So perhaps you have all figured this out already, but I was excited to figure out how to finally neatly get all the data frames, lists, vectors, etc. out of a nested list. It is as easy as nesting ...
Here is some code to run Phylip’s contrast application from R and get the output within R to easily manipulate yourself. Importantly, the code is written specifically for trait pairs only as the re...
—UPDATE: I am now using code formatting from gist.github, so I replaced the old prettyR code (sorry guys). The github way is much easier and prettier. I hope readers like the change.
I wrote earli...
Here is an approach for comparing two methods of adjusting branch lengths on trees: bladj in the program Phylocom and a fxn written by Gene Hunt at the Smithsonian.
Get the code and example files ...