(R) From a larger tree, extract the subtree induced from a specified set of tips. Requires ape.

subtree.induced.R

# extract subtree induced from a set of tips
subtree.induced <- function (phy, tip) {
    if (!inherits(phy, "phylo")) {
        stop("object \"phy\" is not of class \"phylo\"");
    }
    Ntip <- length(phy$tip.label);
    
    # convert to indices if strings passed in
    if (is.character(tip)) {
        idx <- match(tip, phy$tip.label);
        
        # stop on bad tip names
        # alternative is to warn but probably not ideal
        if (any(is.na(idx))) {
            um <- c("umatched tip labels:\n", paste(tip[which(is.na(idx))], collapse=" "));
            stop(um);
        }
        tip <- idx;
    } else {
        # check that passed in indices are all valid
        out.of.range <- tip > Ntip;
        if (any(out.of.range)) {
            warning("some tip numbers were larger than the number of tips: they were ignored");
            tip <- tip[!out.of.range];
        }
    }
    # get complement tip indices to drop
    toDrop <- setdiff(1:Ntip, tip);
    drop.tip(phy, toDrop);
}