Package: ape
Version: 2.7-3
-Date: 2011-06-14
+Date: 2011-06-21
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, Klaus Schliep, Korbinian Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
CHANGES IN APE VERSION 2.7-3
-NEW FEATURES
+BUG FIXES
- o There is a new predict() method for compar.gee().
+ o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
+ position = 0). (Thanks to Liam Revell for digging this bug out.)
and four conversion methods to the classes "phylo", "networx",
"network", and "igraph".
+ o The new function rTraitMult does multivariate traits simulation
+ with user-defined models.
+
o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
is not plotted but the graphical device is set and the
coordinates are saved as usual.
o boot.phylo() now displays a progress bar by default (can be off
if 'quiet = TRUE').
+ o There is a new predict() method for compar.gee().
+
BUG FIXES
presence of identical or nearly identical sequences.
+OTHER CHANGES
+
+ o The data bird.families, bird.orders, cynipids, and woodmouse are
+ now provided as .rda files.
+
+
CHANGES IN APE VERSION 2.7-1
-## bind.tree.R (2011-03-02)
+## bind.tree.R (2011-06-21)
## Bind Trees
y$edge[1] <- x$edge[i, 1]
## delete i-th edge in x:
x$edge <- x$edge[-i, ]
- i <- i - 1L
if (wbl) x$edge.length <- x$edge.length[-i]
+ i <- i - 1L
}
x$tip.label <- x$tip.label[-where]
## renumber the tips that need to:
-## rTrait.R (2011-04-02)
+## rTrait.R (2011-06-16)
## Trait Evolution
rTraitMult <-
function(phy, model, p = 1, root.value = rep(0, p), ancestor = FALSE,
- as.factor = NULL, ...)
+ asFactor = NULL, trait.labels = paste("x", 1:p, sep = ""), ...)
{
phy <- reorder(phy, "pruningwise")
n <- length(phy$tip.label)
el <- phy$edge.length
if (is.null(el)) el <- numeric(N)
+ environment(model) <- environment() # to find 'p'
+
for (i in N:1) x[des[i], ] <- model(x[anc[i], ], el[i], ...)
if (ancestor) {
rownames(x) <- phy$tip.label
}
x <- as.data.frame(x)
- if (!is.null(as.factor)) {
- for (i in as.factor) {
+ names(x) <- trait.labels
+ if (!is.null(asFactor)) {
+ for (i in asFactor) {
y <- x[, i]
x[, i] <- factor(y, labels = LETTERS[1:length(unique(y))])
}
}
\author{Emmanuel Paradis}
\seealso{
- \code{\link{rTraitDisc}}, \code{\link{ace}}
+ \code{\link{rTraitDisc}}, \code{\link{rTraitMult}}, \code{\link{ace}}
}
\examples{
data(bird.orders)
}
\author{Emmanuel Paradis}
\seealso{
- \code{\link{rTraitCont}}, \code{\link{ace}}
+ \code{\link{rTraitCont}}, \code{\link{rTraitMult}}, \code{\link{ace}}
}
\examples{
data(bird.orders)