[REVIEW]: Climate variability indices for ecological and crop models in R: the climatrends package

[editorialbot]

Submitting author: @kauedesousa (Kauê de Sousa) Repository: https://github.com/AgrDataSci/climatrends Branch with paper.md (empty if default branch): Version: v0.2 Editor: @KristinaRiemer Reviewers: @dlebauer, @istfer Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/03d54683d5c1d7759519070442ef4500"><img src="https://joss.theoj.org/papers/03d54683d5c1d7759519070442ef4500/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/03d54683d5c1d7759519070442ef4500/status.svg)](https://joss.theoj.org/papers/03d54683d5c1d7759519070442ef4500)

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

@dlebauer & @istfer, 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 @KristinaRiemer 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 @istfer

📝 Checklist for @dlebauer

[editorialbot]

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:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (888.4 files/s, 174866.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            24           1246            323           4183
R                               20           1029           1462           2010
XML                              2              0              0            749
TeX                              2             53              0            464
CSS                              4             99             49            431
Markdown                         5            162              0            376
JavaScript                       6             69             42            301
SVG                              2              0              1            193
JSON                             1              0              0            187
Rmd                              1             46             55             43
YAML                             2              1              0              7
-------------------------------------------------------------------------------
SUM:                            69           2705           1932           8944
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 3153

[editorialbot]

Failed to discover a Statement of need section in paper

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.02419 is OK
- 10.1029/2005JD006119 is OK
- 10.1016/j.jrurstud.2018.09.018 is OK
- 10.1201/9781315369006-13 is OK
- 10.1073/pnas.1813720116 is OK
- 10.5067/MODIS/MYD11A1.006 is OK
- 10.1038/sdata.2015.66 is OK
- 10.21105/joss.01035 is OK
- 10.32614/RJ-2018-009 is OK
- 10.2307/2845499 is OK
- 10.1038/s41598-018-26681-1 is OK
- 10.1371/journal.pone.0065401 is OK
- 10.1038/nclimate3061 is OK
- 10.1007/978-3-662-56233-8 is OK
- 10.1038/nclimate2242 is OK
- 10.1073/pnas.1920816117 is OK
- 10.1007/s00180-020-00959-3 is OK
- 10.5067/MODIS/MYD11A1.006 is OK
- 10.1155/2016/8065985 is OK
- 10.1007/978-0-387-78341-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[istfer]

Review checklist for @istfer

Conflict of interest

• [X] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 https://github.com/AgrDataSci/climatrends?
• [X] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [X] Contribution and authorship: Has the submitting author (@kauedesousa) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [X] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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

• [ ] 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [ ] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[KristinaRiemer]

Hi @dlebauer & @istfer, could we get an idea of your timelines for completing your reviews? Thanks!

[istfer]

Hi @KristinaRiemer and @kauedesousa, I still need the next (whole) week to complete my review, thank you for your understanding!

[KristinaRiemer]

It's all good, I'm not trying to rush anyone, just want to stay up to date on plans! Thanks @istfer!

[dlebauer]

Apologies, its on my list for next week.

[dlebauer]

Review checklist for @dlebauer

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 https://github.com/AgrDataSci/climatrends?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@kauedesousa) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [ ] Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
• [ ] 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).
• [ ] 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[KristinaRiemer]

Thanks for making progress on your reviews @istfer & @dlebauer. Let me know if any of you need any help or have questions.

[istfer]

Hi @KristinaRiemer, @kauedesousa and @dlebauer,

I'm done with the first pass of the review checklist. The remaining issues (unchecked items) are mostly about the software paper itself and as follows:

1. Documentation: a clear statement of need text is missing from the documentation
2. A section titled "Statement of need" is also missing in the paper
3. State of the field is not described in the paper
4. Quality of the writing is good (maybe a bit too jarnogy for non-specialists) in general but the text is too long for JOSS standards which I believe means structural editing is needed
5. References are in general in place, but I had this question regarding the cbean dataset. Not exactly sure how to link this dataset to the paper & package, but I considered it an issue under "appropriate citation of datasets" hence left the box unchecked for now.

Opened up issues in the climatrends repository accordingly. I'll keep an eye on the activities in the repository but feel free to ping me as needed.

[KristinaRiemer]

Hi everyone, just want to let you all know that I'm going to be on vacation for the next three weeks. @istfer, thank you for finishing your first round of review, and hopefully @kauedesousa will have the chance to address your comments and ask any relevant questions. @dlebauer should also aim to have the initial review complete within the next week or so. Thank you all!

[KristinaRiemer]

/ooo July 15 until August 5

[dlebauer]

I've reviewed the paper, I still need to review the functionality and will submit a PR with suggestions for improving clarity of the text.

I concur with issues @istfer pointed out - esp. the lack of statement of need, description of state of field / related software, and the cbean dataset.

[kauedesousa]

Thanks for the reviews @istfer and @dlebauer

I'm in a duty travel and will work in your comments next week.

[KristinaRiemer]

Hi @dlebauer, have you had a chance to review the software for the functionality items yet?

[dlebauer]

@KristinaRiemer trying, but currently failing to build https://github.com/AgrDataSci/climatrends/issues/16

[kauedesousa]

I am working on updates but got stuck in other adm things. Better if you try the CRAN version which is more stable. Another issue is that NASAPower, which was used for the Scandinavia example, changed the API and don't allow calls for more than 1 year. The issue was already reported to the 'nasapower' developer, but there is not so much he can do https://github.com/ropensci/nasapower/issues/71. I am working in a solution from the climatrends side which probably will involve a loop or lapply.

[arfon]

:wave: folks. Just checking in here. @KristinaRiemer – are we still waiting for the author to make changes here?

[kauedesousa]

I planning to work on these reviews over the next two weeks. Sorry for the long silent, I was traveling a lot (I am returning from one travel today).

[KristinaRiemer]

Thank you for the check in @arfon.

@dlebauer are you still unable to get the dev version of the package to build? Same errors?

@kauedesousa it looks like there are still a handful of open issues from the reviewers, how is the progress on those going?

[dlebauer]

@KristinaRiemer it installs now, though my review is still blocked by https://github.com/AgrDataSci/climatrends/issues/18

[kthyng]

Hi @kauedesousa! From a quick glance, it looks like this review process is waiting on your response to comments so far. When will you be able to work on this?

[kauedesousa]

I am finally back from my duty travels that started in June (Tanzania, Uganda, Kenya, Tanzania again, Norway, Brazil, Cuba, France, Colombia and Nigeria). I started the work on the issues highlighted by the reviewers.