@ -44,15 +44,20 @@ test_that("TreesConsistentWithTwoSplits works", {
 
   Test <- function(n, a, b, score) {
     logScore <- log(score)
+    l2Score <- log2(score)
 
-    expect_equal(score, TreesConsistentWithTwoSplits(n, a, b))
-    expect_equal(score, TreesConsistentWithTwoSplits(n, b, a))
-    expect_equal(score, TreesConsistentWithTwoSplits(n, n - a, n - b))
-    expect_equal(score, TreesConsistentWithTwoSplits(n, n - b, n - a))
-    expect_equal(logScore, LnTreesConsistentWithTwoSplits(n, a, b))
-    expect_equal(logScore, LnTreesConsistentWithTwoSplits(n, b, a))
-    expect_equal(logScore, LnTreesConsistentWithTwoSplits(n, n - a, n - b))
-    expect_equal(logScore, LnTreesConsistentWithTwoSplits(n, n - b, n - a))
+    expect_equal(TreesConsistentWithTwoSplits(n, a, b), score)
+    expect_equal(TreesConsistentWithTwoSplits(n, b, a), score)
+    expect_equal(TreesConsistentWithTwoSplits(n, n - a, n - b), score)
+    expect_equal(TreesConsistentWithTwoSplits(n, n - b, n - a), score)
+    expect_equal(Log2TreesConsistentWithTwoSplits(n, a, b), l2Score)
+    expect_equal(Log2TreesConsistentWithTwoSplits(n, b, a), l2Score)
+    expect_equal(Log2TreesConsistentWithTwoSplits(n, n - a, n - b), l2Score)
+    expect_equal(Log2TreesConsistentWithTwoSplits(n, n - b, n - a), l2Score)
+    expect_equal(LnTreesConsistentWithTwoSplits(n, a, b), logScore)
+    expect_equal(LnTreesConsistentWithTwoSplits(n, b, a), logScore)
+    expect_equal(LnTreesConsistentWithTwoSplits(n, n - a, n - b), logScore)
+    expect_equal(LnTreesConsistentWithTwoSplits(n, n - b, n - a), logScore)
   }
 
   Test(8, 3, 0, 315)

diff --git a/tests/testthat/test-tree_distance_kc.R b/tests/testthat/test-tree_distance_kc.R
@@ -1,5 +1,10 @@
 library("TreeTools", quietly = TRUE)
 
+test_that("KC fails gracefully", {
+  expect_error(KendallColijn(BalancedTree(8), BalancedTree(1:8)),
+               "Leaves must bear identical labels.")
+})
+
 test_that("KC vector calculations", {
 
   bal7 <- ape::read.tree(text = "(((t1,t2),(t3,t4)),((t5,t6),t7));")
@@ -45,9 +50,11 @@ test_that("KCDiameter() calculated", {
   Test(4)
   Test(40)
   tree1 <- ape::read.tree(text = "(a, (b, (c, (d, (e, (f, (g, h)))))));")
+  expect_equal(KendallColijn(tree1), 0)
   tree2 <- ape::read.tree(text = "(a, ((b, c), (d, (e, (f, (g, h))))));")
   tree3 <- ape::read.tree(text = "(a, (b, (c, (d, (e, (f, g))))));")
   trees <- c(tree1, tree2, tree3)
   expect_equal(KCDiameter(trees),
                c(KCDiameter(tree1), KCDiameter(tree2), KCDiameter(tree3)))
+  expect_equal(KCDiameter(list(tree1, tree2, tree3)), KCDiameter(trees))
 })