JOSS reviewer comments - submission 6561

[adriancorrendo]

Review checklist for @adriancorrendo

General checks

• Contribution and authorship: Has the submitting author (@LeoEgidi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

• Commits come only from @LeoEgidi. Could you please confirm the role of the rest of the authors?

Functionality

1 > * [ ] Functionality: Have the functional claims of the software been confirmed?

• I’m afraid there is no example in the paper of at least a line of code running any package functions. Could you please try to include something short with a line of code to run the key/s function/s?

2 > * [ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

• It sounds silly, but authors only indicate how to do it from github (although the code line to do it from CRAN is there). I think it could be good to use something like this on the README
  :

** You can install the CRAN version of pivmet with:
install.packages("pivmet")

** You can install the development version from GitHub with: …

3 > * [ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

Pivmet repo does not include any automated tests through continuous integration tools. @LeoEgidi, could you please revise this point? I could not find these tests like: R-CMD, codecov, appveyor.

4 > * [ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

I could not find community guidelines documentation. Please, see an example here…https://www.tidymodels.org/contribute/

Software paper

5 > * [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?

I consider authors fail to provide a comparison of what potentially similar packages are available or mentioning how do people is figuring out for similar tasks without pivmet. Could you please offer a brief overview to readers?

6 > * [x] Typo on L59

Please, could you check for a potential typo at line 59 where it says..."Figure ??"

[LeoEgidi]

Commits come only from @LeoEgidi. Could you please confirm the role of the rest of the authors?

Sure. The other authors developed some original code and deeply worked at the current project, however, since they are not very fluent with Github, I am the responsible for the Github commits and edits

[LeoEgidi]

Dear @adriancorrendo ,
I worked at the paper review. Thanks a lot for your valuable and precious comments.
I provide here a complete list of answers to your single points.
Of course, I am available for any clarification or doubt.

1. I’m afraid there is no example in the paper of at least a line of code running any package functions. Could you please try to include something short with a line of code to run the key/s function/s?

Done. We added the relevant lines of R code for both the examples reported in the paper, see #Example 1 and #Example 2

2. It sounds silly, but authors only indicate how to do it from github (although the code line to do it from CRAN is there). I think it could be good to use something like this on the README
   :
   ** You can install the CRAN version of pivmet with:
   install.packages("pivmet")

** You can install the development version from GitHub with: …

Thanks, done: we added the suggested intructions in the README.rmd and README.md files.

3. Pivmet repo does not include any automated tests through continuous integration tools. @LeoEgidi, could you please revise this point? I could not find these tests like: R-CMD, codecov, appveyor.

Done. We added new tests in the 'tests/testthat' subfolder to monitor and check the performance of the main functions of the package.

4. I could not find community guidelines documentation. Please, see an example here…https://www.tidymodels.org/contribute/

Thanks, done. We included a new "CODE OF CONDUCT" in the main repo, where we declare and suggest how to contribute and report bugs.

5. I consider authors fail to provide a comparison of what potentially similar packages are available or mentioning how do people is figuring out for similar tasks without pivmet. Could you please offer a brief overview to readers?

Done. We added a new paragraph in the paper, at the end of the "Statement of need", where we offer a brief overview of the main packages related to pivmet.

6. Please, could you check for a potential typo at line 59 where it says..."Figure ??"

Done, it should be fixed right now.

[adriancorrendo]

Thank you, @LeoEgidi ! Great job with the reviews.
Just have a comment regarding #3 Automated tests.
Including the tests with testthat is fine, but I meant adding something like R-CMD, codecov, "passing" badges on the readme. With these badges people will instantly see if the package passed the tests. Ideally, codecov will show what percentage of functions are "covered" with the tests you specified. Could you try at least adding the R-CMD ?

To add the R-CMD for example, you can use usethis::use_github_action()

Thanks,
Adrian

[adriancorrendo]

Hi @LeoEgidi , please take my last comment as a "suggestion" rather than a required revision. I'm happy with your work on my revisions.

Congratulations for your package.

Best regards,
Adrian

[LeoEgidi]

Thanks a lot @adriancorrendo for your nice suggestions and approval!
I added the R-CMD in the readme through your suggested function, thanks a lot!