Make a phylogeny from species names alone

rOpenSci package: taxize

There is only functionality for plants right now in taxize. We hope to add more taxan groups soon.

Load libraries


splist <- c("Helianthus annuus", "Collomia grandiflora", "Rosa californica", "Datura wrightii", "Mimulus bicolor", "Nicotiana glauca","Madia sativa", "Bartlettia scaposa")

Phylomatic is a web service with an API that we can use to get a phylogeny. Fetch phylogeny from phylomatic

phylogeny <- phylomatic_tree(splist)

Format tip-labels

phylogeny$tip.label <- capwords(phylogeny$tip.label, onlyfirst = TRUE)

Plot phylogeny