Submission: refnet

[aurielfournier]

Summary

• What does this package do? (explain in 50 words or less): refnet is a package to read, organize, geocode, analyze, and visualize Clarivate Web of Knowledge/Web of Science, format reference data files for scientometric, social network, and Science of Science analyses.

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

Package: refnet
Type: Package
Title: Thomson Reuters Web of Knowledge/Science and ISI Reference Data Tools
Version: 0.6
Date: 2018-08-26
Authors@R: c(person("Auriel M.V. Fournier", "Developer", role = c("aut"),
                     email = "aurielfournier@gmail.com"),
              person("Forrest R. Stevens", "Developer", role = "aut"),
              person("Matthew E. Boone", "Developer", role = "aut"),
              person("Emilio Bruna", "Developer", role=c("aut","cre"), 
              email="embruna@ufl.edu"))
Maintainer: Emilio Bruna <embruna@ufl.edu>
Description: This function reads Thomson Reuters Web of Knowledge/Science and ISI format reference data files into an R friendly data format and can optionally write the converted data to a friendly CSV format.
License: GPL-3
Imports: maptools, maps, rworldmap, RecordLinkage, Matrix, igraph, network, sna, Hmisc, ggplot2, stringi, stringr, ggmap, Rdpack, tidyr, dplyr, tibble
RoxygenNote: 6.1.0
RdMacros: Rdpack
Suggests: testthat, utils
VignetteBuilder: utils
Encoding: UTF-8

• URL for the package (the development repository, not a stylized html page): https://github.com/embruna/refnet

• Please indicate which category or categories from our package fit policies this package falls under *and why(? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):

Data extraction and munging, since it takes data from one format, and transforms it into something that is useful, and also matches up records among authors.

[Note, the link for the package fit, does not lead to that page anymore, and I couldn't find anything about package fit in the linked policies]

•   Who is the target audience and what are scientific applications of this package?  

Scientists interested in studying the networks of a particular author, subject area or journal.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

•   If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

https://github.com/ropensci/onboarding/issues/247

Requirements

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

• [X] does not violate the Terms of Service of any service it interacts with.
• [X] has a CRAN and OSI accepted license.
• [X] contains a README with instructions for installing the development version.
• [X] includes documentation with examples for all functions.
• [X] contains a vignette with examples of its essential functions and uses.
• [X] has a test suite.
• [X] has continuous integration, including reporting of test coverage, using services such as Travis CI, Coveralls and/or CodeCov.
• [X] 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

• [yes] Do you intend for this package to go on CRAN?
• [yes] Do you wish to automatically submit to the Journal of Open Source Software? If so:
  • [X] The package has an obvious research application according to JOSS's definition.
  • [X] The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • [not yet] The package is deposited in a long-term repository with the DOI:
  • (Do not submit your package separately to JOSS)
• [no] Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
  • [ ] The package is novel and will be of interest to the broad readership of the journal.
  • [ ] The manuscript describing the package is no longer than 3000 words.
  • [ ] You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see MEE's Policy on Publishing Code)
  • (Scope: Do consider MEE's Aims and Scope for your manuscript. We make no guarantee that your manuscript will be within MEE scope.)
  • (Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
  • (Please do not submit your package separately to Methods in Ecology and Evolution)

Detail

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

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

• 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:

Heather Piwowar @hpiwowar

[maelle]

Cool! I'll come back to this thread tomorrow, it's getting late here.

[maelle]

Approved! Thanks @embruna @aurielfournier @birderboone for submitting and @njahn82 @bmkramer for your reviews! :grin:

To-dos:

• [x] Transfer the repo to rOpenSci's "ropensci" GitHub organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You'll be made admin once you do.
• [x] Add the rOpenSci footer to the bottom of your README " [![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)"
• [x] Fix all links to the GitHub repo to point to the repo under the ropensci organization.
• [x] If you already had a pkgdown website, fix its URL to point to https://docs.ropensci.org/package_name and deactivate the automatic deployment you might have set up, since it will not be built centrally like for all rOpenSci packages, see https://devguide.ropensci.org/ci.html#even-more-ci-ropensci-docs. In addition, in your DESCRIPTION file, include the docs link in the URL field alongside the link to the GitHub repository, e.g.: URL: https://docs.ropensci.org/foobar (website) https://github.com/ropensci/foobar
• [x] Add a mention of the review in DESCRIPTION via rodev::add_ro_desc().
• [x] Fix any links in badges for CI and coverage to point to the ropensci URL. We no longer transfer Appveyor projects to ropensci Appveyor account so after transfer of your repo to rOpenSci's "ropensci" GitHub organization the badge should be [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/ropensci/pkgname?branch=master&svg=true)](https://ci.appveyor.com/project/individualaccount/pkgname).
• [x] We're starting to roll out software metadata files to all ropensci packages via the Codemeta initiative, see https://github.com/ropensci/codemetar/#codemetar for how to include it in your package, after installing the package - should be easy as running codemetar::write_codemeta() in the root of your package.
• [x] Activate Zenodo watching the repo
• [x] Tag and create a release so as to create a Zenodo version and DOI
• [x] Submit to JOSS at https://joss.theoj.org/papers/new, using the rOpenSci GitHub repo URL. When a JOSS "PRE REVIEW" issue is generated for your paper, add the comment: This package has been reviewed by rOpenSci: https://LINK.TO/THE/REVIEW/ISSUE, @maelle

Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them "rev"-type contributors in the Authors@R field (with their consent). More info on this here.

Welcome aboard! We'd love to host a blog post about your package - either a short introduction to it with one example or a longer post with some narrative about its development or something you learned, and an example of its use. If you are interested, review the instructions, and tag @stefaniebutland in your reply. She will get in touch about timing and can answer any questions.

We've put together an online book with our best practice and tips, this chapter starts the 3d section that's about guidance for after onboarding. Please tell us what could be improved, the corresponding repo is here.

[embruna]

Hi All, a quick update:

The following have been COMPLETED

• Transfer the repo to rOpenSci's "ropensci" GitHub

• Add the rOpenSci footer to the bottom of your README

• Fix all links to the GitHub repo to point to the repo under the ropensci organization.

• Fix any links in badges for CI and coverage to point to the ropensci URL.

I'm finishing the following as soon as I am done with class:

• Add a mention of the review in DESCRIPTION via rodev::add_ro_desc().
• Including Metadata
• I'm awaiting approval from one last reviewer

At that point I will create the Zeonodo 1.0 version and mint the DOI, and submit to JOSS. Should be done shortly.

[embruna]

Hi @noamross and @maelle, a couple quick questions:

1) I've written some code that helps users more quickly narrow down the names to review after doing the disambiguation, but we decided not to include it in the package. I have it on my own github (link here) and point to it in the vignette. Is that ok, or should this also be transferred over to the ROpenSci repo?

2) It's currently versioned as v0.6. Should it be posted as v1.0?

3) I'm just waiting to hear back from a reviewer. I'll wait until Monday noon, at which time I'll do the Zenodo stuff and submit to JOSS.

[maelle]

1. Maybe it could become a tech note (https://ropensci.org/technotes), or a vignette in refsplitr?

2. That's up to you. :slightly_smiling_face:

3. Ok!

[embruna]

OK, @noamross and @maelle: refsplitr should be ready for Zendo v1.0.0

The only unexpected thing that came up was that our title (or rather, the text after the colon in refsplitr: --- needed to be fixed. It was inconsistent within the repo (different in readme and description) and far longer than CRAN-style. So it is now as follows:

refsplitr: author name disambiguation, author georeferencing, and mapping of coauthorship networks with Web of Science data.

I was a actually a bit concerned because Clarivate's webpage is clear:

Do not incorporate any Clarivate Analytics product names into your company's product names. link

However, a quick search on CRAN reveals several other packages wth "Web of Science" in the title, so I just left it in. If you prefer it be removed let me know. Otherwise, I will freeze v1.0.0 with Zenodo at the end of the day.

[maelle]

I think the package isn't a company product? But I'm not a lawyer.

In any case I think you'll need to write it 'Web of Science' in DESCRIPTION.

[embruna]

Submitted to JOSS, and Zenodo archived as v0.9.0 with doi 10.5281/zenodo.3608285. Once the JOSS review is complete and I can include the details in the paper.rm file. At that point I'll freeze v1.0. A minor thing, and maybe unnecessary. But I wanted 1.0 to be a complete package with no details to be filled in.

[maelle]

Ok! I don't see the submission at https://joss.theoj.org/papers yet.

[embruna]

Yes, still listed as "pending"...I'll check on it periodically throughout the day.

[maelle]

I've just checked again. Please ping me if you see it appear. :wink:

[maelle]

Paper accepted at JOSS 🎉 so closing this issue.