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.
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
Stable CRAN version
Or dev version
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)
brranchingin R doing
citation(package = 'brranching')
crulfor http requests (#25)
phylomatic()function changed to
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)
phylomatic_local()to expect a logical (
FALSE) instead of a "true" or "false". (#15)
ape::read.tree(), which handles the result of
phylomatic_local()the tree from Zanne et al. is also available by using