mid.edge.ages: mid.edge.ages obtans the ages of the mid point of the...

In sebastianduchene/NELSI: NELSI: Nucleotide EvoLution Simulator

mid.edge.ages obtans the ages of the mid point of the branches of a phylogenetic tree. It is not necessary for the tree to be ultrametric.

Description

mid.edge.ages produces a vector of length = number of edges of the tree with the mid.age of the branchies. Assuming that the tree is a chronogram.

Usage

mid.edge.ages(phylo)

Arguments

phylo

A phylogenetic tree of class 'phylo'. The branch lengths should be units of time.

Details

None

Value

A vector of length = number of edges in the tree. Each value is the median branch age.

Note

None

Author(s)

David Duchene

References

None

See Also

allnode.times produces the ages of internal nodes and tips.

Examples

set.seed(12345)
myTree <- rcoal(10)

plot(myTree)
midAges <- mid.edge.ages(myTree)
edgelabels(round(midAges, 2)) 

## The function is currently defined as
function (phylo) 
{
    require(phangorn)
    rootage <- max(allnode.times(phylo))
    if (is.ultrametric(phylo) == TRUE) {
        midages <- vector()
        for (i in 1:length(phylo$edge.length)) {
            if (phylo$edge[i, 2] > length(phylo$tip.label)) {
                recent.node.age <- branching.times(phylo)[(phylo$edge[i, 
                  2] - length(phylo$tip.label))]
                halflength <- phylo$edge.length[i]/2
                midages[i] <- recent.node.age + halflength
            }
            else {
                midages[i] <- phylo$edge.length[i]/2
            }
        }
        return(midages)
    }
    else {
        nodetimes <- vector()
        extantedgelen <- max(phylo$edge.length[as.vector(which(phylo$edge[, 
            1] == as.numeric(names(which(branching.times(phylo) == 
            min(branching.times(phylo)))))))])
        addedval <- abs(min(branching.times(phylo))) + extantedgelen
        for (i in 1:length(branching.times(phylo))) {
            nodetimes[i] <- (rootage/(max(branching.times(phylo)) + 
                addedval)) * (branching.times(phylo) + addedval)[i]
        }
        brlen <- vector()
        for (i in 1:length(phylo$edge.length)) {
            brlen[i] <- (rootage/(max(branching.times(phylo)) + 
                addedval)) * phylo$edge.length[i]
        }
        midages <- vector()
        for (i in 1:length(brlen)) {
            if (phylo$edge[i, 2] > length(phylo$tip.label)) {
                daughter.node.age <- nodetimes[(phylo$edge[i, 
                  2] - length(phylo$tip.label))]
                halflength <- brlen[i]/2
                midages[i] <- daughter.node.age + halflength
            }
            else {
                parent.node.age <- nodetimes[(phylo$edge[i, 1] - 
                  length(phylo$tip.label))]
                midages[i] <- parent.node.age - (brlen[i]/2)
            }
        }
        return(round(midages, 5))
    }
  }

sebastianduchene/NELSI documentation built on Sept. 5, 2024, 3:08 a.m.