Add tools for filtering trees and matrices by taxa

[cjgrady]

We want to create PD metrics for species having ancient traits for the ancient angiosperms project. I can do this by subsetting the PAM to only include species that have each of the traits and then running the stats from there.

This sort of functionality is basically the same process that I have used (and need to continue to use) for some of the other projects (example: subsettting all angiosperms to get palms or some other group for Stephen). It would probably also be used to subset using sites as well. This is something that I have had to do often enough that it makes sense to have a tool for it and then it can be part of an automated workflow.

Look at the sync PAM and tree scripts that I have written before to make sure I can compute multi-species statistics. These tools should either be incorporated into one, or they need to be able to replicate this functionality.

Also consider making these data wranglers for matrix and tree types.

Matrix filtering inputs:

• Input matrix
• Species, column names, or column indicies to keep
• Sites to keep (either manually, by a rule, or intersecting with a shapefile or something)
• Some method for ordering columns and maybe rows

Tree filtering:

• Taxa to keep
• Suppress unifurcations or not

This issue may need to be split out, especially for data wranglers. If that is the case, closing condition for this issue would be some version 1 scripts for matrix and tree filters.