R/drop.tip2.R

In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

drop.tip2 <- 
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\"")
    Ntip <- length(phy$tip.label)
    if (is.character(tip)) 
        tip <- which(phy$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]
    if (subtree) {
        trim.internal <- TRUE
        tr <- reorder(phy, "pruningwise")
        N <- .C("node_depth", as.integer(Ntip), as.integer(Nnode), 
            as.integer(tr$edge[, 1]), as.integer(tr$edge[, 2]), 
            as.integer(Nedge), double(Ntip + Nnode), DUP = FALSE, 
            PACKAGE = "ape")[[6]]
    }
    wbl <- !is.null(phy$edge.length)
    edge1 <- phy$edge[, 1]
    edge2 <- phy$edge[, 2]
    keep <- !logical(Nedge)
    if (is.character(tip)) 
        tip <- which(phy$tip.label %in% tip)
    if (!rooted && subtree) {
        phy <- root(phy, (1:Ntip)[-tip][1])
        root.edge <- 0
    }
    keep[match(tip, edge2)] <- FALSE
    if (trim.internal) {
        ints <- edge2 > Ntip
        repeat {
            sel <- !(edge2 %in% edge1[keep]) & ints & keep
            if (!sum(sel)) 
                break
            keep[sel] <- FALSE
        }
        if (subtree) {
            subt <- edge1 %in% edge1[keep] & edge1 %in% edge1[!keep]
            keep[subt] <- TRUE
        }
        if (root.edge && wbl) {
            degree <- tabulate(edge1[keep])
            if (degree[ROOT] == 1) {
                j <- integer(0)
                repeat {
                  i <- which(edge1 == NEWROOT & keep)
                  j <- c(i, j)
                  NEWROOT <- edge2[i]
                  degree <- tabulate(edge1[keep])
                  if (degree[NEWROOT] > 1) 
                    break
                }
                keep[j] <- FALSE
                if (length(j) > root.edge) 
                  j <- 1:root.edge
                NewRootEdge <- sum(phy$edge.length[j])
                if (length(j) < root.edge && !is.null(phy$root.edge)) 
                  NewRootEdge <- NewRootEdge + phy$root.edge
                phy$root.edge <- NewRootEdge
            }
        }
    }
    if (!root.edge) 
        phy$root.edge <- NULL
    phy$edge <- phy$edge[keep, ]
    if (wbl) 
        phy$edge.length <- phy$edge.length[keep]
    TERMS <- !(phy$edge[, 2] %in% phy$edge[, 1])
    oldNo.ofNewTips <- phy$edge[TERMS, 2]
    n <- length(oldNo.ofNewTips)
    phy$edge[TERMS, 2] <- rank(phy$edge[TERMS, 2])
    if (subtree || !trim.internal) {
        tips.kept <- oldNo.ofNewTips <= Ntip & !(oldNo.ofNewTips %in% 
            tip)
        new.tip.label <- character(n)
        new.tip.label[tips.kept] <- phy$tip.label[-tip]
        node2tip <- oldNo.ofNewTips[!tips.kept]
        new.tip.label[!tips.kept] <- if (subtree) {
            paste("[", N[node2tip], "_tips]", sep = "")
        }
        else {
            if (is.null(phy$node.label)) 
                rep("NA", length(node2tip))
            else phy$node.label[node2tip - Ntip]
        }
        if (!is.null(phy$node.label)) 
            phy$node.label <- phy$node.label[-(node2tip - Ntip)]
        phy$tip.label <- new.tip.label
    }
    else phy$tip.label <- phy$tip.label[-tip]
    if (!is.null(phy$node.label)) 
        phy$node.label <- phy$node.label[sort(unique(phy$edge[, 
            1])) - Ntip]
    phy$Nnode <- dim(phy$edge)[1] - n + 1L
    newNb <- integer(n + phy$Nnode)
    newNb[NEWROOT] <- n + 1L
    sndcol <- phy$edge[, 2] > n
    phy$edge[sndcol, 2] <- newNb[phy$edge[sndcol, 2]] <- (n + 
        2):(n + phy$Nnode)
    phy$edge[, 1] <- newNb[phy$edge[, 1]]
    storage.mode(phy$edge) <- "integer"
    phy <- collapse.singles(phy)
    
    # handle non-standard node-labels (e.g. from BEAST output):
	# ---------------------------------------------------------
	sdtnames <- c("edge", "edge.length", "Nnode", "tip.label", 		"node.label")
	if (!all(names(phy) %in% sdtnames)){
		id <- which(!names(phy) %in% sdtnames)
		drop <- edge1[which(!keep)] - Ntip
		for (i in id){
			phy[[i]] <- phy[[i]][-drop]
		}
	}	
	phy    
}