Package: ape
-Version: 3.0-1
-Date: 2012-02-17
+Version: 3.0-2
+Date: 2012-02-27
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, Korbinian Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
+ CHANGES IN APE VERSION 3.0-2
+
+
+NEW FEATURES
+
+ o The new function alex (alignment explorator) zooms in a DNA
+ alignment and opens the result in a new window.
+
+
+
CHANGES IN APE VERSION 3.0-1
o read.GenBank() has been updated to work with EFetch 2.0.
+ o unroot() on trees in "pruningwise" order did not respect this
+ attribute
+
CHANGES IN APE VERSION 3.0
--- /dev/null
+## alex.R (2012-03-27)
+
+## Alignment Explorer With Multiple Devices
+
+## Copyright 2012 Emmanuel Paradis
+
+## This file is part of the R-package `ape'.
+## See the file ../COPYING for licensing issues.
+
+alex <- function(x, ...)
+{
+ n <- nrow(x)
+ s <- ncol(x)
+ devmain <- dev.cur()
+ on.exit(dev.set(devmain))
+ NEW <- TRUE
+ cat("Click on two opposite corners of the zone you want to zoom-in.
+Right-click to exit.\n")
+ repeat {
+ xy <- locator(2)
+ if (is.null(xy)) break
+ xy <- lapply(xy, function(x) sort(round(x)))
+ i1 <- xy$y[1L]; i2 <- xy$y[2L]
+ j1 <- xy$x[1L]; j2 <- xy$x[2L]
+ if (i1 > n || j1 > s) cat("Try again!\n") else {
+ if (i1 <= 0) i1 <- 1L
+ if (j1 <= 0) j1 <- 1L
+ if (i2 > n) i2 <- n
+ if (j2 > s) j2 <- s
+ if (NEW) {
+ dev.new()
+ devsub <- dev.cur()
+ NEW <- FALSE
+ } else dev.set(devsub)
+ image(x[i1:i2, j1:j2], xaxt = "n", ...)
+ atx <- axTicks(1)
+ axis(1, atx, labels = (j1:j2)[atx])
+ title(sub = paste("From", sQuote(deparse(substitute(x)))))
+ dev.set(devmain)
+ }
+ }
+}
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
- if (dim(phy$edge)[1] < 3)
+ N <- dim(phy$edge)[1]
+ if (N < 3)
stop("cannot unroot a tree with less than three edges.")
+
## delete FIRST the root.edge (in case this is sufficient to
## unroot the tree, i.e. there is a multichotomy at the root)
if (!is.null(phy$root.edge)) phy$root.edge <- NULL
if (!is.rooted(phy)) return(phy)
- ## We remove one of the edges coming from the root, and
- ## eventually adding the branch length to the other one
- ## also coming from the root.
- ## In all cases, the node deleted is the 2nd one (numbered
- ## nb.tip+2 in 'edge'), so we simply need to renumber the
- ## nodes by adding 1, except the root (this remains the
- ## origin of the tree).
- nb.tip <- length(phy$tip.label)
- ROOT <- nb.tip + 1L
- EDGEROOT <- which(phy$edge[, 1] == ROOT)
- ## j: the target where to stick the edge
- ## i: the edge to delete
- if (phy$edge[EDGEROOT[1], 2] == ROOT + 1L) {
- j <- EDGEROOT[2]
- i <- EDGEROOT[1]
+
+ n <- length(phy$tip.label)
+ ROOT <- n + 1L
+
+### EDGEROOT[1]: the edge to delete
+### EDGEROOT[2]: the target where to stick the edge to delete
+
+### If the tree is in pruningwise order, then the last two edges
+### are those connected to the root; the node situated in
+### phy$edge[N - 2L, 1L] will be the new root...
+
+ ophy <- attr(phy, "order")
+ if (!is.null(ophy) && ophy == "pruningwise") {
+ NEWROOT <- phy$edge[N - 2L, 1L]
+ EDGEROOT <- c(N, N - 1L)
} else {
- j <- EDGEROOT[1]
- i <- EDGEROOT[2]
+
+### ... otherwise, we remove one of the edges coming from
+### the root, and eventually adding the branch length to
+### the other one also coming from the root.
+### In all cases, the node deleted is the 2nd one (numbered
+### nb.tip+2 in 'edge'), so we simply need to renumber the
+### nodes by adding 1, except the root (this remains the
+### origin of the tree).
+
+ EDGEROOT <- which(phy$edge[, 1L] == ROOT)
+ NEWROOT <- ROOT + 1L
}
- ## This should work whether the tree is in pruningwise or
- ## cladewise order.
- phy$edge <- phy$edge[-i, ]
- nodes <- phy$edge > ROOT # renumber all nodes except the root
- phy$edge[nodes] <- phy$edge[nodes] - 1L
+
+ ## make sure EDGEROOT is ordered as described above:
+ if (phy$edge[EDGEROOT[1L], 2L] != NEWROOT)
+ EDGEROOT <- EDGEROOT[2:1]
+
+ phy$edge <- phy$edge[-EDGEROOT[1L], ]
+
+ s <- phy$edge == NEWROOT # renumber the new root
+ phy$edge[s] <- ROOT
+
+ s <- phy$edge > NEWROOT # renumber all nodes greater than the new root
+ phy$edge[s] <- phy$edge[s] - 1L
+
if (!is.null(phy$edge.length)) {
- phy$edge.length[j] <- phy$edge.length[j] + phy$edge.length[i]
- phy$edge.length <- phy$edge.length[-i]
+ phy$edge.length[EDGEROOT[2L]] <-
+ phy$edge.length[EDGEROOT[2L]] + phy$edge.length[EDGEROOT[1L]]
+ phy$edge.length <- phy$edge.length[-EDGEROOT[1L]]
}
+
phy$Nnode <- phy$Nnode - 1L
- if (!is.null(phy$node.label))
- phy$node.label <- phy$node.label[-2]
+
+ if (!is.null(phy$node.label)) {
+ if (NEWROOT == n + 2L)
+ phy$node.label <- phy$node.label[-1]
+ else {
+ lbs <- phy$node.label
+ tmp <- lbs[NEWROOT - n]
+ lbs <- lbs[-c(1, NEWROOT)]
+ phy$node.label <- c(tmp, lbs)
+ }
+ }
phy
}
-## vcv.phylo.R (2012-02-09)
+## vcv.phylo.R (2012-02-21)
## Phylogenetic Variance-Covariance or Correlation Matrix
}
}
- diag(vcv) <- xx[1:n]
+ diag.elts <- 1 + 0:(n - 1)*(n + 1)
+ vcv[diag.elts] <- xx[1:n]
if (corr) {
- ## This is inspired from the code of `cov2cor' (2005-09-08):
- M <- vcv
- Is <- sqrt(1/M[1 + 0:(n - 1)*(n + 1)])
- vcv[] <- Is * M * rep(Is, each = n)
- vcv[1 + 0:(n - 1)*(n + 1)] <- 1
+ ## This is inspired from the code of cov2cor (2005-09-08):
+ Is <- sqrt(1 / vcv[diag.elts])
+ ## below 'vcv[] <- ...' has been changed to 'vcv <- ...'
+ ## which seems to be twice faster for n = 1000 and
+ ## respects the additional attributes (2012-02-21):
+ vcv <- Is * vcv * rep(Is, each = n)
+ vcv[diag.elts] <- 1
}
dimnames(vcv)[1:2] <- list(phy$tip.label)
-
vcv
}
--- /dev/null
+\name{alex}
+\alias{alex}
+\title{Alignment Explorer With Multiple Devices}
+\description{
+ This function helps to explore DNA alignments by zooming in. The user
+ clicks twice defining the opposite corners of the portion which is
+ extracted and drawned on a new window.
+}
+\usage{
+alex(x, ...)
+}
+\arguments{
+ \item{x}{an object of class \code{"DNAbin"}.}
+ \item{\dots}{further arguments to pass to \code{image.DNAbin}.}
+}
+\details{
+ This function works with a DNA alignment (freshly) plotted on an
+ interactive graphical device (i.e., not a file) with \code{image}.
+ After calling \code{alex}, the user clicks twice defining a rectangle
+ in the alignment, then this portion of the alignment is extacted and
+ plotted on a \emph{new} window. The user can click as many times on
+ the alignment. The process is stopped by a right-click. If the user
+ clicks twice outside the alignment, a message ``Try again!'' is
+ printed.
+
+ Each time \code{alex} is called, the alignment is plotted on a new
+ window without closing or deleting those possibly already plotted.
+
+ In all cases, the device where \code{x} is plotted is the active
+ window after the operation. It should \emph{not} be closed during the
+ whole process.
+}
+\value{NULL}
+\author{Emmanuel Paradis}
+\seealso{
+ \code{\link{image.DNAbin}}, \code{\link{trex}}
+}
+\examples{
+\dontrun{
+data(woodmouse)
+image(woodmouse)
+alex(woodmouse)
+}}
+\keyword{hplot}
}
\details{
These three functions compute the probabilities to observe \code{x}
- species starting from a single one after time units \code{t} (assumed
- to be continuous). The first one is a short-cut for the second with
- \code{mu = 0} and with default values for the two other parameters.
+ species starting from a single one after time \code{t} (assumed to be
+ continuous). The first function is a short-cut for the second one with
+ \code{mu = 0} and with default values for the two other arguments.
\code{dbdTime} is for time-varying \code{lambda} and \code{mu}
specified as \R functions.
The returned value is, logically, zero for values of \code{x} out of
range, i.e., negative or zero for \code{dyule} or if \code{conditional
= TRUE}. However, it is not checked if the values of \code{x} are
- non-integers and the probabilities are computed and returned.
+ positive non-integers and the probabilities are computed and returned.
The details on the form of the arguments \code{birth}, \code{death},
\code{BIRTH}, \code{DEATH}, and \code{fast} can be found in the links
\alias{trex}
\title{Tree Explorer With Multiple Devices}
\description{
- This functions requires a plotted tree: the user is invited to click
+ This function requires a plotted tree: the user is invited to click
close to a node and the corresponding subtree (or clade) is plotted on
a new window.
}
#define X(i, j) i - 1 + *n * (j - 1)
-#define DINDEX(i, j) n * (i - 1) - i*(i - 1)/2 + j - i - 1
-
-int give_index(int i, int j, int n)
-{
- if (i > j) return(DINDEX(j, i));
- else return(DINDEX(i, j));
-}
-
void distDNA_indelblock(unsigned char *x, int *n, int *s, double *d)
{
int i1, i2, s1, s2, target, N, start_block, end_block;
projects / ape.git / commitdiff