R/subtreez.R

In iteRates: Parametric rate comparison

subtreez <- function(tree, From, To, wait = FALSE) 
{
    N.tip <- Ntip(tree)
    N.node <- Nnode(tree)
    start <- N.tip + From
    limit <- N.tip + To
    sub <- list(N.node[From:To])
    u <- 0
    for (k in start:limit) {
        u <- u + 1
        if (wait == TRUE) 
            cat("wait... Node", u, "out of", N.node, "treated\n")
        fils <- NULL
        pere <- res <- k
        repeat {
            for (i in 1:length(pere)) fils <- c(fils, tree$edge[, 
                2][tree$edge[, 1] == pere[i]])
            res <- c(res, fils)
            pere <- fils
            fils <- NULL
            if (length(pere) == 0) 
                break
        }
        len <- res[res > N.tip]
        #if (u == 1) {
         #   tree2 <- tree
          #  len <- (N.tip + 1):limit
        #}
        #else {
            len.tip <- res[res < N.tip + 1]
            vec <- 1:length(tree$tip.label)
            len.tip.stay <- setdiff(vec, len.tip)
            tree2 <- drop.tip2.6(tree, len.tip.stay)
       # }
        sub[[u]] <- tree2
        sub[[u]]$name <- k
        sub[[u]]$Ntip <- Ntip(tree2)
        sub[[u]]$Nnode <- Nnode(tree2)
        if (is.null(tree$node.label)) 
            sub[[u]]$node.label <- len
    }
    return(sub)
    cat("\n")
}