Convert to ropensci style

[bomeara]

We seem to have a mix of styles: Google's R style guide and some other style. We should convert all to use ropensci's style: https://github.com/ropensci/onboarding/blob/master/packaging_guide.md. They'd be a good home for rphylotastic, folks are used to their style and their domain, and it's been battle-tested.

[bomeara]

See especially https://github.com/ropensci/onboarding/blob/master/packaging_guide.md#funvar

[bomeara]

I've done most of this now. We need to play a bit with the species list functions -- the first parameter tends to be user id, but should probably rewrite that to have it cached somewhere and just pass in the thing we want to change (i..e, the species to change)