Updating the partitioned RAD analysis

I ended up rewriting the RAD scripts so they do split out a new dataset and set of trees for each locus... the workflow goes like this:

1. Generate a set of topologies using NNI. Use: genTrees [fixed today to return unique trees, which it wasn't necessarily doing before]
2. Export locus and unique set of trees for each locus, and a files with the tree indices for each locus. Use: gen.RAD.loci.datasets 
3. Make the resulting sh files executable: use chmod u+rwx raxml.batch.* then execute using sh. note that the export is currently written for Linux and defaults to my directory structure
4. read in the info files to get likelihood for each tree, the index files to get original tree index, and then apply those likelihoods to the trees: use match.lnL.to.trees. I see now that the way the index is written is a bit awkward. What I want from the index is to know which new tree points to which old tree... but what the index actually gives me is, for each old tree, which other old tree that tree is identical to. I guess I can get what I want by just taking unique(treeIndex)... okay, that works.

Okay! that all runs fine... I'm back to the problem of deciding whom to favor and disfavor. I've scrapped all the old SWUL code, which was convoluted and hard to follow and inappropriately named (it's no longer successive weighting, but locus-partitioned data exploration). 

Figuring this part out now...

Plot at the end: how many loci favor each tree, how many disfavor each tree, how many don't vote, and favoring - disfavoring