gen.RAD.loci.datasets: Generate datasets for partitioned RAD analysis

Description

This function takes a set of trees (typically from genTrees), RAD loci, and some parameters about how taxa to include in the datasets, how many taxa at minimum need to be included in the datasets, and whether only variable loci will be included.

Usage

gen.RAD.loci.datasets(rads, trees = "none", loci = "all",
                      taxa = "all", minTaxa = 4, 
                      onlyVariable = TRUE, fileBase = "DEFAULT",
                      splitInto = 1,
                      cores = 2,
                      raxSinglePath = "raxmlHPC-AVX",
                      raxMultiPath = "raxmlHPC-PTHREADS-AVX",
                      header = "#!/bin/sh")

Arguments

rads

an object of class pyRAD.loci

trees

a set of trees, or 'none' if no trees are being used (e.g., if you just want to export loci one-by-one for analysis)

loci

a vector of locus names to include in analysis, or 'all.' Typically, use 'all' here, because part of what this function does is subset loci for you based on criteria you provide

taxa

a vector of taxa to include in analysis, or 'all' for all taxa

minTaxa

an integer, specifying the minimum number of taxa required to export a locus

onlyVariable

either TRUE or FALSE depending on whether loci should be variable or not to be exported

fileBase

base name for the directories and files created by this function; defaults to a handy dated format

splitInto

the number of folders to split files into for analysis, in case you want to run several instances of RAxML to get through analysis more quickly

cores

the number of processing cores to use for the RAxML full-matrix analysis

raxSinglePath

the path to your RAxML executable, single-core installation

raxMultiPath

the path to your RAxML executable, multi-core installation

header

header for the top of your shell scripts / bash files; not necessary for a Windows batch file (.bat), but defaults to the header needed for a Linux shell script

Value

no value. Called for the side effect of the files it exports.

Details

This function subsets the treeset you give it for all the loci imported, then matched loci and treesets and a batch file for calculating the likelihood of all trees for each locus. It is called for the side-effect of writing all these files. All files are exported to a series of folders equal in number to splitInto + 1. As currently written, the folder with the suffix .0 holds all batch files, an index of trees that matches the trees you hand to the function (as trees) with the trees it returns in each subset, and the .info output files that are used by get.raxml.treeLikelihoods as well as the site-likelihood files. The alignments and trees, as well as the reduced alignments created by RAxML, remain in the split folders (1 through splitInto). This function is the workhorse of the partitioned RAD analysis and is time-consuming to run. It could be executed in parallel and should be in future versions. What is most time-consuming is that for every treeset exported, the function makes sure that all trees are unique (see unique.multiPhylo from ape).

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.