From 5cbff387ee39cd855f7e7dbc34d5c480c0d72860 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Thu, 29 Feb 2024 07:58:16 +0000
Subject: [PATCH] KCDiameter.multiPhylo() (#114)

---
 DESCRIPTION                            |  2 +-
 NEWS.md                                |  5 ++++-
 R/parallel.R                           |  2 +-
 R/tree_distance_kendall-colijn.R       | 10 ++++++----
 man/KendallColijn.Rd                   |  2 +-
 man/StartParallel.Rd                   |  2 +-
 tests/testthat/test-tree_distance_kc.R |  6 ++++++
 7 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b4790f17c..da45e9d3f 100644
--- 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 = "martin.smith@durham.ac.uk", 
                     role = c("aut", "cre", "cph", "prg"), 
diff --git a/NEWS.md b/NEWS.md
index 81ffcde89..bbce4f2c4 100644
--- 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
index 541172194..1e86e1ee1 100644
--- 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
index d88724941..3657c0828 100644
--- 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))
+}
\ No newline at end of file
diff --git a/man/KendallColijn.Rd b/man/KendallColijn.Rd
index cbea16de3..dbf9cb956 100644
--- a/man/KendallColijn.Rd
+++ b/man/KendallColijn.Rd
@@ -113,8 +113,8 @@ tree3 <- ape::read.tree(text = "(a, (b, (c, (d, (e, ((f, g), h))))));")
 trees <- c(tree1, tree2, tree3)
 KendallColijn(trees)
 KendallColijn(trees, Vector = SplitVector)
-KCDiameter(trees)
 KCDiameter(4)
+KCDiameter(trees)
 }
 \references{
 \insertAllCited{}
diff --git a/man/StartParallel.Rd b/man/StartParallel.Rd
index f52611992..71d5efc88 100644
--- a/man/StartParallel.Rd
+++ b/man/StartParallel.Rd
@@ -50,7 +50,7 @@ cluster.
 \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/tests/testthat/test-tree_distance_kc.R b/tests/testthat/test-tree_distance_kc.R
index 3f055b594..30063673f 100644
--- 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)))
 })