From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Sat, 20 Dec 2008 16:45:04 +0000 (+0000)
Subject: bug fixed in ltt.plot.R
X-Git-Url: https://git.donarmstrong.com/?p=ape.git;a=commitdiff_plain;h=3f528bd2c47301b64ed03bd28039bbf22a7510ad

bug fixed in ltt.plot.R

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@56 6e262413-ae40-0410-9e79-b911bd7a66b7
---

diff --git a/ChangeLog b/ChangeLog
index 8891e33..5a22435 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -9,6 +9,9 @@ BUG FIXES
       multiple lines with different numbers of lines and/or with
       comments inserted within the trees).
 
+    o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
+      the number of lineages with non-binary trees.
+
 
 
 		CHANGES IN APE VERSION 2.2-2
diff --git a/DESCRIPTION b/DESCRIPTION
index 74b1a1d..7c5ae46 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.2-3
-Date: 2008-11-24
+Date: 2008-12-20
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
   Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
diff --git a/R/ltt.plot.R b/R/ltt.plot.R
index 2a0179c..6421e8b 100644
--- a/R/ltt.plot.R
+++ b/R/ltt.plot.R
@@ -1,4 +1,4 @@
-## ltt.plot.R (2008-02-22)
+## ltt.plot.R (2008-12-20)
 
 ##    Lineages Through Time Plot
 
@@ -10,6 +10,7 @@
 ltt.plot <- function(phy, xlab = "Time", ylab = "N", ...)
 {
     if (class(phy) != "phylo") stop('object "phy" is not of class "phylo"')
+    if (!is.binary.tree(phy)) phy <- multi2di(phy)
     time <- sort(branching.times(phy), decreasing = TRUE)
     N <- 1:(length(time) + 1)
     plot.default(-c(time, 0), N, xlab = xlab, ylab = ylab,
@@ -18,6 +19,7 @@ ltt.plot <- function(phy, xlab = "Time", ylab = "N", ...)
 
 ltt.lines <- function(phy, ...)
 {
+    if (!is.binary.tree(phy)) phy <- multi2di(phy)
     time <- sort(branching.times(phy), decreasing = TRUE)
     N <- 1:(length(time) + 1)
     lines(-c(time, 0), N, type = "S", ...)
@@ -27,6 +29,7 @@ mltt.plot <- function(phy, ..., dcol = TRUE, dlty = FALSE, legend = TRUE,
                       xlab = "Time", ylab = "N", log = "")
 {
     ltt.xy <- function(phy) {
+        if (!is.binary.tree(phy)) phy <- multi2di(phy)
         x <- -c(sort(branching.times(phy), decreasing = TRUE), 0)
         names(x) <- NULL
         y <- 1:length(x)