-## drop.tip.R (2010-11-24)
+## drop.tip.R (2012-11-29)
## Remove Tips in a Phylogenetic Tree
-## Copyright 2003-2010 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))
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
+ if (!length(tip)) return(phy)
Ntip <- length(phy$tip.label)
## find the tips to drop:
if (is.character(tip))
tip <- which(phy$tip.label %in% tip)
}
+ if (!length(tip)) return(phy)
if (any(tip > Ntip))
warning("some tip numbers were higher than the number of tips")
if (is.null(phy$node.label)) rep("NA", length(node2tip))
else phy$node.label[node2tip - Ntip]
}
- if (!is.null(phy$node.label))
- phy$node.label <- phy$node.label[-(node2tip - Ntip)]
+# if (!is.null(phy$node.label))
+# phy$node.label <- phy$node.label[-(node2tip - Ntip)]
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$Nnode
## The block below renumbers the nodes so that they conform
- ## to the "phylo" format -- same as in root()
- newNb <- integer(n + phy$Nnode)
+ ## to the "phylo" format, same as in root()
+ newNb <- integer(Ntip + Nnode)
newNb[NEWROOT] <- n + 1L
sndcol <- phy$edge[, 2] > n
## executed from right to left, so newNb is modified before phy$edge:
(n + 2):(n + phy$Nnode)
phy$edge[, 1] <- newNb[phy$edge[, 1]]
storage.mode(phy$edge) <- "integer"
+ if (!is.null(phy$node.label)) # update node.label if needed
+ phy$node.label <- phy$node.label[which(newNb > 0) - Ntip]
collapse.singles(phy)
}