-## drop.tip.R (2011-05-19)
+## drop.tip.R (2012-10-06)
## Remove Tips in a Phylogenetic Tree
-## Copyright 2003-2011 Emmanuel Paradis
+## Copyright 2003-2012 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
if (wbl) phy$edge.length <- phy$edge.length[keep]
TIPS <- phy$edge[, 2] <= Ntip
tip <- phy$edge[TIPS, 2]
- phy$tip.label <- phy$tip.label[sort(tip)] # <- added sort to avoid shuffling of tip labels (2010-07-21)
+ ## Fix by Ludovic Mallet and Mahendra Mariadassou (2011-11-21):
+ name <- vector("character", length(tip))
+ name[order(tip)] <- phy$tip.label[tip]
+ phy$tip.label <- name
+ ## End of fix
## keep the ordering so no need to reorder tip.label:
phy$edge[TIPS, 2] <- order(tip)
if (!is.null(phy$node.label))
phy$tip.label <- c(phy$tip.label, new.tip.label)
}
- ## update node.label if needed:
- if (!is.null(phy$node.label))
- phy$node.label <- phy$node.label[sort(unique(phy$edge[, 1])) - Ntip]
-
phy$Nnode <- dim(phy$edge)[1] - n + 1L # update phy$Nnode
## The block below renumbers the nodes so that they conform
- ## to the "phylo" format -- same as in root()
+ ## to the "phylo" format, same as in root()
newNb <- integer(n + phy$Nnode)
newNb[NEWROOT] <- n + 1L
sndcol <- phy$edge[, 2] > n
(n + 2):(n + phy$Nnode)
phy$edge[, 1] <- newNb[phy$edge[, 1]]
storage.mode(phy$edge) <- "integer"
+ if (!is.null(phy$node.label)) { # update node.label if needed
+ newNb[is.na(newNb)] <- 0L
+ phy$node.label <- phy$node.label[order(newNb[newNb > 0])]
+ }
collapse.singles(phy)
}