[REVIEW]: `rOPTRAM`: Implementation of the OPTRAM Algorithm in `R`

[editorialbot]

Submitting author: !--author-handle-->@micha-silver<!--end-author-handle-- (Micha Silver) Repository: https://github.com/ropensci/rOPTRAM Branch with paper.md (empty if default branch): Version: v0.3.0 Editor: !--editor-->@kthyng<!--end-editor-- Reviewers: !--reviewers-list-->@kthyng<!--end-reviewers-list-- Archive: 10.5281/zenodo.13257767

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/da6075f8a6b47ad603a2ec4849ef3fb3"><img src="https://joss.theoj.org/papers/da6075f8a6b47ad603a2ec4849ef3fb3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/da6075f8a6b47ad603a2ec4849ef3fb3/status.svg)](https://joss.theoj.org/papers/da6075f8a6b47ad603a2ec4849ef3fb3)

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

@kthyng, 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 @kthyng 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

@kthyng, please create your checklist typing: @editorialbot generate my checklist

[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]

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

OK DOIs

- 10.1126/science.abq4062 is OK
- 10.1016/j.rse.2017.05.041 is OK
- 10.3390/rs12182936 is OK
- 10.1016/j.jag.2020.102113 is OK
- 10.1016/B978-0-12-420022-7.00008-2 is OK
- 10.5194/hess-21-5009-2017 is OK
- 10.3390/s22239143 is OK
- 10.3390/s16081308 is OK
- 10.3390/rs14153801 is OK
- 10.1016/j.rse.2018.04.029 is OK
- 10.1016/j.rse.2015.04.007 is OK
- 10.3390/s7081612 is OK
- 10.1029/2020EA001108 is OK
- 10.3389/fdata.2019.00037 is OK
- 10.1080/01431169608949021 is OK
- 10.1016/j.jag.2022.102817 is OK
- 10.3390/rs12121980 is OK
- 10.1016/j.agwat.2022.107975 is OK
- 10.1029/2021JG006411 is OK
- 10.1016/j.rse.2022.113443 is OK
- 10.3390/rs12203377 is OK
- 10.1016/j.rse.2023.113736 is OK
- 10.5194/esd-2017-4-RC1 is OK
- 10.1016/j.cosust.2020.11.005 is OK
- 10.32614/CRAN.package.CDSE is OK
- 10.1029/2007GB002952 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (2123.6 files/s, 222117.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               24            238           1163           1588
CSV                             17              0              0            828
Markdown                         5            268              0            824
TeX                              3             40              0            516
JSON                             1              0              0            283
JavaScript                       8             22             15            144
YAML                             3             26             16            110
Rmd                              4            234            552             62
SVG                              1              0              0             40
Bourne Shell                     1              4             11             24
-------------------------------------------------------------------------------
SUM:                            67            832           1757           4419
-------------------------------------------------------------------------------

Commit count by author:

   584  Micha Silver
    56  micha-silver
    30  Ron Beiden
     5  Natalya
     1  Maëlle Salmon

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1199

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

[kthyng]

Here is the rOpenSci review: https://github.com/ropensci/software-review/issues/612

[kthyng]

@micha-silver So just to be clear we use the review your software already went through with rOpenSci. My next step is to get an archive for your software from something like Zenodo. Looks like you don't have one yet with your rOpenSci review. Could you do that step now, archive the reviewed version of your package with Zenodo or another archiving system and report the DOI here?

[micha-silver]

Hi @kthyng I've added a release on Zenodo: The DOI is here

Thanks,

[kthyng]

Ok great! A few things:

• I see the version on Zenodo is different than the version here. Which was reviewed, and therefore the version we should have associated with this JOSS/rOpenSci publication?
• Can you update the title and author list on Zenodo to exactly match the JOSS paper?
• Please read through your paper again to make sure everything is perfect since it will be published shortly.

[micha-silver]

• I see the version on Zenodo is different than the version here. Which was reviewed, and therefore the version we should have associated with this JOSS/rOpenSci publication?

The current version of the package is 0.3.0, the same as the release on Zenodo. Maybe I need some guidance on the nuances of "version", "tag" , and "release".

> packageVersion("rOPTRAM")
[1] ‘0.3.0.0’

• Can you update the title and author list on Zenodo to exactly match the JOSS paper?

I see on Zenodo that I can add an "Additional title". Is that sufficient?

Regarding authors, we have some contributors to the package who were not involved in the paper at all. So they are not included. And one author who did not contribute to the package, but is a coauthor of the paper. ??

• Please read through your paper again to make sure everything is perfect since it will be published shortly.

OK

[kthyng]

@editorialbot set v0.3.0 as version

[editorialbot]

Done! version is now v0.3.0

[kthyng]

I see on Zenodo that I can add an "Additional title". Is that sufficient?

Regarding authors, we have some contributors to the package who were not involved in the paper at all. So they are not included. And one author who did not contribute to the package, but is a coauthor of the paper.

It is not a requirement to change the title and author list to match the Zenodo archive — the idea is to make one cohesive set of archives to represent this review of your software between your rOpenSci review, your JOSS DOI, and your Zenodo DOI, thus keeping the same title and author list across them.

The additional title is a different field; if you want to change the metadata to match for this purpose you can directly alter the title and author list.

Yes, it is common for there to be minor contributors to the code who do not rise to the authorship level of the package, but if they should be included then perhaps they should have been included as authors? Just to clarify, the paper itself is a tiny piece of this software publishing and is meant to represent the software package but is not the item being published here — it is the software. Not all authors have to contribute code but they would have contributed to the package in other ways typically like ideas for the software over time.

[micha-silver]

Hi @kthyng Thanks for the explanations.

I have changed the Zenodo title, following your suggestion, to match with the title in the package. And, after checking with the other package contributors, I added them as authors to the Zenodo release. So we should be good now.

One clarification: after the review of the package was completed, I added the reviewers' names as package contributors (with "role" = "rev"). But they do not appear as authors of the paper in Zenodo. Is that the norm?

[kthyng]

One clarification: after the review of the package was completed, I added the reviewers' names as package contributors (with "role" = "rev"). But they do not appear as authors of the paper in Zenodo. Is that the norm?

If you're asking where they appear on the Zenodo page based on this role assignment, I am not sure, sorry! But it looks good from the JOSS perspective now. Ready?

[micha-silver]

@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:

[kthyng]

@micha-silver Should I proceed with finalizing your submission?

[micha-silver]

@kthyng We made a few last minute grammatical edits. And I also added as an author the package contributor who was missing from the Zenodo release. So, yes, please go ahead and finalize.

[kthyng]

@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:

[kthyng]

@micha-silver Did you intend to have your author list different on your paper and Zenodo?

[micha-silver]

@kthyng No, I liked your suggestion to get the package contributors and paper authors in line. Is there still some discrepancy?

I see that I skipped the package contributor Dong Zhe as author. :face_with_diagonal_mouth: Give me another day to double check...

[kthyng]

I'm seeing

vs.

between the paper and Zenodo, so multiple discrepancies.

[micha-silver]

OK, now I've got 5 contributors, also added as paper authors. (The only exception now is Maelle Salomon from rOpenSci - she helped with a minor code error, so her name was added to the github repository, but no involvement with the paper. And as I mentioned, the package reviewers were added to the package, but not as paper authors.) Thanks for all your assistance.

[kthyng]

@editorialbot accept

[editorialbot]

Paper is not ready for acceptance yet, the archive is missing

[kthyng]

@editorialbot set 10.5281/zenodo.13257767 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.13257767

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Silver given-names: Micha orcid: "https://orcid.org/0000-0002-1128-1325" - family-names: Beiden given-names: Ron - family-names: Dong given-names: Zhe orcid: "https://orcid.org/0009-0007-5298-8355" - family-names: Panov given-names: Natalya - family-names: Karnieli given-names: Arnon orcid: "https://orcid.org/0000-0001-8065-9793" doi: 10.5281/zenodo.13257767 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Silver given-names: Micha orcid: "https://orcid.org/0000-0002-1128-1325" - family-names: Beiden given-names: Ron - family-names: Dong given-names: Zhe orcid: "https://orcid.org/0009-0007-5298-8355" - family-names: Panov given-names: Natalya - family-names: Karnieli given-names: Arnon orcid: "https://orcid.org/0000-0001-8065-9793" date-published: 2024-08-22 doi: 10.21105/joss.07086 issn: 2475-9066 issue: 100 journal: Journal of Open Source Software publisher: name: Open Journals start: 7086 title: "rOPTRAM: Deriving Soil Moisture from Satellite Imagery in R" type: article url: "https://joss.theoj.org/papers/10.21105/joss.07086" volume: 9 title: "rOPTRAM: Deriving Soil Moisture from Satellite Imagery in R" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5798
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07086
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congratulations on your new publication @micha-silver! Many thanks to reviewers @harryeslick and @obrl-soil for your time, hard work, and expertise!! JOSS and rOpenSci wouldn't be able to function nor succeed without your efforts.

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.07086/status.svg)](https://doi.org/10.21105/joss.07086)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.07086">
  <img src="https://joss.theoj.org/papers/10.21105/joss.07086/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07086/status.svg
   :target: https://doi.org/10.21105/joss.07086

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[micha-silver]

Congratulations on your new publication @micha-silver! Many thanks to reviewers @harryeslick and @obrl-soil for your time, hard work, and expertise!! JOSS and rOpenSci wouldn't be able to function nor succeed without your efforts.

@kthyng We appreciate your help and advice.