[REVIEW]: **geostan**: An R package for Bayesian spatial analysis

[editorialbot]

Submitting author: @ConnorDonegan (Connor Donegan) Repository: https://github.com/ConnorDonegan/geostan Branch with paper.md (empty if default branch): JOSS Version: V0.3.0 Editor: @jbytecode Reviewers: @wcjochem, @becarioprecario Archive: Pending

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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) 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

@wcjochem & @becarioprecario, 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 @becarioprecario

[editorialbot]

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

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (828.9 files/s, 146986.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            41           1300            133           6559
R                               29            213           2464           3141
TeX                              3             63              0            493
CSS                              3             98             52            442
JavaScript                       3             64             32            256
Markdown                         3             93              0            240
Rmd                              3            191            295            125
XML                              1              0              0            123
YAML                             3              3              4             85
SVG                              1              0              1             11
Bourne Shell                     2              4              2              4
C/C++ Header                     1              0              1              0
-------------------------------------------------------------------------------
SUM:                            93           2029           2984          11479
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1047

[editorialbot]

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

OK DOIs

- 10.31219/osf.io/3ey65 is OK
- 10.1016/j.spasta.2020.100450 is OK
- 10.3390/ijerph18136856 is OK
- 10.2307/2532039 is OK
- 10.1111/j.1467-8306.2005.00484.x is OK
- 10.1016/C2017-0-01015-7 is OK
- 10.1111/j.1538-4632.2007.00708.x is OK
- 10.1016/j.apgeog.2013.08.013 is OK
- 10.1007/s13524-016-0499-1 is OK
- 10.1016/j.csda.2008.07.033 is OK
- 10.1002/(sici)1097-0258(19970415)16:7<741::aid-sim501>3.0.co;2-1 is OK
- 10.1002/(sici)1097-0258(19980930)17:18<2025::aid-sim865>3.0.co;2-m is OK
- 10.1111/j.2517-6161.1974.tb00999.x is OK
- 10.1007/BF00116466 is OK
- 10.1177/0962280216660421 is OK
- 10.1016/j.sste.2019.100301 is OK
- 10.18637/jss.v063.i18 is OK
- 10.1080/10618600.2016.1172487 is OK
- 10.5281/zenodo.1308151 is OK
- 10.18637/jss.v092.i10 is OK
- 10.1214/17-BA1091 is OK
- 10.1111/j.1538-4632.1995.tb00338.x 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:

[jbytecode]

Dear @wcjochem and @becarioprecario

This is the review thread. Firstly, type

@editorialbot generate my checklist

to generate your own checklist. In that checklist, there are 20 check items. Whenever you complete the corresponding task, you can check off them. The review process is interactive so you can always interact with the authors, reviewers, and the editor. You can also create issues and pull requests in the target repo. Please do mention this thread's URL in the issues so we can keep tracking what is going on out of our world.

Please do not hesitate to ask me anything, anytime.

Thank you in advance!

[jbytecode]

Dear @wcjochem and @becarioprecario

Could you please update your status on how is going your review and generate your task lists?

Thank you in advance.

[jbytecode]

@editorialbot remind @wcjochem in two days

[editorialbot]

Reminder set for @wcjochem in two days

[jbytecode]

@editorialbot remind @becarioprecario in two days

[editorialbot]

Reminder set for @becarioprecario in two days

[jbytecode]

Thanks @editorialbot !

[editorialbot]

You are welcome

[editorialbot]

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

[editorialbot]

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

[ConnorDonegan]

@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]

@wcjochem, @becarioprecario - could you please update your status?

Can I kindly ask you to create your check list first?

Thank you in advance.

[wcjochem]

Hi @jbytecode when I agreed to review this submission I said I couldn't start until after 15 September. So I have only started my review and it is ongoing. Thanks.

[jbytecode]

@wcjochem - I am so sorry for bothering and pinging you too much, my bad! I totally forgot your deadline. Thank you for reminding that.

[jbytecode]

@becarioprecario - could you please update your status? We have failed to get a life signal from you. Setting a deadline for us would be great, if possible. Thank you in advance.

[jbytecode]

Dear @becarioprecario,

This is the last reminder. Since you never sent a response, I assume that you are so much busy to reply messages, and/or you are not able to receive notifications. If you don't set a deadline for us until 15th October, I will try to find another reviewer for this issue.

Thank you in advance.

[becarioprecario]

Hi,

Sorry for the delay. I will try to send the review by the end of the week.

Best,

Virgilio

El 13 oct 2022, a las 11:20, Mehmet Hakan Satman @.@.>> escribió:

Dear @becarioprecariohttps://github.com/becarioprecario,

This is the last reminder. Since you never sent a response, I assume that you are so much busy to reply messages, and/or you are not able to receive notifications. If you don't set a deadline for us until 15th October, I will try to find another reviewer for this issue.

Thank you in advance.

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/4716#issuecomment-1277299612, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABYD6WSVIO4RWQRSZ6H5V7LWC7H6DANCNFSM573GXAFQ. You are receiving this because you were mentioned.Message ID: @.***>

[jbytecode]

@becarioprecario - I am happy to hear from you. I will be waiting for your review. Thank you for the response.

[becarioprecario]

Review checklist for @becarioprecario

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/ConnorDonegan/geostan?
• [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 (@ConnorDonegan) 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
• [x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 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?
• [x] 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)?
• [x] 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?

[becarioprecario]

I have read the paper now. These are some comments that perhaps require changes in the main paper:

• Authorship. The geostan package has been vdeveloped by two authors but only one appears listed in the paper. Is there any particular reason for this?
• BayesX is also an R package to fit Bayesian spatial models that should be mentioned.
• Lines 55-59. Does the package relies on other R packages to compute these statistics and plots?
• Line 74. If there is a model that will be included in a forthcoming version I would wait to have these models implemented to actually publish the paper. It seems that the SAR model is already there, so the paper can be updated and this sentence rephrased.
• Line 81. INLA can also include user-defined models
• Citation format. When the references are included in a sentence which is between parentheses I believe that they are written using the wrong formant, e.g., "(... Author1 et al. (2022) ...)" instead of "(... Autho1 et al., 2022, ...)"

[jbytecode]

@ConnorDonegan - could you please apply the corrections as suggested by our reviewer? Thank you in advance.

[ConnorDonegan]

Thank you @becarioprecario and @jbytecode, I will respond and submit revisions by this Thursday (Oct. 20).

[wcjochem]

Review checklist for @wcjochem

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/ConnorDonegan/geostan?
• [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 (@ConnorDonegan) 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
• [x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 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?
• [x] 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)?
• [x] 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?

[ConnorDonegan]

@editorialbot generate pdf