Use Phylomatic locally on your own machine from R

phylo
phylogenetics
r
Tags: #<Tag:0x00007f57fadbf0e8> #<Tag:0x00007f57fadbee68> #<Tag:0x00007f57fadbebe8>

#1

Given the new availability of Phylocom in R (https://discuss.ropensci.org/t/phylocom-is-coming-to-r/557), we can now make using Phylomatic in our brranching package a much better experience. Before we required users to venture out into the web, download Phylomatic, and install it themselves. That version of Phylomatic requires awk or gawk which are not straight-forward to install and use across operating systems.

Phylomatic is also available in Phylocom as it turns out. The interface is slightly different though, so we can’t expose the same interface as we did to the other Phylomatic.

We have a draft function in brranching, see brranching::phylomatic_local2().

Installation

this will also install phylocomr from github if you don’t have it already

devtools::install_github("ropensci/brranchigh")
library(brranching)
library(taxize)
library(ape)

Example usage

Get a list of 200 plant taxon names

spp <- names_list("species", 200)
#> Phylogenetic tree with 178 tips and 129 internal nodes.
#> 
#> Tip labels:
#> 	paspalum_reclinatum, eragrostis_longiramea, bromus_brevis, muhlenbergia_brandegeei, schizostachyum_undulatum, digitaria_curvinervis, ...
#> Node labels:
#> 	euphyllophyte, seedplants, magnoliales_to_asterales, poales_to_asterales, , , ...
#> 
#> Rooted; includes branch lengths.

Using the new interface to phylocomr, lets use Phylomatic with the default stored tree R20120829

(tree <- phylomatic_local2(spp))

Visualize

plot(collapse.singles(tree), no.margin = TRUE, show.tip.label = FALSE)

Todo

We’ll continue to write tests and more examples for the new interface to Phylomatic, so things may change a bit. In addition, we’ll rename brranching::phylomatic_local2() to brranching::phylomatic_local() which will replace the current version in the package.

let us know

Let us know if you have any problems with brranching, have feature requests, etc.