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

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.

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)
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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)
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Meta

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