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.
Stable CRAN version
install.packages("brranching")
Or dev version
install.packages("devtools")devtools::install_github("ropensci/brranching")
library("brranching")
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)
brranching
in R doing citation(package = 'brranching')
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)rbladj()
function now using phylocomr::ph_bladj
instead of shelling out to Phylocom via system
(#30) (#35)phylomatic_local()
, see ?phylomatic_trees
phylomatic_names()
and the README on using NCBI Entrez API keysbladj
(#18)httr
with crul
for http requests (#25)verbose
param in phylomatic()
function changed to mssgs
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)clean
parameter in phylomatic()
and phylomatic_local()
to expect a logical (TRUE
or FALSE
) instead of a "true" or "false". (#15)phytools::read.newick()
instead of ape::read.tree()
, which handles
the result of clean=FALSE
in phylomatic()
and phylomatic_local()
(#16)storedtree
parameter of phylomatic()
and
phylomatic_local()
the tree from Zanne et al. is also available by using
storedtree="zanne2014"
(#19)