phylocomr-package {phylocomr}

Phylocom interface

Description

phylocomr gives you access to Phylocom, specifically the Phylocom C library (https://github.com/phylocom/phylocom/), licensed under BSD 2-clause (http://www.opensource.org/licenses/bsd-license.php)

Details

This package isn't doing system calls to a separately installed Phylocom instance - but actually includes Phylocom itself in the package.

Phylocom is usually used either on the command line or through the R package picante, which has duplicated some of the Phylocom functionality.

In terms of performance, some functionality will be faster here than in picante, but the maintainers of picante have re-written some Phylocom functionality in C/C++, so performance should be similar in those cases.

A note about files

As a convenience you can pass ages, sample and trait data.frame's, and phylogenies as strings, to phylocomr functions. However, phylocomr has to write these data.frame's/strings to disk (your computer's file system) to be able to run the Phylocom code on them. Internally, phylocomr is writing to a temporary file to run Phylocom code, and then the file is removed.

In addition, you can pass in files instead of data.frame's/strings. These are not themselves used. Instead, we read and write those files to temporary files. We do this for two reasons. First, Phylocom expects the files its using to be in the same directory, so if we control the file paths that becomes easier. Second, Phylocom is case sensitive, so we simply standardize all taxon names by lower casing all of them. We do this case manipulation on the temporary files so that your original data files are not modified.

Package API

• ecovolve()/ph_ecovolve() - interface to ecovolve executable, and a higher level interface

• phylomatic()/ph_phylomatic() - interface to phylomatic executable, and a higher level interface

• phylocom() - interface to phylocom executable

• ph_aot() - higher level interface to aot

• ph_bladj() - higher level interface to bladj

• ph_comdist()/ph_comdistnt() - higher level interface to comdist

• ph_comstruct() - higher level interface to comstruct

• ph_comtrait() - higher level interface to comtrait

• ph_pd() - higher level interface to Faith's phylogenetic diversity

Author(s)

Scott Chamberlain

Jeroen Ooms