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

[editorialbot]

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

Status

Status badge code:

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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:

@editorialbot generate my checklist

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @bauer-alex

📝 Checklist for @paulrougieux

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.40 s (674.5 files/s, 171656.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           161           6341            513          30417
JavaScript                       4           2099           1928           7019
R                               69           2505           7122           5989
Rmd                             19           1120           1746            590
XML                              1              0              0            486
Markdown                         5            118              0            370
YAML                             7             27             11            368
TeX                              1             16              0            146
CSS                              2              0              0             22
SVG                              1              0              1             11
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           271          12226          11321          45419
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1360

[bluefoxr]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.38 s (711.8 files/s, 181124.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           161           6341            513          30417
JavaScript                       4           2099           1928           7019
R                               69           2505           7122           5989
Rmd                             19           1120           1746            590
XML                              1              0              0            486
YAML                             7             27             11            368
Markdown                         5            119              0            360
TeX                              1             16              0            146
CSS                              2              0              0             22
SVG                              1              0              1             11
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           271          12227          11321          45409
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1350

[bluefoxr]

I am getting slightly conflicting word counts from the wordcount addin in R studio which points to approx 1200 words as opposed to the bot which counts more. I have removed quite a bit of text - @bauer-alex could you let me know how close to 1000 you need because I added some extra text on the request of the other reviewer. Thanks

[bauer-alex]

@editorialbot generate pdf

[editorialbot]

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

[bauer-alex]

Thanks for the quick changes @bluefoxr. For the word count I get 1,097 words (again, excluding headers, figure captions, references and acknowledgements). Seeing that - as you mention - the paper grew a little during the revision process, this is fine for me.

The only open task from my previous message is to name it Microsoft Excel instead of only Excel. Then you get my go for publication.

[bluefoxr]

Thanks also for the quick reply, I have just made the last change - somehow I overlooked that one: https://github.com/bluefoxr/COINr/commit/b0c33138bdb56fbc66fe761dfc0ee57efa677d2a

[bauer-alex]

Perfect!

[bauer-alex]

@editorialbot generate pdf

[editorialbot]

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

[bauer-alex]

@jbytecode I'm happy with the changes made and ticked all my checkboxes. You can move on with the publication process.

[jbytecode]

@bauer-alex, @paulrougieux - thank you for your valuable reviews and spending your time.

I think I can now start my editorial tasks.

Thank you.

[jbytecode]

@editorialbot check references

[editorialbot]

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

- 10.1111/j.1467-985x.2005.00350.x may be a valid DOI for title: Uncertainty and sensitivity analysis techniques as tools for the quality assessment of composite indicators
- 10.1016/j.envsoft.2019.01.012 may be a valid DOI for title: Why so many published sensitivity analyses are false: A systematic review of sensitivity analysis practices

INVALID DOIs

- None

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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

[bluefoxr]

@jbytecode thank you I have merged the pull request

[jbytecode]

@bluefoxr - please review the pull request that I have just sent and apply it if you are agreed with the changes.

Thank you in advance.

[bluefoxr]

@jbytecode thanks for your input - I have merged that as well.

[jbytecode]

@editorialbot check references

[editorialbot]

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
- 10.1111/j.1467-985x.2005.00350.x is OK
- 10.1016/j.envsoft.2019.01.012 is OK
- 10.1007/s11205-021-02688-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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

[jbytecode]

@bluefoxr - please check the PR again

[bluefoxr]

Thanks, merged, I just added a word

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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

[jbytecode]

Dear @bluefoxr

• [X] The paper and the bibtex look nicer now. Thank you.
• [x] Please read the paper pdf carefully, one more time, correct any issue if exists. Please perform a full grammar check.
• [x] Create a tagged release in the software repository. Report the version here. The version should be in form of vx.y.z, e.g. v1.2.3.
• [x] Create a Zenodo archive of the repository in https://zenodo.org/
• [x] The Zenodo archive (with the same name/title with the JOSS paper) should have the correct metadata, e.g. author names, ORCIDs, the title of the archive. Please set the archive title as the paper title.
• [x] Please provide the tagged release id, zenodo archive DOI, and Zenodo archive URL here.

Thank you in advance.

[jbytecode]

@bluefoxr - could you please update your status and set a deadline for us? thank you in advance.

[bluefoxr]

@jbytecode I am aiming to complete your checklist by the end of the day, if not by tomorrow. I just made some minor last edits to the paper and will now proceed to tag and archive the repo as requested.

[bluefoxr]

@jbytecode could I ask which zenodo community, if any, the software should be archived in? Am I free to choose or is there a JOSS policy/requirement? Thanks.

[jbytecode]

@bluefoxr - The latest snapshot should be registered as a tagged archive in github and should be also registered on an outer service such as Zenodo.org. Yes, this process is required in JOSS submissions. Thank you in advance.

[jbytecode]

@bluefoxr - Please take a look at the https://joss.readthedocs.io/en/latest/submitting.html?highlight=zenodo#the-review-process

[bluefoxr]

@jbytecode I have now archived the package on Zenodo. Details are:

• GitHub tagged release: https://github.com/bluefoxr/COINr/releases/tag/v1.1.0
• Zenodo DOI: https://doi.org/10.5281/zenodo.7180388
• Zenodo link: https://zenodo.org/record/7180389#.Y0PzBnZBzN8

Please let me know if it is OK like this or I need to change something. Thanks.

[jbytecode]

@bluefoxr - could you please check the author metadata and ORCHID for all co-authors in Zenodo archive? It seems there is some missing info (at least an Orchid)

[bluefoxr]

@jbytecode I can't see anything missing - only three of the authors have ORCIDs, and it corresponds to the JOSS paper as far as I can see? Is there something specific missing?

[jbytecode]

@editorialbot set v1.1.0 as version

[editorialbot]

Done! version is now v1.1.0

[jbytecode]

@editorialbot set 10.5281/zenodo.7180388 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7180388

[jbytecode]

@editorialbot check references

[editorialbot]

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
- 10.1111/j.1467-985x.2005.00350.x is OK
- 10.1016/j.envsoft.2019.01.012 is OK
- 10.1007/s11205-021-02688-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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

[jbytecode]

@bauer-alex, @paulrougieux - thank you so much, again and again, for your contributions, review, and time!

@bluefoxr - Now it is okay to me, thank you for correcting and crafting things.

I am now recommending an accept!

[jbytecode]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...