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: refsplitr
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/refsplitr

• 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.

#247

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, Coveralls 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

• [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:
  • The package has an obvious research application according to JOSS's definition.
  • 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

[sckott]

Thanks very much for your submission @aurielfournier - we're discussing now and will get back to you soon

[maelle]

Thanks for your submission @aurielfournier! I see the package doesn't have any test and doesn't have continuous integration yet. I suggest we put the submission on hold while you sort that, unless you can and want to add this within a week or so? There is some guidance in this guide, and I am happy to answer any question here or via Slack!

I was also looking at the dependencies, there are many of them in DESCRIPTION and

• at least one doesn't seem used at all in the package (stringi)
• it seems you have written the NAMESPACE by hand? We'd prefer you to use @importFrom (or even just pkg::fun when calling the function) and @export tags in R files. I wouldn't recommend importing whole packages unless needed. See http://r-pkgs.had.co.nz/namespace.html#imports

[maelle]

@aurielfournier for info I've just added the holding label, please update this thread once you have had time to work on the package, and ask me any question.

[aurielfournier]

Thanks @maelle I and my co-authors are working on it, but its taken a bit longer then we expected. Appreciate your patience!

[maelle]

No problem, and happy to help if I/we can!

[aurielfournier]

@maelle package now has tests and continuous integration.

I removed stringi from the DESCRIPTION file.

I have fixed the issues from the NAMESPACE file.

Huge thanks to my coauthor @birderboone for doing the heavy lifting to get this over the finish line!

I think we are ready for review now. If you have any other things that need to be addressed let me know.

Thanks!

[maelle]

👋 @aurielfournier @birderboone! Awesome, thanks to both of you! A few comments before I do the last editor checks:

• Could you please add the Travis badge at the top of the README?
• The Travis build is failing. To fix this (both WARNING and NOTEs)
  • "Undocumented arguments in documentation object 'references_read'
    ‘include_all’" Update the docs
  • prefix utils functions e.g. utils::flush.console()
  • For some variables you might need to create such a file: https://github.com/ropensci/opencage/blob/master/R/globalVariables.R to define them as global variables (the ones that appear in NOTEs). Unless they come up in dplyr function in which case you can write e.g. mutate(df, y = .data$a + .data$x) to make the NOTE disappear see this vignette
  • Reg JOSS in rtimicropem I put the paper in a paper/ folder https://github.com/ropensci/rtimicropem/tree/master/paper and buildignored it usethis::use_build_ignore("paper/") or something like that.
• Once the Travis build passes please add a code coverage report. Run usethis::use_coverage("codecov") which will give you stuff to add to the Travis config file, browse codecov maybe (I can't remember) and give you the code to paste in the README to get a badge.
• I see two issues about postal codes (leading zeros, Brazil code), do they need to be fixed before review?
• Regarding the other issues I admire the naming scheme. Just in case you ignored that, GitHub also has a milestone feature: https://help.github.com/articles/about-milestones/
• Please add a code of conduct and contributing guide (this can be extremely short) https://ropensci.github.io/dev_guide/collaboration.html#friendlyfiles No need to add the PR and issue templates yet.