match.lnL.to.trees: Match the likelihoods returned on a subset of trees for numerous loci to the trees originally input

Description

This function reads in tree likelihoods for a series of loci exported from gen.RAD.loci.datasets and matches those up to the trees originally created. Because gen.RAD.loci.datasets only exports trees that include the taxa in each locus exported, these likelihoods are matched up to all trees in the original dataset that are compatible with each pruned tree.

Usage

match.lnL.to.trees(directory = "getwd()",
                   lnLprefix = "RAxML_info.",
		   lnLsuffix = ".lnL",
                   treeIndexFile = "tree.index.lines.txt",
		   locus.names = NULL, ...)

Arguments

Value

A matrix of likelihoods, with loci as rows and the original trees as columns

Details

The idea behind this function is that we want to let loci vote only on trees they are qualified to vote on. In an earlier implementation, each locus was forced to vote on every tree, unpruned, and the results were simply noisy. Here, we take a set of trees and, for each locus out a treeset pruned to just that taxon set for each taxon set. We then calculate the site likelihoods based on those treesets. Every locus is, in fact, evaluating every tree, but because many trees become topologically identical after pruning, we have to set an equal score to trees that are topologically identical... and which trees are topologically identical differs among loci.

References

Hipp A.L., Eaton D.A.R., Cavender-Bares J., Fitzek E., Nipper R. & Manos P.S. (Accepted pending revision). A framework phylogeny of the American oak clade based on sequenced RAD data. PLoS ONE.