-## drop.tip.R (2009-05-10)
+## drop.tip.R (2009-06-23)
## Remove Tips in a Phylogenetic Tree
}
drop.tip <-
- function(phy, tip, trim.internal = TRUE, subtree = FALSE, root.edge = 0)
+ function(phy, tip, trim.internal = TRUE, subtree = FALSE,
+ root.edge = 0, rooted = is.rooted(phy))
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
- phy <- reorder(phy)
+
Ntip <- length(phy$tip.label)
+ ## find the tips to drop:
+ if (is.character(tip))
+ tip <- which(phy$tip.label %in% tip)
+
+ if (!rooted && subtree) {
+ phy <- root(phy, (1:Ntip)[-tip][1])
+ root.edge <- 0
+ }
+
+ phy <- reorder(phy)
NEWROOT <- ROOT <- Ntip + 1
Nnode <- phy$Nnode
Nedge <- dim(phy$edge)[1]
edge1 <- phy$edge[, 1] # local copies
edge2 <- phy$edge[, 2] #
keep <- !logical(Nedge)
+
## find the tips to drop:
if (is.character(tip))
tip <- which(phy$tip.label %in% tip)
+
+ if (!rooted && subtree) {
+ phy <- root(phy, (1:Ntip)[-tip][1])
+ root.edge <- 0
+ }
+
## delete the terminal edges given by `tip':
keep[match(tip, edge2)] <- FALSE
if (trim.internal) {
- internals <- edge2 <= Ntip
+ ints <- edge2 > Ntip
## delete the internal edges that do not have anymore
## descendants (ie, they are in the 2nd col of `edge' but
## not in the 1st one)
repeat {
- sel <- !(edge2 %in% edge1[keep]) & internals & keep
+ sel <- !(edge2 %in% edge1[keep]) & ints & keep
if (!sum(sel)) break
keep[sel] <- FALSE
}
if (!root.edge) phy$root.edge <- NULL
- ## upate the tree; 1) drop the edges and tip labels
+ ## drop the edges
phy$edge <- phy$edge[keep, ]
if (wbl) phy$edge.length <- phy$edge.length[keep]
- phy$tip.label <- phy$tip.label[-tip]
- ## 2) renumber the remaining tips now
- TIPS <- phy$edge[, 2] <= Ntip
- ## keep the ordering so no need to reorder tip.label:
- phy$edge[TIPS, 2] <- rank(phy$edge[TIPS, 2])
- ## 3) update node.label if needed
- if (!is.null(phy$node.label))
- phy$node.label <- phy$node.label[sort(unique(phy$edge[, 1])) - Ntip]
- Ntip <- length(phy$tip.label) # 4) update Ntip
- ## make new tip labels if necessary
+ ## find the new terminal edges (works whatever 'subtree' and 'trim.internal'):
+ TERMS <- !(phy$edge[, 2] %in% phy$edge[, 1])
+
+ ## get the old No. of the nodes and tips that become tips:
+ oldNo.ofNewTips <- phy$edge[TERMS, 2]
+
+ n <- length(oldNo.ofNewTips) # the new number of tips in the tree
+
+ ## assumes that the ordering of tips is unchanged:
+ phy$edge[TERMS, 2] <- 1:n
+
+ ## make new tip labels if necessary:
if (subtree || !trim.internal) {
- new.trms <- !(phy$edge[, 2] %in% phy$edge[, 1]) & phy$edge[, 2] > Ntip
- node2tip <- phy$edge[new.trms, 2]
- if (subtree)
- new.lab <- paste("[", N[node2tip], "_tips]", sep = "")
- else {
- new.lab <-
- if (is.null(phy$node.label)) rep("NA", length(node2tip))
- else phy$node.label[node2tip - Ntip]
+ ## 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$tip.label[-tip]
+ ## get the numbers of the nodes that become tips:
+ node2tip <- oldNo.ofNewTips[!tips.kept]
+ new.tip.label[!tips.kept] <- if (subtree) {
+ paste("[", N[node2tip], "_tips]", sep = "")
+ } else {
+ if (is.null(phy$node.label)) rep("NA", length(node2tip))
+ else phy$node.label[node2tip - Ntip]
}
- ## change the #'s in the edge matrix
- new.tip <- Ntip + 1:length(node2tip)
- phy$edge[new.trms, 2] <- new.tip
- phy$tip.label[new.tip] <- new.lab
- Ntip <- length(phy$tip.label)
if (!is.null(phy$node.label))
phy$node.label <- phy$node.label[-(node2tip - Ntip)]
- }
- phy$Nnode <- dim(phy$edge)[1] - Ntip + 1L # 3) update phy$Nnode
+ 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$edge[, 1])) - Ntip]
+
+ phy$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(Ntip + phy$Nnode)
- newNb[NEWROOT] <- Ntip + 1L
- sndcol <- phy$edge[, 2] > Ntip
+ newNb <- integer(n + phy$Nnode)
+ newNb[NEWROOT] <- n + 1L
+ sndcol <- phy$edge[, 2] > n
## executed from right to left, so newNb is modified before phy$edge:
phy$edge[sndcol, 2] <- newNb[phy$edge[sndcol, 2]] <-
- (Ntip + 2):(Ntip + phy$Nnode)
+ (n + 2):(n + phy$Nnode)
phy$edge[, 1] <- newNb[phy$edge[, 1]]
storage.mode(phy$edge) <- "integer"
collapse.singles(phy)
\title{Remove Tips in a Phylogenetic Tree}
\usage{
drop.tip(phy, tip, trim.internal = TRUE, subtree = FALSE,
- root.edge = 0)
+ root.edge = 0, rooted = is.rooted(phy))
extract.clade(phy, node, root.edge = 0)
}
\arguments{
\item{root.edge}{an integer giving the number of internal branches to
be used to build the new root edge. This has no effect if
\code{trim.internal = FALSE}.}
+ \item{rooted}{a logical indicated whether the tree must be treated as
+ rooted or not. This allows to force the tree to be considered as
+ unrooted (see examples).}
\item{node}{a node number or label.}
}
\description{
plot(drop.tip(bird.families, tip))
plot(drop.tip(bird.families, tip, trim.internal = FALSE))
data(bird.orders)
-plot(drop.tip(bird.orders, 6:23, subtree = TRUE), font = 1)
-plot(drop.tip(bird.orders, c(1:5, 20:23), subtree = TRUE), font = 1)
-
+plot(drop.tip(bird.orders, 6:23, subtree = TRUE))
+plot(drop.tip(bird.orders, c(1:5, 20:23), subtree = TRUE))
+plot(drop.tip(bird.orders, c(1:20, 23), subtree = TRUE))
+plot(drop.tip(bird.orders, c(1:20, 23), subtree = TRUE, rooted = FALSE))
### Examples of the use of `root.edge'
tr <- read.tree(text = "(A:1,(B:1,(C:1,(D:1,E:1):1):1):1):1;")
drop.tip(tr, c("A", "B"), root.edge = 0) # = (C:1,(D:1,E:1):1);
projects / ape.git / commitdiff