+ CHANGES IN APE VERSION 2.6-1
+
+
+BUG FIXES
+
+ o as.hclust.phylo() failed with trees with node labels (thanks to
+ Filipe Vieira for the fix).
+
+
+
CHANGES IN APE VERSION 2.6
o pic() now returns a vector with the node labels of the tree (if
available) as names.
+ o write.tree() and read.tree() have been substantially thanks to
+ contributions by Klaus Schliep.
+
CHANGES IN APE VERSION 2.5-3
Package: ape
-Version: 2.6
-Date: 2010-09-27
+Version: 2.6-1
+Date: 2010-09-30
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, Korbinian Strimmer, Damien de Vienne
+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>
Depends: R (>= 2.6.0)
Suggests: gee
PAR <- matrix(NA, boot, np)
i <- 1L
while (i <= boot) {
- cat("i =", i, "\n")
+ cat("\rDoing bootstrap no.", i, "\n")
x <- sort(sample(x, replace = TRUE))
o <- try(nlminb(ip, foo, control = list(trace = 0, eval.max = 500),
upper = upper, lower = lower))
cat("Parameter estimates:\n")
names(estim) <- c("rate index", "estimate", "std-err")
print(estim, row.names = FALSE)
- cat("\nScaled likelihoods at the root (type 'x$lik.anc' to get them for all nodes):\n")
+ cat("\nScaled likelihoods at the root (type '...$lik.anc' to get them for all nodes):\n")
print(x$lik.anc[1, ])
}
}
-## as.matching.R (2007-12-23)
+## as.matching.R (2010-09-29)
## Conversion Between Phylo and Matching Objects
-## Copyright 2005-2007 Emmanuel Paradis
+## Copyright 2005-2010 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
obj <- list(edge = edge)
if (!is.null(x$tip.label)) obj$tip.label <- x$tip.label
else obj$tip.label <- as.character(1:nb.tip)
+ obj$Nnode <- nb.node
class(obj) <- "phylo"
read.tree(text = write.tree(obj))
}
-## as.phylo.R (2010-04-06)
+## as.phylo.R (2010-09-30)
## Conversion Among Tree Objects
n <- length(x$tip.label)
bt <- rev(branching.times(x))
N <- length(bt)
- nm <- as.numeric(names(bt))
+ nm <- x$Nnode:1 + n # fix by Filipe G. Vieira (2010-09-30)
merge <- matrix(NA, N, 2)
for (i in 1:N) {
ind <- which(x$edge[, 1] == nm[i])
-## read.nexus.R (2009-11-21)
+## read.nexus.R (2010-09-27)
## Read Tree File in Nexus Format
-## Copyright 2003-2009 Emmanuel Paradis
+## Copyright 2003-2009 Emmanuel Paradis and 2010 Klaus Schliep
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
edge[j, 1] <<- current.node
node <<- node + 1
edge[j, 2] <<- current.node <<- node
+ index[node] <<- j # set index
j <<- j + 1
}
add.terminal <- function() {
edge[j, 1] <<- current.node
edge[j, 2] <<- tip
+ index[tip] <<- j # set index
tip.label[tip] <<- tpc[k]
k <<- k + 1
tip <<- tip + 1
j <<- j + 1
}
go.down <- function() {
- l <- which(edge[, 2] == current.node)
+ l <- index[current.node]
node.label[current.node - nb.tip] <<- tpc[k]
k <<- k + 1
current.node <<- edge[l, 1]
edge[nb.edge, 1] <- 0 # see comment above
edge[nb.edge, 2] <- node #
+ index <- numeric(nb.edge + 1)
+ index[node] <- nb.edge
## j: index of the line number of edge
## k: index of the line number of tpc
## tip: tip number
j <- k <- tip <- 1
-
for (i in 2:nsk) {
if (skeleton[i] == "(") add.internal() # add an internal branch (on top)
if (skeleton[i] == ",") {
if (skeleton[i - 1] == ")") go.down() # go down one level
}
}
-# if(node.label[1] == "NA") node.label[1] <- ""
edge <- edge[-nb.edge, ]
obj <- list(edge = edge, tip.label = tip.label,
Nnode = nb.node, node.label = node.label)
-## read.tree.R (2009-04-27)
+## read.tree.R (2010-09-27)
## Read Tree Files in Parenthetic Format
-## Copyright 2002-2009 Emmanuel Paradis and Daniel Lawson
+## Copyright 2002-2010 Emmanuel Paradis, Daniel Lawson and Klaus Schliep
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
add.internal <- function() {
edge[j, 1] <<- current.node
edge[j, 2] <<- current.node <<- node <<- node + 1L
+ index[node] <<- j # set index
j <<- j + 1L
}
add.terminal <- function() {
edge[j, 1] <<- current.node
edge[j, 2] <<- tip
+ index[tip] <<- j # set index
X <- unlist(strsplit(tpc[k], ":"))
tip.label[tip] <<- X[1]
edge.length[j] <<- as.numeric(X[2])
j <<- j + 1L
}
go.down <- function() {
- l <- which(edge[, 2] == current.node)
+ l <- index[current.node]
X <- unlist(strsplit(tpc[k], ":"))
node.label[current.node - nb.tip] <<- X[1]
edge.length[l] <<- as.numeric(X[2])
edge.length <- numeric(nb.edge)
edge <- matrix(0L, nb.edge, 2)
current.node <- node <- as.integer(nb.tip + 1) # node number
- edge[nb.edge, 2] <- node #
+ edge[nb.edge, 2] <- node
+ index <- numeric(nb.edge + 1) # hash index to avoid which
+ index[node] <- nb.edge
## j: index of the line number of edge
## k: index of the line number of tpc
-## write.tree.R (2009-06-16)
+## write.tree.R (2010-09-27)
## Write Tree File in Parenthetic Format
-## Copyright 2002-2009 Emmanuel Paradis and Daniel Lawson
+## Copyright 2002-2010 Emmanuel Paradis, Daniel Lawson, and Klaus Schliep
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
phy$tip.label <- checkLabel(phy$tip.label)
if (nodelab) phy$node.label <- checkLabel(phy$node.label)
f.d <- paste("%.", digits, "g", sep = "")
- cp <- function(s) STRING <<- paste(STRING, s, sep = "")
+ cp <- function(x){
+ STRING[k] <<- x
+ k <<- k + 1
+ }
add.internal <- function(i) {
cp("(")
- br <- which(phy$edge[, 1] == i)
- for (j in br) {
- desc <- phy$edge[j, 2]
- if (desc > n) add.internal(desc)
- else add.terminal(j)
- if (j != br[length(br)]) cp(",")
+ desc <- kids[[i]]
+ for (j in desc) {
+ if (j > n) add.internal(j)
+ else add.terminal(ind[j])
+ if (j != desc[length(desc)]) cp(",")
}
cp(")")
- if (nodelab) cp(phy$node.label[i - n])
+ if (nodelab) cp(phy$node.label[ind[i] - n])
if (brl) {
cp(":")
- cp(sprintf(f.d, phy$edge.length[which(phy$edge[, 2] == i)]))
+ cp(sprintf(f.d, phy$edge.length[ind[i]]))
}
}
add.terminal <- function(i) {
cp(sprintf(f.d, phy$edge.length[i]))
}
}
+
n <- length(phy$tip.label)
- STRING <-
- if (output.tree.names) paste(tree.names, "(", sep = "") else "("
- 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(",")
+
+ ## borrowed from phangorn:
+ parent <- phy$edge[, 1]
+ children <- phy$edge[, 2]
+ kids <- vector("list", n + phy$Nnode)
+ for (i in 1:length(parent))
+ kids[[parent[i]]] <- c(kids[[parent[i]]], children[i])
+
+ ind <- match(1:max(phy$edge), phy$edge[, 2])
+
+ LS <- 4*n + 5
+ if (brl) LS <- LS + 4*n
+ if (nodelab) LS <- LS + n
+ STRING <- character(LS)
+ k <- 1
+ if (output.tree.names) cp(tree.names)
+ cp("(")
+ k <- 2
+ getRoot <- function(phy)
+ phy$edge[, 1][!match(phy$edge[, 1], phy$edge[, 2], 0)][1]
+ root <- getRoot(phy) # replaced n+1 with root - root has not be n+1
+ desc <- kids[[root]]
+ for (j in desc) {
+ if (j > n) add.internal(j)
+ else add.terminal(ind[j])
+ if (j != desc[length(desc)]) cp(",")
}
+
if (is.null(phy$root.edge)) {
cp(")")
if (nodelab) cp(phy$node.label[1])
cp(sprintf(f.d, phy$root.edge))
cp(";")
}
- if (file == "") return(STRING)
- cat(STRING, file = file, append = append, sep = "\n")
+ STRING <- paste(STRING, collapse = "")
+ if (file == "")
+ return(STRING)
+ else cat(STRING, file = file, append = append, sep = "\n")
}
-
Significant bug fixes were provided by Cécile Ané, James Bullard,
Otto Cordero, Éric Durand, Olivier François, Rich FitzJohn, Bret
Larget, Nick Matzke, Michael Phelan, Elizabeth Purdom, Dan Rabosky,
-Klaus Schliep, Tim Wallstrom, Li-San Wang, Yan Wong, Peter Wragg,
+Filipe Vieira, Tim Wallstrom, Li-San Wang, Yan Wong, Peter Wragg,
and Janet Young. Contact me if I forgot someone.
Kurt Hornik, of the R Core Team, helped in several occasions to
\examples{
data(woodmouse)
woodmouse
-summary(woodmouse)
-summary(woodmouse, 15, 6)
-summary(woodmouse[1:5, 1:300], 15, 6)
+print(woodmouse, 15, 6)
+print(woodmouse[1:5, 1:300], 15, 6)
### Just to show how distances could be influenced by sampling:
dist.dna(woodmouse[1:2, ])
dist.dna(woodmouse[1:3, ])
\examples{
plot(rlineage(0.1, 0)) # Yule process with lambda = 0.1
plot(rlineage(0.1, 0.05)) # simple birth-death process
-b <- function(t) 1/(1 + exp(0.1*t - 2)) # logistic
-layout(matrix(1:2, 1))
-plot(rlineage(b, 0.01))
-plot(rbdtree(b, 0.01))
+b <- function(t) 1/(1 + exp(0.2*t - 1)) # logistic
+layout(matrix(0:3, 2, byrow = TRUE))
+curve(b, 0, 50, xlab = "Time", ylab = "")
+mu <- 0.07
+segments(0, mu, 50, mu, lty = 2)
+legend("topright", c(expression(lambda), expression(mu)),
+ lty = 1:2, bty = "n")
+plot(rlineage(b, mu), show.tip.label = FALSE)
+title("Simulated with 'rlineage'")
+plot(rbdtree(b, mu), show.tip.label = FALSE)
+title("Simulated with 'rbdtree'")
}
\keyword{datagen}
projects / ape.git / commitdiff