Joss-reviews: [REVIEW]: Gravity: Estimation Methods for Gravity Models in R

[whedon]

Submitting author: @pachamaltese (Mauricio Vargas)
Repository: https://github.com/pachamaltese/gravity
Version: v0.9.0
Editor: @yochannah
Reviewer: @DiegoKoz
Archive: 10.5281/zenodo.1491873

Status

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@DiegoKoz, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @yochannah know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @DiegoKoz

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v0.9.0)?
• [x] Authorship: Has the submitting author (@pachamaltese) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

Software paper

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @DiegoKoz it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[pachamaltese]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[pachamaltese]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[pachamaltese]

@yochannah Hi! Is it just me or commiting is super weird today?

[yochannah]

YES! GitHub is playing up I think.

[pachamaltese]

@yochannah just to inform that github became funnier again
I added some feedback from @DiegoKoz and @paulofelipe to the repo, and therefore I updated the version to 0.9 after many iterations

[DiegoKoz]

Hi! I'll open new issues in the original repo with the comments I did in the previous repo, and link them here

[DiegoKoz]

Hi! I'll open new issues in the original repo with the comments I did in the previous repo, and link them here

https://github.com/pachamaltese/gravity/issues/8
https://github.com/pachamaltese/gravity/issues/4

---

This are the remaining two. the rest of the suggestions are already implemented

[DiegoKoz]

@pachamaltese please add a plain-text license

[DiegoKoz]

@pachamaltese please add __Community guidelines__:

clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

[DiegoKoz]

@pachamaltese please add Community guidelines:

clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

You add them in README.rmd instead of README.md and it is not display in the github page

[DiegoKoz]

@yochannah just to inform that github became funnier again
I added some feedback from @DiegoKoz and @paulofelipe to the repo, and therefore I updated the version to 0.9 after many iterations

I think this is the last thing that remains pending. @yochannah how do we proceed with this?

[yochannah]

@DiegoKoz @pachamaltese I note there are a couple of issues in the gravity repo suggested by @DiegoKoz - do you feel like these need to be addressed before we accept?

[pachamaltese]

Hi. Yes, please!
Let me tweak one of the functions a bit, if I am sleepless maybe I optimize
it a lot.

On Sun, Nov 4, 2018, 7:19 PM Yo Yehudi <[email protected] wrote:

@DiegoKoz https://github.com/DiegoKoz @pachamaltese
https://github.com/pachamaltese I note there are a couple of issues in
the gravity repo suggested by @DiegoKoz https://github.com/DiegoKoz -
do you feel like these need to be addressed before we accept?

—
You are receiving this because you were mentioned.
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https://github.com/openjournals/joss-reviews/issues/1038#issuecomment-435713509,
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[DiegoKoz]

@yochannah what should we do with the fact that @pachamaltese upgraded the version and its no longer v0.8.2?

[pachamaltese]

@DiegoKoz @yochannah I can always go back to 0.8.2
I just followed http://r-pkgs.had.co.nz/release.html#release-version

[DiegoKoz]

@DiegoKoz @yochannah I can always go back to 0.8.2
I just followed http://r-pkgs.had.co.nz/release.html#release-version

yes, it's fine, but I don't understand if @yochannah should update de info of the review, or I just accept that item.

Besides de issue you are working on, the rest is fine for me and I think we could accept the review

[yochannah]

we can update the version in the issue above, don't worry :)

[yochannah]

... done. I think versions end up bumped a lot during our review process, since there are usually lot of suggestions and improvements made

[pachamaltese]

@yochannah @DiegoKoz
Hi!! First of all, thanks a lot for the valuable feedback.
I closed all issues except https://github.com/pachamaltese/gravity/issues/5 after doing various improvements. PPML would requiere extensive coding and that issue is more performance related than user input's checks or statistical concerns.
After all the improvements I updated to v0.9.0 and, IMO, I consider the package to be ready.

[yochannah]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[yochannah]

@pachamaltese I've made a PR with a few minor grammar edits for the paper: https://github.com/pachamaltese/gravity/pull/12 - Oh wait, I see you have already merged it, nice!

[yochannah]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[yochannah]

@pachamaltese - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? Also take note of the authors list - it may pick my typo contribution up - you'll need to manually edit the metadata to remove me.

[pachamaltese]

@yochannah my apologies for the delay, here is the upload with the source and binary build https://zenodo.org/record/1490783#.W_GhIuhKhPY

[yochannah]

@whedon set http://doi.org/10.21105/joss.01038 as archive

[whedon]

OK. 10.21105/joss.01038 is the archive.

[yochannah]

Okay! @arfon I think we're ready to accept this one. 🎉 🎆

Thanks @DiegoKoz for reviewing and @pachamaltese for your patience - I know it's been a long process for this paper!

[arfon]

@yochannah my apologies for the delay, here is the upload with the source and binary build https://zenodo.org/record/1490783#.W_GhIuhKhPY

:wave: thanks for making the archive DOI. Unfortunately what you have done won't work. The DOI you have used with Zenodo is the DOI that _JOSS_ will issue (https://doi.org/10.21105/joss.01038). Instead, you need another DOI for the software archive.

When you have a new DOI, please notify us here and we'll proceed with accepting the paper.

[pachamaltese]

@arfon Hi. It is updated now :)
https://zenodo.org/record/1491873#.W_MW5OhKhPY

[arfon]

@whedon set 10.5281/zenodo.1491873 as archive

[whedon]

OK. 10.5281/zenodo.1491873 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/72

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/72, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/73
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01038
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[arfon]

@DiegoKoz - many thanks for your review here and to @yochannah for editing this submission ✨

@pachamaltese - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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