CHANGES IN APE VERSION 2.4-1
+NEW FEATURES
+
+ o rtree() and rcoal() now accept a numeric vector for the 'br'
+ argument.
+
+
BUG FIXES
o bind.tree() failed when 'y' had no root edge.
Package: ape
Version: 2.4-1
-Date: 2009-10-27
+Date: 2009-11-03
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>
-## rtree.R (2000-05-13)
+## rtree.R (2009-11-03)
## Generates Random Trees
phy$tip.label <-
if (is.null(tip.label)) paste("t", sample(n), sep = "")
else sample(tip.label)
- if (is.function(br)) phy$edge.length <- br(nbr, ...)
+ if (!is.null(br)) {
+ phy$edge.length <-
+ if (is.function(br)) br(nbr, ...) else rep(br, length.out = nbr)
+ }
phy$Nnode <- n - 2L + rooted
class(phy) <- "phylo"
phy
edge <- matrix(NA, nbr, 2)
## coalescence times by default:
x <- if (is.character(br)) 2*rexp(n - 1)/(as.double(n:2) * as.double((n - 1):1))
- else br(n - 1, ...)
+ else if (is.numeric(br)) rep(br, length.out = n - 1) else br(n - 1, ...)
if (n == 2) {
edge[] <- c(3L, 3L, 1:2)
edge.length <- rep(x, 2)
\arguments{
\item{object}{An object inheriting from class \code{corPhyl}.}
\item{data}{The data to use. If it contains rownames, they are matched with the tree tip labels, otherwise data are supposed to be in the same order than tip labels and a warning is sent.}
- \item{...}{some methods for this generic require additional arguments. None are used in this method.}
+ \item{\dots}{some methods for this generic require additional arguments. None are used in this method.}
}
\description{
Initialize a \code{corPhyl} correlation structure object.
lengths.}
\item{scale}{a positive number, comparison of branch lengths is made
after scaling (i.e., dividing) them by this number.}
- \item{...}{further arguments passed to or from other methods.}
+ \item{\dots}{further arguments passed to or from other methods.}
}
\description{
This function makes a global comparison of two phylogenetic trees.
\arguments{
\item{x}{a matrix or a list containing the DNA sequences, or an object
of class \code{"alignment"}.}
- \item{...}{further arguments to be passed to or from other methods.}
+ \item{\dots}{further arguments to be passed to or from other methods.}
}
\details{
For \code{as.alignment}, the sequences given as argument should be
}
\arguments{
\item{x}{an object to be converted into another class.}
- \item{...}{further arguments to be passed to or from other methods.}
+ \item{\dots}{further arguments to be passed to or from other methods.}
\item{phy}{an object of class \code{"phylo"}.}
}
\description{
\arguments{
\item{side}{a numeric value specifying the side where the axis is
plotted: 1: below, 2: left, 3: above, 4: right.}
- \item{...}{further arguments to be passed to \code{axis}.}
+ \item{\dots}{further arguments to be passed to \code{axis}.}
}
\description{
This function adds a scaled axis on the side of a phylogeny plot.
\arguments{
\item{phy}{an object of class \code{"phylo"}.}
\item{x}{an object of class \code{"birthdeath"}.}
- \item{...}{further arguments passed to the \code{print} function.}
+ \item{\dots}{further arguments passed to the \code{print} function.}
}
\description{
This function fits by maximum likelihood a birth-death model to the
\item{scope}{<unused>.}
\item{quiet}{a logical specifying whether to display a warning message
about eventual ``marginality principle violation''.}
- \item{...}{further arguments to be passed to \code{drop1}.}
+ \item{\dots}{further arguments to be passed to \code{drop1}.}
}
\description{
\code{compar.gee} performs the comparative analysis using generalized
this must be one of the followings: (i) \code{"Grafen"} (the
default), (ii) a numeric vector, or (iii) a function.}
\item{power}{The power at which heights must be raised (see below).}
- \item{...}{further argument(s) to be passed to \code{method} if it is
+ \item{\dots}{further argument(s) to be passed to \code{method} if it is
a function.}
}
\description{
consensus(..., p = 1, check.labels = TRUE)
}
\arguments{
- \item{...}{either (i) a single object of class \code{"phylo"}, (ii) a
+ \item{\dots}{either (i) a single object of class \code{"phylo"}, (ii) a
series of such objects separated by commas, or (iii) a list
containing such objects.}
\item{p}{a numeric value between 0.5 and 1 giving the proportion for a
in unconstrained form (the same used in the optimization
algorithm). If 'FALSE' the coefficients are returned in
"natural", possibly constrained, form. Defaults to 'TRUE'}
- \item{...}{some methods for these generics require additional arguments.
+ \item{\dots}{some methods for these generics require additional arguments.
None are used in these methods.}
}
\description{
returned in unconstrained form (the same used in the optimization
algorithm). If 'FALSE' the coefficients are returned in "natural",
possibly constrained, form. Defaults to 'TRUE'}
- \item{...}{some methods for these generics require additional
+ \item{\dots}{some methods for these generics require additional
arguments. None are used in these methods.}
}
\description{
in unconstrained form (the same used in the optimization
algorithm). If 'FALSE' the coefficients are returned in
"natural", possibly constrained, form. Defaults to 'TRUE'}
- \item{...}{some methods for these generics require additional arguments.
+ \item{\dots}{some methods for these generics require additional arguments.
None are used in these methods.}
}
\description{
information.}
\item{labels}{a logical specifying whether to return the labels; by
default only the numbers are returned.}
- \item{...}{further arguments to be passed to or from other methods.}
+ \item{\dots}{further arguments to be passed to or from other methods.}
}
\description{
This function allows to identify a clade on a plotted tree by clicking
\item{plot}{
a logical. If \code{TRUE}, then the tree is plotted with the specified group \code{tips} highlighted.
}
- \item{...}{
+ \item{\dots}{
further arguments passed to \code{plot}.
}
}
\item{xlab}{a character string (or a variable of mode character)
giving the label for the x-axis (default is "Time").}
\item{ylab}{idem for the y-axis (default is "N").}
- \item{...}{in the cases of \code{ltt.plot()} and \code{ltt.lines()}
+ \item{\dots}{in the cases of \code{ltt.plot()} and \code{ltt.lines()}
these are further (graphical) arguments to be passed to
\code{plot()} or \code{lines()}, respectively (see \code{Details:}
on how to transform the axes); in the case \code{mltt.plot()} these
modified; \code{TRUE} by default.}
\item{nodes}{a logical specifying whether node labels are to be
modified; \code{TRUE} by default.}
- \item{...}{further arguments to be passed to or from other methods.}
+ \item{\dots}{further arguments to be passed to or from other methods.}
}
\description{
This is a generic function with methods for character vectors, trees
\item{nperm}{the number of times to permute the data.}
\item{graph}{a logical indicating whether to produce a summary graph
(by default the graph is not plotted).}
- \item{...}{further arguments to be passed to \code{plot()} (to add a
+ \item{\dots}{further arguments to be passed to \code{plot()} (to add a
title, change the axis labels, and so on).}
}
\description{
\item{x2}{a numeric vector giving the coordinates of the observations
on the \emph{y}-axis. Both \code{x1} and \code{x2} must be specified
to be used.}
- \item{...}{further arguments to be passed to \code{plot()}.}
+ \item{\dots}{further arguments to be passed to \code{plot()}.}
}
\description{
The function \code{mst} finds the minimum spanning tree between a set of
title).}
\item{col}{a colour used for the segments showing the AIC values (blue
by default).}
- \item{...}{further arguments passed to or from other methods.}
+ \item{\dots}{further arguments passed to or from other methods.}
}
\description{
This function calls PhyML and fits successively 28 models of DNA
\item{col.fun}{the color function to use.}
\item{plot.node.values}{Should character values used as node labels?}
\item{ask}{Ask before each plot?}
- \item{...}{Further parameters to pass to the plot.phylo function.}
+ \item{\dots}{Further parameters to pass to the plot.phylo function.}
}
\details{
This function produces one plot by selected ancestral character. It
\item{tip.color}{the colours used for the tip labels, eventually
recycled (see examples).}
\item{layout}{the number of trees to be plotted simultaneously.}
- \item{...}{further arguments to be passed to \code{plot} or to
+ \item{\dots}{further arguments to be passed to \code{plot} or to
\code{plot.phylo}.}
}
\description{
\item{i}{indices of the tree(s) to select from a list; this may be a
vector of integers, logicals, or names.}
\item{name}{a character string specifying the tree to be extracted.}
- \item{...}{further arguments passed to or from other methods.}
+ \item{\dots}{further arguments passed to or from other methods.}
}
\description{
These functions prints a compact summary of a phylogeny, or a list of,
(the default).}
\item{tip.label}{a character vector giving the tip labels; if not
specified, the tips "t1", "t2", ..., are given.}
- \item{br}{an R function used to generate the branch lengths
- (\code{rtree}; use \code{NULL} to simulate only a topology), or the
- coalescence times (\code{rcoal}). For the latter, a genuine
- coalescent tree is simulated by default.}
- \item{...}{further argument(s) to be passed to \code{br}.}
+ \item{br}{one of the following: (i) an R function used to generate the
+ branch lengths (\code{rtree}; use \code{NULL} to simulate only a
+ topology), or the coalescence times (\code{rcoal}); (ii) a character
+ to simulate a genuine coalescent tree for \code{rcoal} (the
+ default); or (iii) a numeric vector for the branch lengths or the
+ coalescence times.}
+ \item{\dots}{further argument(s) to be passed to \code{br}.}
\item{N}{an integer giving the number of trees to generate.}
}
\description{
\item{MINEPS}{Parameter for the grid search for \code{epsilon} in \code{find.skyline.epsilon}.}
- \item{...}{Any of the above parameters.}
+ \item{\dots}{Any of the above parameters.}
}
\description{
\arguments{
\item{x}{an object of class \code{"phylo"}.}
\item{wait}{a logical indicating whether the node beeing processed should be printed (useful for big phylogenies).}
- \item{...}{further arguments passed to \code{plot.phylo}.}
+ \item{\dots}{further arguments passed to \code{plot.phylo}.}
}
\details{
This function aims at easily exploring very large trees. The main argument is
}
\arguments{
\item{object, phy}{an object of class \code{"phylo"}.}
- \item{...}{further arguments passed to or from other methods.}
+ \item{\dots}{further arguments passed to or from other methods.}
\item{internal.only}{a logical indicating whether to return the number
of internal nodes only (the default), or of internal and terminal
(tips) nodes (if \code{FALSE}).}
write.nexus(..., file = "", translate = TRUE, original.data = TRUE)
}
\arguments{
- \item{...}{either (i) a single object of class \code{"phylo"}, (ii) a
+ \item{\dots}{either (i) a single object of class \code{"phylo"}, (ii) a
series of such objects separated by commas, or (iii) a list
containing such objects.}
\item{file}{a file name specified by either a variable of mode character,
extracted subtrees.}
\item{col}{a vector of colours used to show where the subtrees are in
the main tree, or a function .}
- \item{...}{further arguments passed to \code{plot.phylo}.}
+ \item{\dots}{further arguments passed to \code{plot.phylo}.}
}
\details{
This function aims at exploring very large trees. The main argument is
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