- o root() failed with resolve.root = TRUE when the root was already
- the specified root.
+ o root() failed with 'resolve.root = TRUE' when the root was
+ already the specified root.
o Several bugs were fixed in mlphylo().
o Several bugs were fixed in mlphylo().
+ o collapsed.singles() did not propagate the 'Nnode' and
+ 'node.labels' elements (thanks to Elizabeth Purdom for the fix.
+
Package: ape
Version: 2.2-1
Package: ape
Version: 2.2-1
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
-## collapse.singles.R (2006-07-15)
+## collapse.singles.R (2008-06-19)
## Collapse "Single" Nodes
## Collapse "Single" Nodes
{
elen <- tree$edge.length
xmat <- tree$edge
{
elen <- tree$edge.length
xmat <- tree$edge
+ ## added by Elizabeth Purdom (2008-06-19):
+ node.lab<-tree$node.label
+ nnode<-tree$Nnode
+ ntip<-length(tree$tip.label)
+ ## end
singles <- NA
while (length(singles) > 0) {
## changed by EP to make it slightly more efficient:
singles <- NA
while (length(singles) > 0) {
## changed by EP to make it slightly more efficient:
xmat[xmat > i] <- xmat[xmat > i] - 1 ## adjust indices
## END
elen[prev.node] <- elen[prev.node] + elen[next.node]
xmat[xmat > i] <- xmat[xmat > i] - 1 ## adjust indices
## END
elen[prev.node] <- elen[prev.node] + elen[next.node]
+ ## added by Elizabeth Purdom (2008-06-19):
+ if(!is.null(node.lab)) node.lab<-node.lab[-c(i-ntip)]
+ nnode<-nnode-1
+ ## end
elen <- elen[-next.node]
}
}
tree$edge <- xmat
tree$edge.length <- elen
elen <- elen[-next.node]
}
}
tree$edge <- xmat
tree$edge.length <- elen
+ ## added by Elizabeth Purdom (2008-06-19):
+ tree$node.label<-node.lab
+ tree$Nnode<-nnode
+ ## end
comments, or bug reports: thanks to all of you!
Significant bug fixes were provided by James Bullard, Éric Durand,
comments, or bug reports: thanks to all of you!
Significant bug fixes were provided by James Bullard, Éric Durand,
-Olivier François, Bret Larget, Klaus Schliep, Li-San Wang, and
-Yan Wong. Contact me if I forgot someone.
+Olivier François, Bret Larget, Elizabeth Purdom, Klaus Schliep,
+Li-San Wang, and Yan Wong. Contact me if I forgot someone.
Kurt Hornik, of the R Core Team, helped in several occasions to
fix some problems and bugs.
Kurt Hornik, of the R Core Team, helped in several occasions to
fix some problems and bugs.