Fetch 'Phylogenies' from Many Sources

Includes methods for fetching 'phylogenies' from a variety of sources, including the 'Phylomatic' web service (< http://phylodiversity.net/phylomatic>), and 'Phylocom' (< https://github.com/phylocom/phylocom/>).


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

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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News

brranching 0.4.0

NEW FEATURES

  • in the phylomatic_local() function now using phylocomr::ph_phylomatic instead of shelling out to Phylocom via system. A number of parameters are gone due to the change internally (#30) (#35)
  • in the rbladj() function now using phylocomr::ph_bladj instead of shelling out to Phylocom via system (#30) (#35)
  • added a package vignette (#31) (#34) thanks @fozy81
  • added new dataset of four phylogenetic trees that can be used in phylomatic_local(), see ?phylomatic_trees

MINOR IMPROVEMENTS

  • added docs to phylomatic_names() and the README on using NCBI Entrez API keys

brranching 0.3.0

NEW FEATURES

  • gains new function bladj (#18)
  • replaced httr with crul for http requests (#25)

MINOR IMPROVEMENTS

  • fix links to readme images (#29) (#26)
  • verbose param in phylomatic() function changed to mssgs

brranching 0.2.0

NEW FEATURES

  • Added function phylomatic_local() to use Phylomatic locally. Phylomatic is a set of Awk scripts, which have to be downloaded by the user. After downloading, this function uses the local version of Phylomatic (Same as that that runs as a web service). This is advantageous especially when dealing with large queries. (#13)

MINOR IMPROVEMENTS

  • Fixed clean parameter in phylomatic() and phylomatic_local() to expect a logical (TRUE or FALSE) instead of a "true" or "false". (#15)
  • A related change to that above, changed reading newick strings to use phytools::read.newick() instead of ape::read.tree(), which handles the result of clean=FALSE in phylomatic() and phylomatic_local() (#16)
  • Documented that in the storedtree parameter of phylomatic() and phylomatic_local() the tree from Zanne et al. is also available by using storedtree="zanne2014" (#19)

brranching 0.1.0

NEW FEATURES

  • Released to CRAN.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("brranching")

0.4.0 by Scott Chamberlain, 5 months ago


https://github.com/ropensci/brranching


Report a bug at http://github.com/ropensci/brranching/issues


Browse source code at https://github.com/cran/brranching


Authors: Scott Chamberlain [aut, cre]


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


MIT + file LICENSE license


Imports crul, curl, ape, taxize, phytools, phylocomr

Suggests testthat, knitr


Depended on by aptg.


See at CRAN