R/clade.members.R

In caper: Comparative Analyses of Phylogenetics and Evolution in R

clade.members <- function(x, phy, tip.labels = FALSE, include.nodes = FALSE) {
    # NEW2OLD: CONVERTED...

    # returns a vector of the tips that descend from an identified node
    if (!inherits(phy, "phylo")) stop("Phylogeny required")

    NallNodes <- max(phy$edge)
    Ntips <- max(phy$edge) - phy$Nnode

    if (!(x %in% 1:NallNodes)) stop("Node not in range for phylogeny")

    # find the children of the node, append them to the vector of nodes (x)
    # and remove the parent, until all the nodes in the vector are tips...
    # now updated to keep track of parents...

    intN <- x[x > Ntips]
    descNode <- numeric(length = 0)

    while (length(intN) > 0) {
        minIntN <- min(intN)
        childOfMinIntN <- with(phy, edge[, 2][which(edge[, 1] == minIntN)])

        descNode <- c(descNode, minIntN)
        x <- c(x[x != minIntN], childOfMinIntN)

        intN <- x[x > Ntips]
    }

    RET <- unique(x)

    if (tip.labels) {
        RET <- phy$tip.label[x]
    }

    if (include.nodes) {
        RET <- list(tips = RET, nodes = descNode)
    }

    return(RET)
}

clade.members.list <- function(phy, tips = FALSE, tip.labels = FALSE, include.nodes = FALSE) {
    # OLD2NEW CONVERTED

    # returns a list of vectors showing the tips
    # subtending from each node in the tree
    if (!inherits(phy, "phylo")) stop("Phylogeny required")

    nodes <- 1:max(phy$edge)

    if (!tips) nodes <- nodes[nodes > length(nodes) - phy$Nnode]

    clade.list <- mapply(clade.members, nodes, MoreArgs = list(phy = phy, tip.labels = tip.labels, include.nodes = include.nodes), SIMPLIFY = FALSE)
    names(clade.list) <- nodes

    return(clade.list)
}

## "all.clades" <-
## function(phy, tips=FALSE, tip.labels=FALSE){
##
##     .Deprecated("clade.members.list")
##     clade.members.list(phy, tips=FALSE, tip.labels=FALSE)
## }