NEW FEATURES
+ o The new function is.monophyletic tests the monophyly of a group.
+
o There is now a c() method for lists of class "DNAbin".
o yule.cov() now fits the null model, and its help page has been
the fix. With other improvements, this function is now about 6
times faster.
+ o write.tree() failed with objects of class "multiPhylo".
+
OTHER CHANGES
o rcoal() is now faster.
+
+DEPRECATED & DEFUNCT
+
o klastorin() has been removed.
Package: ape
Version: 2.3-1
-Date: 2009-06-12
+Date: 2009-06-19
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
## find the tips to drop:
if (is.character(tip))
tip <- which(phy$tip.label %in% tip)
- trms <- edge2 <= Ntip
## delete the terminal edges given by `tip':
keep[match(tip, edge2)] <- FALSE
if (trim.internal) {
- ## delete the internal edges that do not have descendants
- ## anymore (ie, they are in the 2nd column of `edge' but
+ internals <- edge2 <= Ntip
+ ## delete the internal edges that do not have anymore
+ ## descendants (ie, they are in the 2nd col of `edge' but
## not in the 1st one)
repeat {
- sel <- !(edge2 %in% edge1[keep]) & !trms & keep
+ sel <- !(edge2 %in% edge1[keep]) & internals & keep
if (!sum(sel)) break
keep[sel] <- FALSE
}
if (subtree) {
## keep the subtending edge(s):
subt <- edge1 %in% edge1[keep] & edge1 %in% edge1[!keep]
- ## <FIXME> 'if (... ' needed below?
- if (any(subt)) keep[which(subt)] <- TRUE
+ keep[subt] <- TRUE
}
if (root.edge && wbl) {
degree <- tabulate(edge1[keep])
--- /dev/null
+## ace.R (2009-06-19)
+
+## Ancestral Character Estimation
+
+## Copyright 2009 Johan Nylander and Emmanuel Paradis
+
+## This file is part of the R-package `ape'.
+## See the file ../COPYING for licensing issues.
+
+is.monophyletic <-
+ function(phy, tips, reroot = !is.rooted(phy), plot = FALSE, ...)
+{
+ if (!inherits(phy, "phylo"))
+ stop("object 'phy' is not of class 'phylo'")
+ if (length(tips) == 1) return(TRUE)
+ n <- length(phy$tip.label)
+ if (length(tips) == n) return(TRUE)
+ ROOT <- n + 1
+ if (is.numeric(tips)) {
+ if (any(tips > n))
+ stop("incorrect tip#: should not be greater than the number of tips")
+ tips <- sort(tips)
+ }
+ if (is.character(tips))
+ tips <- which(phy$tip.label %in% tips)
+
+ if (reroot) {
+ outgrp <- phy$tip.label[-tips][1]
+ phy <- root(phy, outgroup = outgrp, resolve.root = TRUE)
+ rerooted <- TRUE
+ } else rerooted <- FALSE
+
+ phy <- reorder(phy)
+
+ seq.nod <- .Call("seq_root2tip", phy$edge, n, phy$Nnode, PACKAGE = "ape")
+ sn <- seq.nod[tips]
+ newroot <- ROOT
+ i <- 2
+ repeat {
+ x <- unique(unlist(lapply(sn, "[", i)))
+ if (length(x) != 1) break
+ newroot <- x
+ i <- i + 1
+ }
+ desc <- which(unlist(lapply(seq.nod, function(x) any(x %in% newroot))))
+ if (plot) {
+ zoom(phy, tips, subtree = FALSE, ...)
+ if (rerooted)
+ mtext("Input tree arbitrarily rerooted", side = 1, cex = 0.9)
+ }
+ ## assuming that both vectors are sorted:
+ identical(tips, desc)
+} # end of is.monophyletic
-## write.tree.R (2009-05-10)
+## write.tree.R (2009-06-16)
## Write Tree File in Parenthetic Format
write.tree <-
function (phy, file = "", append = FALSE, digits = 10, tree.names = FALSE)
{
+ output.tree.names <- FALSE
if (is.logical(tree.names)) {
output.tree.names <- tree.names
tree.names <- NULL
} else if (is.character(tree.names)) {
output.tree.names <- TRUE
- names(tree) <- tree.names
+ names(phy) <- tree.names
}
if (output.tree.names)
- names(tree) <- checkLabel(names(tree))
+ names(phy) <- checkLabel(names(phy))
if (inherits(phy, "multiPhylo")) {
write.tree(phy[[1]], file = file, append = append,
- digits = digits, tree.names = names[1])
+ digits = digits, tree.names = names(phy)[1])
if (length(phy) > 1)
for (i in 2:length(phy)) write.tree(phy[[i]], file = file,
append = TRUE, digits = digits, tree.names = names(phy)[i])
-## zoom.R (2008-04-16)
+## zoom.R (2009-06-12)
## Zoom on a Portion of a Phylogeny
-## Copyright 2003-2008 Emmanuel Paradis
+## Copyright 2003-2009 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
for (i in 1:n)
if (is.character(focus[[i]]))
focus[[i]] <- which(phy$tip.label %in% focus[[i]]) # fix by Yan Wong
- if (is.function(col))
- if (deparse(substitute(col)) == "grey")
- col <- grey(1:n/n) else col <- col(n)
- ext <- list()
- length(ext) <- n
+ if (is.function(col)) {
+ col <- if (deparse(substitute(col)) == "grey") grey(1:n/n) else col(n)
+ }
+ ext <- vector("list", n)
for (i in 1:n)
ext[[i]] <- drop.tip(phy, phy$tip.label[-focus[[i]]],
subtree = subtree)
--- /dev/null
+\name{is.monophyletic}
+\alias{is.monophyletic}
+\title{
+ Is Group Monophyletic
+}
+\usage{
+is.monophyletic(phy, tips, reroot = NULL, plot = FALSE, ...)
+}
+\description{
+ This function tests whether a list of tip labels is monophyletic on a given tree.
+}
+\arguments{
+ \item{phy}{
+ a phylogenetic tree description of class \code{"phylo"}.
+ }
+ \item{tips}{
+ a vector of mode numeric or character specifying the tips to be tested.
+ }
+ \item{reroot}{
+ a logical. If \code{FALSE}, then the input tree is not unrooted before the test.
+ }
+ \item{plot}{
+ a logical. If \code{TRUE}, then the tree is plotted with the specified group \code{tips} highlighted.
+ }
+ \item{...}{
+ further arguments passed to \code{plot}.
+ }
+}
+\details{
+ If \code{phy} is rooted, the test is done on the rooted tree, otherwise
+ the tree is first unrooted, then arbitrarily rerooted, in order to be
+ independent on the current position of the root. That is, the test
+ asks if \code{tips} could be monophyletic given any favourably rooting
+ of \code{phy}.
+
+ If \code{phy} is unrooted the test is done on an unrooted tree, unless
+ \code{reroot = FALSE} is specified.
+
+ If tip labels in the list \code{tips} are given as characters, they need
+ to be spelled as in the object \code{phy}.
+}
+\value{
+ \code{TRUE} or \code{FALSE}.
+}
+\author{
+ Johan Nylander \email{jnylander@users.sourceforge.net}
+}
+\seealso{
+ \code{\link{which.edge}}, \code{\link{drop.tip}}, \code{\link{mrca}}.
+}
+\examples{
+ ## Test one monophyletic and one paraphyletic group on the bird.orders tree
+ \dontrun{data("bird.orders")}
+ \dontrun{is.monophyletic(phy = bird.orders, tips = c("Ciconiiformes", "Gruiformes"))}
+ \dontrun{is.monophyletic(bird.orders, c("Passeriformes", "Ciconiiformes", "Gruiformes"))}
+ \dontshow{\dontrun{rm(bird.orders)}}
+}
+\keyword{utilities}
+
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