I can haz all the phylogenies
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README.md

brranching

Project Status: Active - The project has reached a stable, usable state and is being actively developed. Build Status codecov.io cran checks rstudio mirror downloads cran version

Description

Brranching is an interface to many different sources of phylogenetic data (currently only from Phylomatic (http://phylodiversity.net/phylomatic/), but more sources to come) that allows users to query for phylogenetic data using taxonomic names.

For brranching::phylomatic_names() function you should get an NCBI Entrez API key. NCBI Entrez doesn't require that you use an API key, but you get higher rate limit with a key, from 3 to 10 requests per second, so do get one. Run taxize::use_entrez() or see https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ for instructions.

Installation

Stable CRAN version

install.packages("brranching")

Or dev version

install.packages("devtools")
devtools::install_github("ropensci/brranching")
library("brranching")

Phylomatic

taxa <- c("Poa annua", "Phlox diffusa", "Helianthus annuus")
tree <- phylomatic(taxa=taxa, get = 'POST')
plot(tree, no.margin=TRUE)

plot of chunk unnamed-chunk-5

You can pass in up to about 5000 names. We can use taxize to get a random set of plant species names.

library("taxize")
spp <- names_list("species", 200)
out <- phylomatic(taxa = spp, get = "POST")
plot(out, show.tip.label = FALSE)

plot of chunk unnamed-chunk-6

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for brranching in R doing citation(package = 'brranching')
  • Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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