Taxonomy data from the web in three languages27 Sep 2013 R ruby python taxonomy
Eduard Szöcs and I started developing a taxonomic toolbelt for the R language a while back , which lets you interact with a multitude of taxonomic databases on the web. We have a paper in F1000Research if you want to find out more (see here).
I thought it would be fun to rewrite some of taxize in other languages to learn more languages. Ruby and Python made the most sense to try. I did try others (Julia, Node), but gave up on those for now. The goal here isn’t to port taxize to Python and Ruby right now - it’s for me to learn myself some coding.
Anyway, here’s use of the same function in three languages: R, Ruby, and Python. The function searches the Global Names Index, but is named slightly differently in R (
gni_search) vs. Ruby/Python (
gniSearch). (yes, I realize the package names aren’t consistent)
Note that there are only a few functions available in the Ruby and Python versions:
- colChildren (Python, not Ruby)
And the behavior of these functions does not necessarily match that in the R version.
One thing I have learned is that packaging in R is much harder than in Python or Ruby. devtools does make R packaging easier, but still…
Then search for a taxonomic name
In a Ruby repl, like
irb, search for a taxonomic name
In a Python repl, like
ipython, search for a taxonomic name