o The new function makeNodeLabel creates and/or modifies node
labels in a flexible way.
+ o read.tree() and write.tree() have been modified so that they can
+ handle individual tree names
+
BUG FIXES
Package: ape
Version: 2.3
-Date: 2009-03-22
+Date: 2009-03-23
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, Vincent Lefort, Pierre Legendre,
- Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein,
- Korbinian Strimmer, Damien de Vienne
+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>
Depends: R (>= 2.6.0)
Suggests: gee
-## read.tree.R (2008-02-18)
+## read.tree.R (2009-03-09)
## Read Tree Files in Parenthetic Format
-## Copyright 2002-2008 Emmanuel Paradis
+## Copyright 2002-2009 Emmanuel Paradis and Daniel Lawson
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
obj
}
-read.tree <- function(file = "", text = NULL, tree.names = NULL,
- skip = 0, comment.char = "#", ...)
+read.tree <- function(file = "", text = NULL, tree.names = NULL, skip = 0,
+ comment.char = "#", keep.multi = FALSE, ...)
{
+ unname <- function(treetext) {
+ tstart <- 1
+ while (substr(treetext, tstart, tstart) != "(" && tstart <= nchar(treetext))
+ tstart <- tstart + 1
+ if (tstart > 1)
+ return(c(substr(treetext, 1, tstart - 1),
+ substr(treetext, tstart, nchar(treetext))))
+ return(c("", treetext))
+ }
if (!is.null(text)) {
if (!is.character(text))
stop("argument `text' must be of mode character")
tree <- scan(file = file, what = "", sep = "\n", quiet = TRUE,
skip = skip, comment.char = comment.char, ...)
}
+ tmp <- lapply(tree, unname)
+ tmpnames <- sapply(tmp, function(x) x[1])
+ tree <- sapply(tmp, function(x) x[2])
+ if (is.null(tree.names) && any(nzchar(tmpnames))) tree.names <- tmpnames
## Suggestion from Eric Durand and Nicolas Bortolussi (added 2005-08-17):
if (identical(tree, character(0))) {
warning("empty character string.")
if(sum(obj[[i]]$edge[, 1] == ROOT) == 1 && dim(obj[[i]]$edge)[1] > 1)
stop(paste("There is apparently two root edges in your file: cannot read tree file.\n Reading Newick file aborted at tree no.", i, sep = ""))
}
- if (Ntree == 1) obj <- obj[[1]] else {
+ if (Ntree == 1 && !keep.multi) obj <- obj[[1]] else {
if (!is.null(tree.names)) names(obj) <- tree.names
class(obj) <- "multiPhylo"
}
-## write.tree.R (2007-12-22)
+## write.tree.R (2009-03-23)
## Write Tree File in Parenthetic Format
-## Copyright 2002-2007 Emmanuel Paradis
+## Copyright 2002-2009 Emmanuel Paradis and Daniel Lawson
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
x
}
-write.tree <- function(phy, file = "", append = FALSE,
- digits = 10)
+write.tree <-
+ function (phy, file = "", append = FALSE, digits = 10, 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
+ }
+ if (output.tree.names)
+ names(tree) <- checkLabel(names(tree))
if (class(phy) == "multiPhylo") {
- write.tree(phy[[1]], file = file,
- append = append, digits = digits)
+ write.tree(phy[[1]], file = file, append = append,
+ digits = digits, tree.names = names[1])
if (length(phy) > 1)
- for (i in 2:length(phy))
- write.tree(phy[[i]], file = file,
- append = TRUE, digits = digits)
+ for (i in 2:length(phy)) write.tree(phy[[i]], file = file,
+ append = TRUE, digits = digits, tree.names = names(phy)[i])
return(invisible(NULL))
}
-
if (class(phy) != "phylo")
- stop('object "phy" is not of class "phylo"')
-
+ stop("object \"phy\" is not of class \"phylo\"")
brl <- !is.null(phy$edge.length)
-
-### Ne serait-il pas plus efficace de créer des node labels vides
-### "" et d'éviter l'évaluation if (nodelab) ????
-### Autre possibilité : créer plusieurs variants de ces fonctions
-### (au moins deux avec/sans edge.length)
-
-### Encore autre chose: les appels à which ne peuvent-ils pas
-### être évités ??? surtout si l'arbre est en cladewise order...
-
nodelab <- !is.null(phy$node.label)
phy$tip.label <- checkLabel(phy$tip.label)
- if (nodelab)
- phy$node.label <- checkLabel(phy$node.label)
-
+ if (nodelab) phy$node.label <- checkLabel(phy$node.label)
f.d <- paste("%.", digits, "g", sep = "")
-
cp <- function(s) STRING <<- paste(STRING, s, sep = "")
add.internal <- function(i) {
cp("(")
br <- which(phy$edge[, 1] == i)
for (j in br) {
desc <- phy$edge[j, 2]
- if (desc > n) add.internal(desc) else add.terminal(j)
- if (j != br[length(br)]) cp(",")
+ if (desc > n)
+ add.internal(desc)
+ else add.terminal(j)
+ if (j != br[length(br)])
+ cp(",")
}
cp(")")
- if (nodelab) cp(phy$node.label[i - n])
+ if (nodelab)
+ cp(phy$node.label[i - n])
if (brl) {
cp(":")
- cp(sprintf(f.d, phy$edge.length[which(phy$edge[, 2] == i)]))
+ cp(sprintf(f.d, phy$edge.length[which(phy$edge[,
+ 2] == i)]))
}
}
add.terminal <- function(i) {
}
}
n <- length(phy$tip.label)
- STRING <- "("
+ if(tree.names){STRING <- paste(tname,"(",sep="")
+ }else STRING <- "("
br <- which(phy$edge[, 1] == n + 1)
for (j in br) {
desc <- phy$edge[j, 2]
- if (desc > n) add.internal(desc) else add.terminal(j)
- if (j != br[length(br)]) cp(",")
+ if (desc > n)
+ add.internal(desc)
+ else add.terminal(j)
+ if (j != br[length(br)])
+ cp(",")
}
if (is.null(phy$root.edge)) {
cp(")")
- if (nodelab) cp(phy$node.label[1])
+ if (nodelab)
+ cp(phy$node.label[1])
cp(";")
- } else {
+ }
+ else {
cp(")")
- if (nodelab) cp(phy$node.label[1])
+ if (nodelab)
+ cp(phy$node.label[1])
cp(":")
cp(sprintf(f.d, phy$root.edge))
cp(";")
}
- if (file == "") return(STRING)
+ if (file == "")
+ return(STRING)
else cat(STRING, file = file, append = append, sep = "\n")
}
+
\alias{read.tree}
\title{Read Tree File in Parenthetic Format}
\usage{
-read.tree(file = "", text = NULL, tree.names = NULL,
- skip = 0, comment.char = "#", ...)
+read.tree(file = "", text = NULL, tree.names = NULL, skip = 0,
+ comment.char = "#", keep.multi = FALSE, ...)
}
\arguments{
\item{file}{a file name specified by either a variable of mode character,
\item{comment.char}{a single character, the remaining of the line
after this character is ignored (this is passed directly to
\code{scan()}).}
- \item{...}{Further arguments to be passed to \code{scan()}.}
+ \item{keep.multi}{if \code{TRUE} and \code{tree.names = NULL} then
+ single trees are returned in \code{"multiPhylo"} format, with any
+ name that is present (see details). Default is \code{FALSE}.}
+ \item{\dots}{further arguments to be passed to \code{scan()}.}
}
\description{
This function reads a file which contains one or several trees in
apparently not a valid Newick format. If there are two root edges
(e.g., "(((A:1,B:1):10):10);"), then the tree is not read and an error
message is issued.
+
+ If there are any characters preceding the first "(" in a line then
+ this is assigned to the name. This is returned when a "multiphylo"
+ object is returned and \code{tree.names = NULL}.
}
\value{
an object of class \code{"phylo"} with the following components:
If several trees are read in the file, the returned object is of class
\code{"multiPhylo"}, and is a list of objects of class \code{"phylo"}.
+ The name of each tree can be specified by \code{tree.names}, or can be
+ read from the file (see details).
}
\references{
Felsenstein, J. The Newick tree format.
in R. \url{http://ape.mpl.ird.fr/misc/FormatTreeR_28July2008.pdf}
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr} and Daniel
+ Lawson \email{dan.lawson@bristol.ac.uk}}
\seealso{
\code{\link{write.tree}}, \code{\link{read.nexus}},
\code{\link{write.nexus}}, \code{\link[base]{scan}} for the basic R
}
\examples{
### An extract from Sibley and Ahlquist (1990)
-cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,",
- "Athene_noctua:7.3):6.3,Tyto_alba:13.5);",
- file = "ex.tre", sep = "\n")
+cat("owls(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);", file = "ex.tre", sep = "\n")
tree.owls <- read.tree("ex.tre")
str(tree.owls)
tree.owls
+tree.owls <- read.tree("ex.tre", keep.multi = TRUE)
+tree.owls
+names(tree.owls)
unlink("ex.tre") # delete the file "ex.tre"
### Only the first three species using the option `text'
TREE <- "((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3);"
\title{Write Tree File in Parenthetic Format}
\usage{
write.tree(phy, file = "", append = FALSE,
- digits = 10)
+ digits = 10, tree.names = FALSE)
}
\arguments{
\item{phy}{an object of class \code{"phylo"}.}
the file (if it exists) is overwritten (\code{FALSE} the default).}
\item{digits}{a numeric giving the number of digits used for printing
branch lengths.}
+ \item{tree.names}{either a logical or a vector of mode character. If
+ \code{TRUE} then any tree names will be written prior to the tree on
+ each line. If character, specifies the name of \code{"phylo"}
+ objects which can be written to the file.}
}
\description{
This function writes in a file a tree in parenthetic format using the
\details{
The node labels and the root edge length, if available, are written in
the file.
+
+ If \code{tree.names == TRUE} then a variant of the Newick format is
+ written for which the name of a tree precedes the Newick format tree
+ (parentheses are eventually deleted beforehand).
}
\references{
Felsenstein, J. The Newick tree format.
\url{http://evolution.genetics.washington.edu/phylip/newick_doc.html}
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr} and Daniel
+ Lawson \email{dan.lawson@bristol.ac.uk}}
\seealso{
\code{\link{read.tree}}, \code{\link{read.nexus}},
\code{\link{write.nexus}}
}
\keyword{manip}
-\keyword{IO}
+\keyword{IO}
\ No newline at end of file
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