Join GitHub today
GitHub is home to over 31 million developers working together to host and review code, manage projects, and build software together.Sign up
rebi - an R-Client for Europe PMC #29
rebi gives access to Europe PubMed Central, an indexing service for life-
It only works with Europe PMC's Articles RESTful API.
Life-science researchers and students, scholars that study the life sciences,
To my knowledge, this is the only package that implements Europe PMC's
This package has been available through rOpenSci since summer 2013. Because I
See also the discussion in the forum:
Here's my review. N.B. According to the submission above, the package has been available through rOpenSci since 2013, but has recently made major upgrades that reflect rOpenSci guidance on package authorship, so it probably is already sufficient. Let me know if you have any questions, or any areas where you'd like me to clarify more.
General comments on code
Comments on specific functions
Improvements to code style?
Comments on documentation?
Do tests pass locally?
Documentation and examples run without issue
ROpenSci Packaging Guidelines
(I spent about 1.5–2 hours on the review).
Hi @toph-allen, sorry for coming back to you after such a long time. Thank you again for your helpful comments and suggestions to improve my package. I have a new version ready that include your remarks. I'll go over them in the following.
Please let me know if you have any further comments.
As suggested, I removed the
Agreed. I moved functions that are commonly used to
Agreed. Added more comprehensive explanations in some places.
As suggested, I clarified both functions. In the documentation of
It comes from the acronym European Bioinformatics Institute (EBI), which hosts Europe PMC. Do you think
I followed the example of other rOpenSci packages like
Again, many thanks for your helpful comments and suggestions.
Quick editor's comment about function naming: We recommend prefixing (e.g,
I'm so sorry I took even longer to respond to your changes—I had been budgeting more time to go through it than it actually took.
Reading through your responses to my suggestions, and looking through the accompanying changes to the code, I don't think I have any further issues.
Regarding the naming of your packages:
I think that renaming the package
All seems in order to me!
@njahn82 I am getting one local error for a test that is skipped on Travis:
Once that's fixed, and you've made all the internal changes for changing the name, I think we're good to go. You should be able to apply your changes to the package in the ropensci repo via a pull request. I'm not sure about whether you have the ability to change that repo's name. @sckott: heads up, we may need to see that a name change populates through our systems properly.
Thanks for letting me know. I realized that the Europe PMC API has started to give a 404 when no citations were found, which is not a nice behavior.
I will fix the error messages and corresponding tests.