examples/simulations/NELSI_RCodeOnly/get.rtt.dist.R

In josephwb/chronosCI: Molecular Dating by Penalised Likelihood and Maximum Likelihood

get.rtt.dist <-
function(phylo){
    di.phylo <- dist.nodes(phylo)
    root.phylo <- phylo$edge[, 1][!(phylo$edge[, 1] %in% phylo$edge[, 2])][1]
    phylo.depth <- max(di.phylo[as.numeric(colnames(di.phylo)) == root.phylo, ])
    node.times <- phylo.depth - di.phylo[as.numeric(rownames(di.phylo)) == root.phylo, ]
    tip.times <- phylo.depth - di.phylo[as.numeric(rownames(di.phylo)) == root.phylo, 1:length(phylo$tip.label)]
    tip.times <- abs(tip.times - max(node.times))
    return(tip.times)
}