Using R to parse time (and taxon names) with GBIF’s API

Update: The taxize package for R now includes a gbif_parse function.


GBIF has recently made a bunch of handy tools available via their revamped API. These tools include a species name parser, which seems very useful for cleaning long lists of taxon names.

Here’s a simple R function that takes a vector of taxon names and parses them using GBIF’s API, extracting, among other details, the genus, species, infraspecific rank and epithet, nothorank (i.e., indicating the taxonomic rank of hybridisation), and authorship.

I’ve created a gist of this function, so you can grab it from github with source_url('https://gist.github.com/johnbaums/6971353/raw/gbif_parse.R') (requires devtools package), or you can just copy and paste it from here.

It’s a bit awkward to include wide tabular output here, but I’ve provided a few examples of the function’s use on github. I haven’t tested the API thoroughly (and the stable version hasn’t yet been released – expected end of 2013), so I’m interested to hear if it “parses” your tests.


EDIT: updated to point to GBIF API v 1.0.
WARNING: currently returns an error when input strings contain certain diacritics.

Advertisements