Comments from Owen

[sckott]

Comments from Own Jones

• [x] My main point for improvement would be that I feel it needs a clearer framing of the problems confronted by the target users of taxize in the introduction. I feel that you jump straight into the solutions before explaining the problem well-enough. I think you should give readers more of an idea of the problems researchers come up against when doing research that needs taxonomic data. The big one that comes to mind is the problem of merging two (or more) sets of data tied to species. For example, a database of geographic range sizes, to a database of body sizes. The first job would be to match up the species but this is very hard due to 1) typos, 2) different taxonomies being used etc.
• [x] IUCN status heading: I would frame this under the heading of: Obtaining ancillary information about my species. You could then highlight the GBIF functionality and invasive species status etc, e.g. for a species I can get geographic distribution info, whether it is invasive in the US, AND its IUCN status.
• [x] Matching species tables with different taxonomic resolution heading: I really didn't understand what you were getting at with this until I read the supplement. Can you include a simple clear example so that the reader can understand the principle without needing to read the supplement?
• [x] He said to not put comments in code, but to bring in to main text. Carl said this too. I don't see the problem, but sure we can change.
• [x] He says about the Interactive name selection section = This is really cool, but in a sense it goes against the fully-programmatic ethos of taxize. I would play this down, and maybe replace with a different example. (What do you think @EDiLD - I think it's still programmatic, since you are doing it from the command line and not in a browser)
• [ ] Incorporate small changes not put in here...(pg 1, pg 9, pg X, pg X)

[eduardszoecs]

Thanks for this usefull comments! A lot of work till the final version - but it will get better and better...

• Points two and three are related . So more information/need here.
• comments in code: For me code and comments belong together - so I don't get this point...
• well we need this - therefore we have it in get_*(). If we have multiple matches the user must decide whichone fits better. (OK-we could say just take species from Animalia and not from plants). For me not so a big problem...

[sckott]

comments in code: For me code and comments belong together - so I don't get this point...

Agreed. I wonder if we should see what journals have the best code highlighting/handling since we have a lot of code in our paper? Maybe PLOS isn't the best, I just dont know.

On the interactive part: Agreed, just leave as is I think.

[sckott]

@EDiLD Can you address the comment from Owen on the section Matching species tables with different...

[sckott]

regarding owens comment on reframing IUCN status - I don't think we should reframe as generally getting any info on a species as we are trying to point out specific use cases that are also brief to explain.

[sckott]

I think you should give readers more of an idea of the problems researchers come up against when doing research that needs taxonomic data. The big one that comes to mind is the problem of merging two (or more) sets of data tied to species.

I think this is more or less (though not exactly) addressed in your section @EDiLD on Matching species tables with different...

[sckott]

I think this is taken care of now with new changes that I will push soon in the Intro

[eduardszoecs]

Yes, will revise the matching section. Probably by the weekend...

[sckott]

@EDiLD I think this is taken care of, reopen if not