KCDiameter.multiPhylo() (#114)

ms609 · Feb 29, 2024 · 5cbff38 · 5cbff38
1 parent 1644628
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: TreeDist
 Type: Package
 Title: Calculate and Map Distances Between Phylogenetic Trees
-Version: 2.7.0.9000
+Version: 2.7.0.9001
 Authors@R: c(person("Martin R.", "Smith",
                     email = "[email protected]", 
                     role = c("aut", "cre", "cph", "prg"), 

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,10 @@
-# TreeDist 2.7.0.9000 (development)
+# TreeDist 2.7.0.9001 (development)
 
 - Fix dead links in documentation
 
+- Fix `KCDiameter.multiPhylo()` for multiple trees.
+
+
 # TreeDist 2.7.0 (2023-10-25)
 
 - Fix calculation error in `StrainCol()`.

diff --git a/R/parallel.R b/R/parallel.R
@@ -21,7 +21,7 @@
 #' @examples
 #' if (interactive()) { # Only run in terminal
 #'   library("TreeTools", quietly = TRUE)
-#'   nCores <- ceiling(detectCores() / 2)
+#'   nCores <- ceiling(parallel::detectCores() / 2)
 #'   StartParallel(nCores) # Takes a few seconds to set up processes
 #'   GetParallel()
 #'   ClusteringInfoDistance(as.phylo(0:6, 100))

diff --git a/R/tree_distance_kendall-colijn.R b/R/tree_distance_kendall-colijn.R
@@ -214,8 +214,8 @@ SplitVector <- function(tree) {
 #' metric.
 #'
 #' @examples
-#' KCDiameter(trees)
 #' KCDiameter(4)
+#' KCDiameter(trees)
 #' @importFrom TreeTools PectinateTree
 #' @rdname KendallColijn
 #' @export
@@ -237,10 +237,12 @@ KCDiameter.numeric <- function(tree) {
   Euclid(nTip - mat[lower.tri(mat)] + 1L, t(mat)[lower.tri(mat)])
 }
 
-#' @export
-KCDiameter.multiPhylo <- KCDiameter.phylo
-
 #' @export
 KCDiameter.list <- function(tree) {
   lapply(tree, KCDiameter)
 }
+
+#' @export
+KCDiameter.multiPhylo <- function(tree) {
+  vapply(tree, KCDiameter, double(1))
+}
diff --git a/man/KendallColijn.Rd b/man/KendallColijn.Rd
diff --git a/man/StartParallel.Rd b/man/StartParallel.Rd
diff --git a/tests/testthat/test-tree_distance_kc.R b/tests/testthat/test-tree_distance_kc.R
@@ -44,4 +44,10 @@ test_that("KCDiameter() calculated", {
   }
   Test(4)
   Test(40)
+  tree1 <- ape::read.tree(text = "(a, (b, (c, (d, (e, (f, (g, h)))))));")
+  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)))
 })