brranching
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/>).
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)
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)
Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
brranchingin R doingcitation(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.
News
brranching 0.4.0
NEW FEATURES
- in the
phylomatic_local()function now usingphylocomr::ph_phylomaticinstead of shelling out to Phylocom viasystem. A number of parameters are gone due to the change internally (#30) (#35) - in the
rbladj()function now usingphylocomr::ph_bladjinstead of shelling out to Phylocom viasystem(#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
httrwithcrulfor http requests (#25)
MINOR IMPROVEMENTS
- fix links to readme images (#29) (#26)
verboseparam inphylomatic()function changed tomssgs
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
cleanparameter inphylomatic()andphylomatic_local()to expect a logical (TRUEorFALSE) instead of a "true" or "false". (#15) - A related change to that above, changed reading newick strings to use
phytools::read.newick()instead ofape::read.tree(), which handles the result ofclean=FALSEinphylomatic()andphylomatic_local()(#16) - Documented that in the
storedtreeparameter ofphylomatic()andphylomatic_local()the tree from Zanne et al. is also available by usingstoredtree="zanne2014"(#19)
brranching 0.1.0
NEW FEATURES
- Released to CRAN.