taxize (version 0.2.0)

phylomatic_format: Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.

Description

Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.

Usage

phylomatic_format(taxa = NA, format = "isubmit", db = "ncbi")

Arguments

taxa

quoted tsn number (taxonomic serial number)

format

output format, isubmit (you can paste in to the Phylomatic website), or 'rsubmit' to use in fxn phylomatic_tree

db

One of "ncbi", "itis", or "apg"

Value

• e.g., "pinaceae/pinus/pinus_contorta", in Phylomatic submission format.

Examples

mynames <- c("Poa annua", "Salix goodingii", "Helianthus annuus")
phylomatic_format(mynames, format='rsubmit')
phylomatic_format(mynames, format='isubmit', db="apg")