roadoi

[njahn82]

Summary

• What does this package do? (explain in 50 words or less):

roadoi interacts with the oaDOI API, a simple web interface that links Digital Object Identifiers (DOIs) and open access full-texts disseminated by both open access journals and repositories.

• Paste the full DESCRIPTION file inside a code block below:

Package: roadoi
Type: Package
Title: Find Free Versions of Scholarly Publications via the oaDOI Service
Version: 0.2
Authors@R: c(
    person("Najko", "Jahn", role = c("aut", "cre"), email = "najko.jahn@gmail.com"))
Description: This web client interfaces oaDOI <https://oadoi.org>, a service finding 
    free full-texts of academic papers by linking DOIs with open access journals and
    repositories. It provides unified access to various data sources for open access
    full-text links including Crossref, Bielefeld Academic Search Engine (BASE) and 
    the Directory of Open Access Journals (DOAJ). API usage is free and no 
    registration is required.
License: MIT + file LICENSE
URL: https://github.com/njahn82/roadoi
BugReports: https://github.com/njahn82/roadoi/issues
LazyData: TRUE
Imports:
    httr,
    jsonlite,
    dplyr,
    plyr,
    miniUI,
    shiny
Suggests:
    roxygen2 (>= 6.0.1),
    testthat,
    knitr,
    covr,
    rmarkdown,
    lubridate,
    rcrossref
RoxygenNote: 6.0.1
VignetteBuilder: knitr

• URL for the package (the development repository, not a stylized html page):

https://github.com/njahn82/roadoi

• Which categories does the package fall under from our package fit policies? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):

data retrieval

• Who is the target audience?

This package aims at academics who want to find openly available full-texts within R. More specifically, roadoi can be beneficial for text-mining because it retrieves links to full-texts, as well as for those studying scholarly communication. This package is also of practical use for scholarly communication librarians and analysts.

• Are there other R packages that accomplish the same thing? If so, what is different about yours?

To my knowledge, there aren't any other R packages on CRAN wrapping the oaDOI-API. However, some R packages allow for searching and retrieving scholarly publications. One example, which is maintained by rOpenSci, is fulltext, a wrapper for searching freely available full-texts across many open access sources.

Requirements

Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.

• has a CRAN and OSI accepted license.

• contains a README with instructions for installing the development version.

• includes documentation with examples for all functions.

• contains a vignette with examples of its essential functions and uses.

• has a test suite.

• has continuous integration, including reporting of test coverage, using
  services such as Travis CI, Coeveralls and/or CodeCov.

• I agree to abide by ROpenSci's Code of Conduct during
  the review process and in maintaining my package should it be accepted.

Publication options

• Do you intend for this package to go on CRAN? <- The package is already available via CRAN
• Do you wish to automatically submit to the Journal of Open Source Software? If so:
  • The package contains a paper.md with a high-level description in the package root or in inst/.
  • The package is deposited in a long-term repository with the DOI:
  • (Do not submit your package separately to JOSS)

Detail

• Does R CMD check (or devtools::check()) succeed? Paste and describe any errors or warnings:

• Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:

• Please indicate which category or categories from our package fit policies this package falls under and why:

I think this package falls best under the data retrieval category, because it supports the discovery of openly available scholarly publications. The oaDOI service itself claims to index more than 90 million articles covering sources like Crossref, a DOI minting agency, or the Bielefeld Academic Search Engine (BASE).

• If this is a resubmission following rejection, please explain the change in circumstances:

• If possible, please provide recommendations of reviewers - those with experience with similar packages and/or likely users of your package - and their GitHub user names:

  • Ross Mounce - rossmounce
  • Tuija Sonkkila - tts

[sckott]

thx for your submission @njahn82

editor checks coming soon

[sckott]

Editor checks:

• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has a CRAN or OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

Editor comments

Currently seeking reviewers. It's a good fit and not overlapping.

• Played a bit with the package:
  • seems like email will take any string - maybe it's worth validating email addresses - seems like they don't server side either, though maybe they are just using it as a string and not validating it
• Ran goodpractice::gp(), not a lot to deal with. Test coverage is quite good. Could shorten line lengths to tidy things up a bit.

It is good practice to

  ✖ write unit tests for all functions, and all package code in general. 81% of code lines are covered by test cases.

    R/oadoi_fetch.r:126:NA
    R/oadoi_fetch.r:127:NA
    R/oadoi_fetch.r:128:NA
    R/oadoi_fetch.r:129:NA
    R/oadoi_fetch.r:130:NA
    ... and 4 more lines

  ✖ avoid long code lines, it is bad for readability. Also, many people prefer editor windows that are about 80 characters wide. Try make your
    lines shorter than 80 characters

    R/oadoiAddins.R:24:1

---

Reviewers: @rossmounce @tts
Due date: 2017-06-12

[njahn82]

Thanks for your suggestions! Email validation is now implemented and the long line is wrapped for better code readability.

[sckott]

cool, thx

[sckott]

Reviewers assigned! Big thx to @rossmounce @tts - due date above

[tts]

Package Review

• As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

• A statement of need clearly stating problems the software is designed to solve and its target audience in README
• Installation instructions: for the development version of package and any non-standard dependencies in README
• Vignette(s) demonstrating major functionality that runs successfully locally
• Function Documentation: for all exported functions in R help
• Examples for all exported functions in R Help that run successfully locally
• Community guidelines including contribution guidelines in the README or CONTRIBUTING, and URL, Maintainer and BugReports fields in DESCRIPTION

Functionality

• Installation: Installation succeeds as documented.
• Functionality: Any functional claims of the software been confirmed.
• Performance: Any performance claims of the software been confirmed.
• Automated tests: Unit tests cover essential functions of the package
  and a reasonable range of inputs and conditions. All tests pass on the local machine.
• Packaging guidelines: The package conforms to the rOpenSci packaging guidelines

Final approval (post-review)

• The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 5

---

General Comments

This is a compact and useful package. For me personally timing was perfect because I had plans to add links to open access fulltext to my latest altmetrics Shiny app aaltovirta. Now links are in place, thanks to your work, @njahn82!

Although I do not really belong to the RStudio addin focus group, I can imagine that there are many people who welcome this functionality too.

Tests

devtools::check() and devtools::test() ran without errors on Ubuntu 16.04.2 LTS, R 3.2.3.

The RStudio addin works as expected.

Documentation

• In oadoi_fetch.R, line 3: acccess --> access
• In oadoi_fetch.R, line 12: adress --> address
• In oadoi_fetch.R, lines 24-57: the following are returned by the function but missing from here: _closed_base_ids, _closed_urls, oa_color_long
• In oadoi_fetch.R, lines 24-57: columns are sorted by name which is fine. However, I wonder if the preceding column numbering is needed at all because as of now, it does not reflect the order of the result tibble. Or is it so that the .Rd command \tabular does not serve very well here?
• In oadoi_fetch.R, line 34: green_base_collections --> _green_base_collections
• In vignette intro.Rmd, line 27: json --> JSON