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[REVIEW]: COINr: An R package for developing composite indicators #4567

Closed editorialbot closed 2 years ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@bluefoxr<!--end-author-handle-- (William Becker) Repository: https://github.com/bluefoxr/COINr Branch with paper.md (empty if default branch): Version: v1.1.0 Editor: !--editor-->@jbytecode<!--end-editor-- Reviewers: @bauer-alex, @paulrougieux Archive: 10.5281/zenodo.7180388

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HTML: <a href="https://joss.theoj.org/papers/187b1759658c96177f8d17f3b55b90a0"><img src="https://joss.theoj.org/papers/187b1759658c96177f8d17f3b55b90a0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/187b1759658c96177f8d17f3b55b90a0/status.svg)](https://joss.theoj.org/papers/187b1759658c96177f8d17f3b55b90a0)

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) by leaving comments 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

@bauer-alex & @paulrougieux, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jbytecode know.

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Checklists

📝 Checklist for @bauer-alex

📝 Checklist for @paulrougieux

editorialbot commented 2 years ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.63 s (478.8 files/s, 147803.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           209           7304            750          34654
JavaScript                      10           6039           5400          20673
R                               46           2026           5900           4991
XML                              1              0              0            630
Rmd                             20           1106           1737            590
CSS                              5             98             52            464
YAML                             3             12              4            312
Markdown                         5             85              0            267
TeX                              1             12              0            111
SVG                              1              0              1             11
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           302          16682          13844          62704
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 1051

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.resglo.2021.100045 is OK
- 10.13140/RG.2.2.14408.75520 is OK
- 10.1007/s10669-020-09784-x is OK
- 10.2760/523877 is OK
- 10.1016/j.omega.2017.04.007 is OK
- 10.1007/s11573-018-0902-z is OK
- 10.1111/ecge.12094 is OK
- 10.1016/j.envsoft.2021.105208 is OK
- 10.1007/s11205-021-02688-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

jbytecode commented 2 years ago

Dear Reviewers: @bauer-alex and @paulrougieux

This is the review thread. Please type

@editorialbot generate my checklist

to generate your task list. In this list, there are 20 review items. Whenever you complete a task, you can check off the corresponding check box.

You can always interact with the author(s), other reviewers, and the editor during the reviewing process. You can also open issues in the target repo and send pull request. Please mention the review page in those issues, so we can keep tracking outside of our world.

Thank you in advance.

jbytecode commented 2 years ago

@editorialbot remind @bauer-alex in 3 days

editorialbot commented 2 years ago

Reminder set for @bauer-alex in 3 days

jbytecode commented 2 years ago

@editorialbot remind @paulrougieux in 3 days

editorialbot commented 2 years ago

Reminder set for @paulrougieux in 3 days

bauer-alex commented 2 years ago

Review checklist for @bauer-alex

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

paulrougieux commented 2 years ago

Review checklist for @paulrougieux

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

paulrougieux commented 2 years ago

@jbytecode @bluefoxr (William Becker) is a former colleague from the Joint Research Centre, a large research organisation, but we were working in different research groups.

danielskatz commented 2 years ago

@paulrougieux - from how long ago?

paulrougieux commented 2 years ago

From a couple of years ago.

danielskatz commented 2 years ago

Can you define a couple?

bluefoxr commented 2 years ago

Hi @danielskatz I invited @paulrougieux since we were short on reviewers. I worked in the European Commission's Joint Research Centre up until March 2020. Paul worked there as well, and still works there. He has a lot of experience in R and has actually used the COINr package (the subject of this paper). I am sure Paul would give an objective review, but if this is too much of a conflict of interest I understand and my apologies.

Edit: for clarity, the research centre has approx 2000 staff on site and we worked in completely separate groups. However I do know Paul personally.

danielskatz commented 2 years ago

Our COI rules use 4 years as the conflict period in this type of situation, so the editor (@jbytecode) now needs to decide whether this COI that we've found should be waived.

bluefoxr commented 2 years ago

@danielskatz Ok thanks for the clarification - I had understood the 4 years was for professional collaborations. Anyway sorry for the confusion here.

danielskatz commented 2 years ago

@bluefoxr - You are correct. I was misremembering the JOSS guidelines, which say that the organizational conflict period is one year, while the collaboration conflict period is four years. So there is no conflict here, and the review can proceed without concern.

bluefoxr commented 2 years ago

@danielskatz fantastic, thanks

jbytecode commented 2 years ago

@paulrougieux thank you for stating the coi issue.

As @danielskatz says, there is no conflict here and we can continue.

bauer-alex commented 2 years ago

@bluefoxr Seems like a very interesting package! I especially appreciate the high effort you put into documenting all functionalities appropriately. I opened some technical and documentation issues in the COINr repository. Once these are dealt with I will take a deeper look over the paper itself.

One additional question: In the GitHub repository you are the only contributor to the package. Could you clarify the contributions of your co-authors?

editorialbot commented 2 years ago

:wave: @bauer-alex, please update us on how your review is going (this is an automated reminder).

editorialbot commented 2 years ago

:wave: @paulrougieux, please update us on how your review is going (this is an automated reminder).

bluefoxr commented 2 years ago

@bluefoxr Seems like a very interesting package! I especially appreciate the high effort you put into documenting all functionalities appropriately. I opened some technical and documentation issues in the COINr repository. Once these are dealt with I will take a deeper look over the paper itself.

One additional question: In the GitHub repository you are the only contributor to the package. Could you clarify the contributions of your co-authors?

@bauer-alex Thanks very much for taking the time to look over the package. I will deal with all the issues you raised although as mentioned expanding the unit testing coverage will take a little while as this is quite a big task.

As regards the co-authors they are included due to a lot of helpful input in conceptualising the package, testing features and providing feedback.

jbytecode commented 2 years ago

Dear @bluefoxr

How is your edits going? Could you please update your status or at least give a deadline for us?

Thank you in advance.

bluefoxr commented 2 years ago

Dear @jbytecode my apologies for the slow reply, I have been away. I have addressed some initial comments previously and I see that there are a number of extra comments to address. Most of these can be dealt with fairly quickly but some, such as the unit testing coverage, will need quite a bit of time to improve. I will see what progress I can make in the next week, after which I will again be away until the beginning of September. Would it be reasonable to ask until end of Sep to deal with this? I am mainly thinking of the time needed to code up all the unit tests. Thanks.

jbytecode commented 2 years ago

Thank you for the response, I just wanted to see whether you are in trouble or not. Have a nice vacation.

bluefoxr commented 2 years ago

No trouble, the reviewers' comments are all reasonable. Thanks and I will update as soon as I can.

jbytecode commented 2 years ago

@editorialbot remind @bluefoxr in two days

editorialbot commented 2 years ago

Reminder set for @bluefoxr in two days

editorialbot commented 2 years ago

:wave: @bluefoxr, please update us on how things are progressing here (this is an automated reminder).

bluefoxr commented 2 years ago

Hi @jbytecode I am away until the beginning of September. I can't do much until then, at which point I will aim to finish all revisions by the end of September if that is OK?

jbytecode commented 2 years ago

@bluefoxr - thank you so much for setting a deadline.

jbytecode commented 2 years ago

Dear @bauer-alex and @paulrougieux - could you please update your status and inform us on how is your review going?

Dear @bluefoxr - I am so sorry if I am bothering you pinging on 26th Sept, I am not sure if it can be considered as the end of the month, but if it is possible, can you update your status and inform us?

Thank you in advance.

bluefoxr commented 2 years ago

Dear @jbytecode I have addressed all the open issues raised by the reviewers so far. Just waiting for @paulrougieux to see if this issue (https://github.com/bluefoxr/COINr/issues/15) can be closed after some revisions I made to the paper. Not sure if the reviewers want to raise further issues at this stage?

paulrougieux commented 2 years ago

Hi, I'll update this evening.

bauer-alex commented 2 years ago

Hi all, I'm on it. Will have some more comments about the content of the paper. Since I'm quite involved in work you'll get my update mid / end next week.

paulrougieux commented 2 years ago

I see 2 issues remaining :

Once these are clarified or fixed, the paper is OK from my side.

bluefoxr commented 2 years ago

Hi @paulrougieux I have made some commits to fix these issues. Please take a look and see if you think they fix the problems. Thanks.

paulrougieux commented 2 years ago

Both issues bluefoxr/COINr#23 and bluefoxr/COINr#15 are fixed, I ticked all boxes in the checklist above.

jbytecode commented 2 years ago

@paulrougieux - Thank you for completing your review and spending your valuable time.

bluefoxr commented 2 years ago

Both issues bluefoxr/COINr#23 and bluefoxr/COINr#15 are fixed, I ticked all boxes in the checklist above.

Thanks @paulrougieux for your valuable input!

bauer-alex commented 2 years ago

@bluefoxr I now took a deeper look over the paper. Here are my final comments: First of all, I really like the style of writing. Nice descriptions with a good depth and useful examples and links to further helpful materials. Good work!

Apart from the following long list of (easily solvable) minor points down below, I only have one major point which is that your paper is too long for JOSS. It should include 1.000 words max, but your text parts (without headers, code blocks, figure captions, acknowledgments, references) currently comprise ~1.360 words.

Minor points:

bluefoxr commented 2 years ago

@bauer-alex thanks for these comments, I will get started and report progress here

bluefoxr commented 2 years ago

For the minor comments, please see commits https://github.com/bluefoxr/COINr/commit/3b4a23a877e838c42adccb37169d617a1e2328a0 up to https://github.com/bluefoxr/COINr/commit/eced2abc6c4c1be4ba1c6b014828138aba332a69 (or perhaps better, the resulting pdf).

I will now have a go at reducing the word count a bit.

bluefoxr commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

Hello @bluefoxr, here are the things you can ask me to do:


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bluefoxr commented 2 years ago

@editorialbot check repository