-## drop.tip.R (2010-07-21)
+## 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 (!rooted && subtree) {
phy <- root(phy, (1:Ntip)[-tip][1])
edge2 <- phy$edge[, 2] #
keep <- !logical(Nedge)
- ## find the tips to drop:
- if (is.character(tip))
- tip <- which(phy$tip.label %in% tip)
-
- if (!rooted && subtree) {
- phy <- root(phy, (1:Ntip)[-tip][1])
- root.edge <- 0
- }
-
## delete the terminal edges given by `tip':
keep[match(tip, edge2)] <- FALSE
## get the old No. of the nodes and tips that become tips:
oldNo.ofNewTips <- phy$edge[TERMS, 2]
+ ## in case some tips are dropped but kept because of 'subtree = TRUE':
+ if (subtree) {
+ i <- which(tip %in% oldNo.ofNewTips)
+ if (length(i)) {
+ phy$tip.label[tip[i]] <- "[1_tip]"
+ tip <- tip[-i]
+ }
+ }
+
n <- length(oldNo.ofNewTips) # the new number of tips in the tree
- ## the tips may not be sorted in increasing order of their
- ## in the 2nd col of edge, so no need to reorder $tip.label
+ ## the tips may not be sorted in increasing order in the
+ ## 2nd col of edge, so no need to reorder $tip.label
phy$edge[TERMS, 2] <- rank(phy$edge[TERMS, 2])
+ phy$tip.label <- phy$tip.label[-tip]
## make new tip labels if necessary:
if (subtree || !trim.internal) {
- ## get the logical indices of the tips that are kept within 'oldNo.ofNewTips':
- tips.kept <- oldNo.ofNewTips <= Ntip & !(oldNo.ofNewTips %in% tip)
- new.tip.label <- character(n)
- new.tip.label[tips.kept] <- phy$tip.label[-tip]
## get the numbers of the nodes that become tips:
- node2tip <- oldNo.ofNewTips[!tips.kept]
- new.tip.label[!tips.kept] <- if (subtree) {
+ node2tip <- oldNo.ofNewTips[oldNo.ofNewTips > Ntip]
+ new.tip.label <- if (subtree) {
paste("[", N[node2tip], "_tips]", sep = "")
} else {
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$node.label[-(node2tip - Ntip)]
- phy$tip.label <- new.tip.label
- } else phy$tip.label <- phy$tip.label[-tip]
-
- ## update node.label if needed:
- if (!is.null(phy$node.label))
- phy$node.label <- phy$node.label[sort(unique(phy$edge[, 1])) - Ntip]
+# if (!is.null(phy$node.label))
+# phy$node.label <- phy$node.label[-(node2tip - Ntip)]
+ phy$tip.label <- c(phy$tip.label, new.tip.label)
+ }
phy$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)
}
+