A general way to bind a phylogeny to replace a given species on another phylogeny

bind.replace.R

# Functions
library(caper)
find.clade <- function(tree, tips){
    clade.mat <- clade.matrix(tree)$clade.matrix
    sums <- rowSums(clade.mat)
    ancestors <- apply(clade.mat, 1, function(x) all(x[tips]==1))
    sums[!ancestors] <- length(tree$tip.label)
    return(unname(which.min(sums)))
}
bind.replace <- function(backbone, donor, replacing.tip.label){
    size <- max(branching.times(donor))
    bind.point <- which(backbone$tip.label == replacing.tip.label)
    tree <- bind.tree(backbone, donor, where=bind.point)
    clade <- find.clade(tree, which(tree$tip.label %in% donor$tip.label))
    which.edge <- which(tree$edge[,2] == clade)
    if(tree$edge.length[which.edge] < size)
        stop("Donor phylogeny too large for backbone phylogeny")
    tree$edge.length[which.edge] <- tree$edge.length[which.edge] - size
    return(tree)
}

# Example
library(geiger)
tree <- sim.bdtree(n=10)
donor <- sim.bdtree(n=3)
donor$tip.label <- letters[seq_along(donor$tip.label)]
plot(tree)
plot(bind.replace(tree, donor, "s4")) #... you should change the tip label to be something you want bound in