phylocomr gives you access to Phylocom, specifically the
Phylocom C library (https://github.com/phylocom/phylocom/),
licensed under BSD 2-clause
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
picante, but the maintainers of
picante have re-written some
Phylocom functionality in C/C++, so performance should be similar in
As a convienence you can pass ages, sample and trait data.frame's, and
phylogenies as strings, to
phylocomr functions. However,
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.
ph_ecovolve() - interface to
and a higher level interface
ph_phylomatic() - interface to
executable, and a higher level interface
phylocom() - interface to
ph_aot() - higher level interface to
ph_bladj() - higher level interface to
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
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