From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Tue, 10 Mar 2009 10:53:04 +0000 (+0000)
Subject: various fixes + del xenarthra
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=fc029e0a1be9a5bd338c941b00842cfad95c0336;p=ape.git

various fixes + del xenarthra

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@65 6e262413-ae40-0410-9e79-b911bd7a66b7
---

diff --git a/ChangeLog b/ChangeLog
index c01a581..b6bffe8 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -15,6 +15,13 @@ BUG FIXES
 
     o drop.tip() shuffled tip labels in some cases.
 
+    o is.ultrametric() now checks the ordering of the edge matrix.
+
+
+OTHER CHANGES
+
+    o The data set xenarthra has been removed.
+
 
 
 		CHANGES IN APE VERSION 2.2-4
diff --git a/DESCRIPTION b/DESCRIPTION
index 65f9a43..1cc4f4a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.3
-Date: 2009-03-04
+Date: 2009-03-10
 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/is.ultrametric.R b/R/is.ultrametric.R
index 476c229..76abc58 100644
--- a/R/is.ultrametric.R
+++ b/R/is.ultrametric.R
@@ -1,19 +1,19 @@
-## is.ultrametric.R (2007-12-18)
+## is.ultrametric.R (2009-03-09)
 
 ##   Test if a Tree is Ultrametric
 
-## Copyright 2003-2007 Emmanuel Paradis
+## Copyright 2003-2009 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
 is.ultrametric <- function(phy, tol = .Machine$double.eps^0.5)
 {
-### the tree must be in cladewise order
     if (class(phy) != "phylo")
       stop('object "phy" is not of class "phylo".')
     if (is.null(phy$edge.length))
       stop("the tree has no branch lengths.")
+    phy <- reorder(phy)
     n <- length(phy$tip.label)
     n.node <- phy$Nnode
 
diff --git a/data/xenarthra.R b/data/xenarthra.R
deleted file mode 100644
index 349802d..0000000
--- a/data/xenarthra.R
+++ /dev/null
@@ -1,39 +0,0 @@
-"xenarthra" <-
-structure(list(edge = structure(c(51, 51, 52, 52, 51, 53, 54,
-55, 56, 57, 57, 56, 58, 59, 59, 60, 60, 58, 61, 61, 62, 62, 55,
-63, 64, 64, 65, 65, 63, 66, 66, 54, 67, 68, 68, 69, 69, 67, 70,
-70, 71, 71, 72, 72, 53, 73, 74, 74, 75, 75, 76, 76, 77, 77, 78,
-79, 79, 80, 80, 78, 81, 81, 73, 82, 83, 83, 82, 84, 85, 86, 87,
-88, 88, 87, 89, 89, 86, 90, 90, 91, 91, 85, 92, 93, 93, 92, 94,
-94, 95, 95, 96, 96, 97, 97, 84, 98, 98, 1, 52, 2, 3, 53, 54,
-55, 56, 57, 4, 5, 58, 59, 6, 60, 7, 8, 61, 9, 62, 10, 11, 63,
-64, 12, 65, 13, 14, 66, 15, 16, 67, 68, 17, 69, 18, 19, 70, 20,
-71, 21, 72, 22, 23, 73, 74, 24, 75, 25, 76, 26, 77, 27, 78, 79,
-28, 80, 29, 30, 81, 31, 32, 82, 83, 33, 34, 84, 85, 86, 87, 88,
-35, 36, 89, 37, 38, 90, 39, 91, 40, 41, 92, 93, 42, 43, 94, 44,
-95, 45, 96, 46, 97, 47, 48, 98, 49, 50), .Dim = c(97, 2)), edge.length = c(0.109894,
-0.022173, 0.066834, 0.047474, 0.427827, 0.002024, 0.025857, 0.022981,
-0.026731, 0.007126, 0.008411, 0.006233, 0.017379, 0.002957, 0.001106,
-0.002583, 0.003687, 0.005152, 0.012123, 0.000671, 0.011783, 0.008738,
-0.008776, 0.011882, 0.035474, 0.038071, 0.012415, 0.012484, 0.025252,
-0.021598, 0.015425, 0.029149, 0.013247, 0.033688, 0.003945, 0.047081,
-0.123258, 0.004856, 0.082597, 0.002941, 0.156433, 0.006792, 0.097117,
-0.220728, 0.009689, 0.00691, 0.12952, 0.00221, 0.086326, 0.000742,
-0.06454, 0.00375, 0.140251, 0.012014, 0.006192, 0.266772, 0.204941,
-0.070565, 0.056994, 0.041168, 0.058614, 0.062632, 0.013307, 0.015539,
-0.112732, 0.168348, 0.003898, 0.00109, 0.014771, 0.001936, 0.050427,
-0.017972, 0.038131, 0.007296, 0.070184, 0.060133, 0.014944, 0.182596,
-0.010519, 0.055868, 0.040506, 0.000379, 0.015614, 0.035851, 0.045494,
-0.024393, 0.059475, 0.005829, 0.081795, 0.00852, 0.09217, 0.003101,
-0.051699, 0.038765, 0.006122, 0.082358, 0.082157), tip.label = c("Didelphis",
-"Macropus", "Vombatus", "Dasypus_no", "Dasypus_ka", "Zaedyus",
-"Chaetophractus", "Euphractus", "Priodontes", "Tolypeutes", "Cabassous",
-"Cyclopes", "Myrmecophaga", "Tamandua", "Bradypus", "Choloepus",
-"Dugong", "Elephas", "Procavia", "Orycteropus", "Macroscelides",
-"Amblysomus", "Echinops", "Tupaia", "Homo", "Cynocephalus", "Lepus",
-"Hystrix", "Mus", "Rattus", "Glaucomys", "Aplodontia", "Scalopus",
-"Erinaceus", "Pteropus", "Cynopterus", "Megaderma", "Hipposideros",
-"Tonatia", "Myotis", "Tadarida", "Diceros", "Equus", "Lama",
-"Sus", "Bos", "Hippopotamus", "Physeter", "Manis", "Felis"),
-    Nnode = 48), .Names = c("edge", "edge.length", "tip.label",
-"Nnode"), class = "phylo")
diff --git a/man/phymltest.Rd b/man/phymltest.Rd
index 737beed..d71789a 100644
--- a/man/phymltest.Rd
+++ b/man/phymltest.Rd
@@ -115,7 +115,7 @@ phymltest(seqfile, format = "interleaved", itree = NULL,
   Guindon, S. and Gascuel, O. (2003) A simple, fast, and accurate
   algorithm to estimate large phylogenies by maximum likelihood.
   \emph{Systematic Biology}, \bold{52}, 696--704.
-  \url{http://atgc.lirmm.fr/phyml/}
+  \url{http://www.atgc-montpellier.fr/phyml/}
 }
 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
 \seealso{
diff --git a/man/xenarthra.Rd b/man/xenarthra.Rd
deleted file mode 100644
index c0e917e..0000000
--- a/man/xenarthra.Rd
+++ /dev/null
@@ -1,35 +0,0 @@
-\name{xenarthra}
-\alias{xenarthra}
-\title{Molecular Phylogeny of Living Xenarthrans}
-\description{
-  This phylogeny was inferred by maximum likelihood analysis of the
-  nuclear gene BRCA1 (breast cancer susceptibility, 2788 sites)
-  sequences for 47 placental and 3 marsupial taxa.
-}
-\usage{
-data(xenarthra)
-}
-\format{
-  The data are stored as an object of class \code{"phylo"} which
-  structure is described in the help page of the function
-  \code{\link{read.tree}}.
-}
-\source{
-  Delsuc, F., Scally, M., Madsen, O., Stanhope, M. J., de Jong, W. W.,
-  Catzeflis, F. M., Springer, M. S. and Douzery, E. J. P. (2002)
-  Molecular phylogeny of living xenarthrans and the impact of character
-  and taxon sampling on the placental tree rooting. \emph{Molecular
-    Biology and Evolution}, \bold{19}, 1656--1671.
-}
-\seealso{
-  \code{\link{read.tree}}
-}
-\examples{
-data(xenarthra)
-plot(xenarthra)
-### remove the margins...
-plot(xenarthra, no.margin = TRUE)
-### ... and use a smaller font size
-plot(xenarthra, no.margin = TRUE, cex = 0.8)
-}
-\keyword{datasets}