[REVIEW]: The ppmData R-package for setting up spatial point process models #4771

editorialbot · 2022-09-19T14:09:58Z

Submitting author: @skiptoniam (Skipton Nicholas Charles Woolley)
Repository: https://github.com/skiptoniam/ppmData
Branch with paper.md (empty if default branch): joss_submission
Version: v1.0.0
Editor: @elbeejay
Reviewers: @OwenWard, @mhesselbarth
Archive: 10.5281/zenodo.7679406

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b5288481bbd5f97602a71ce7b66273ef"><img src="https://joss.theoj.org/papers/b5288481bbd5f97602a71ce7b66273ef/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b5288481bbd5f97602a71ce7b66273ef/status.svg)](https://joss.theoj.org/papers/b5288481bbd5f97602a71ce7b66273ef)

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

@OwenWard & @mhesselbarth, 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 @elbeejay 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 @mhesselbarth

📝 Checklist for @OwenWard

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-09-19T14:09:59Z

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 · 2022-09-19T14:10:02Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (551.2 files/s, 75741.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               16            342            439           1141
C++                              4            166             27            698
XML                              1              0              2            441
TeX                              1             34              0            356
Markdown                         3             60              0            175
C/C++ Header                     2             44              0            126
YAML                             3             20              9             90
Rmd                              2             49            105             73
-------------------------------------------------------------------------------
SUM:                            32            715            582           3100
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-09-19T14:10:03Z

Wordcount for paper.md is 2448

editorialbot · 2022-09-19T14:12:01Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

elbeejay · 2022-09-19T14:13:38Z

@OwenWard and @mhesselbarth instructions for completing your reviews are provided in the top comment of this issue. Please make specific comments pertaining to your review in the ppmData repository itself, and reference this overarching JOSS review issue with a hyperlink, to maintain some connectivity between this review issue and individual repository issues. Feel free to provide a summary of your review here, and please ask any questions that you have about the process in this issue.

I will be asking the bot to provide reminder messages in 4 weeks. Right now we are requesting that our reviewers complete their reviews in 6 weeks if possible; if you need more time please just comment here so that both myself and @skiptoniam are aware.

Thanks!
Jay

elbeejay · 2022-09-19T14:14:12Z

@editorialbot remind @OwenWard in four weeks

editorialbot · 2022-09-19T14:14:13Z

Reminder set for @OwenWard in four weeks

elbeejay · 2022-09-19T14:14:33Z

@editorialbot remind @mhesselbarth in four weeks

editorialbot · 2022-09-19T14:14:34Z

Reminder set for @mhesselbarth in four weeks

editorialbot · 2022-09-19T14:20:22Z

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

OK DOIs

- 10.1890/10-1251.1 is OK
- 10.1111/1467-842X.00128 is OK
- 10.1890/07-2153.1 is OK
- 10.1111/2041-210X.12352 is OK
- 10.1111/2041-210X.12242 is OK
- 10.1111/j.2041-210X.2011.00141.x is OK
- 10.1371/journal.pone.0079168 is OK
- 10.1214/10-AOAS331 is OK
- 10.1111/j.1467-9876.2011.01023.x is OK
- 10.32614/RJ-2018-009 is OK
- 10.18637/jss.v033.i01 is OK

MISSING DOIs

- 10.1111/1365-2656.12071 may be a valid DOI for title: Advancing our thinking in presence-only and used-available analysis
- 10.1214/13-aoas667 may be a valid DOI for title: Finite-sample equivalence in statistical models for presence-only data
- 10.2307/2347614 may be a valid DOI for title: Approximating point process likelihoods with GLIM
- 10.1111/anzs.12337 may be a valid DOI for title: What is the effective sample size of a spatial point process?
- 10.1111/j.1467-9876.2009.00701.x may be a valid DOI for title: Geostatistical inference under preferential sampling
- 10.1111/j.1541-0420.2012.01824.x may be a valid DOI for title: Equivalence of MAXENT and Poisson point process models for species distribution modeling in ecology
- 10.1093/biomet/asv064 may be a valid DOI for title: Going off grid: Computationally efficient inference for log-Gaussian Cox processes
- 10.1002/env.2194 may be a valid DOI for title: Doubly balanced spatial sampling with spreading and restitution of auxiliary totals
- 10.1111/biom.12059 may be a valid DOI for title: BAS: Balanced acceptance sampling of natural resources
- 10.1016/j.spasta.2019.100392 may be a valid DOI for title: Bayesian model based spatiotemporal survey designs and partially observed log Gaussian Cox process
- 10.1111/2041-210x.12782 may be a valid DOI for title: Spatially balanced designs that incorporate legacy sites
- 10.1007/bf01386213 may be a valid DOI for title: On the efficiency of certain quasi-random sequences of points in evaluating multi-dimensional integrals
- 10.1007/bf02985802 may be a valid DOI for title: The elements of statistical learning: data mining, inference, and prediction

INVALID DOIs

- doi:10.1016/j.ecolmodel.2005.03.026 is INVALID (failed connection)

mhesselbarth · 2022-09-21T14:26:49Z

Review checklist for @mhesselbarth

Conflict of interest

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/skiptoniam/ppmData?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@skiptoniam) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

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

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
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)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
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

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, 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?
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?

mhesselbarth · 2022-09-21T16:12:58Z

I added a few first issues directly in the code repository regarding some general code structures. I will have a closer look at the manuscript within the next few days.

OwenWard · 2022-10-04T17:10:45Z

Review checklist for @OwenWard

Conflict of interest

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/skiptoniam/ppmData?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@skiptoniam) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

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

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
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)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
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

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, 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?
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?

elbeejay · 2023-02-24T13:19:42Z

Great, thanks @skiptoniam. At this time we need to finalize the metadata and versioning for the version of ppmData that will be tied to this JOSS publication. I noticed that the work related to the JOSS publication has happened in the "joss_submission" branch, this is also an opportunity to merge it into the "main" branch if you'd like, as the review process is over. Please let me know once you've been able to do the following:

Make a tagged release of your software, and list the version tag of the archived version here.
Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
Please list the DOI of the archived version here.
(if necessary) Re-release the package on CRAN so that the "JOSS version" matches one in a package repository

Thanks again to @OwenWard and @mhesselbarth for their work reviewing this package.

skiptoniam · 2023-02-27T03:00:06Z

@elbeejay Thanks.

I have made a release: https://github.com/skiptoniam/ppmData/releases/tag/v1.0.0
Archived the software here: https://doi.org/10.5281/zenodo.7679406
I am yet to put the software on CRAN, but will do so soon.

elbeejay · 2023-02-27T13:20:35Z

@editorialbot check references

elbeejay · 2023-02-27T13:20:48Z

@editorialbot generate pdf

editorialbot · 2023-02-27T13:22:05Z

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

OK DOIs

- 10.1890/10-1251.1 is OK
- 10.1111/1467-842X.00128 is OK
- 10.1016/j.ecolmodel.2005.03.026 is OK
- 10.1890/07-2153.1 is OK
- 10.1111/1365-2656.12071 is OK
- 10.1111/2041-210X.12352 is OK
- 10.1214/13-aoas667 is OK
- 10.1111/2041-210X.12242 is OK
- 10.1111/j.2041-210X.2011.00141.x is OK
- 10.1371/journal.pone.0079168 is OK
- 10.1214/10-AOAS331 is OK
- 10.1111/j.1467-9876.2011.01023.x is OK
- 10.2307/2347614 is OK
- 10.1111/anzs.12337 is OK
- 10.1111/j.1467-9876.2009.00701.x is OK
- 10.1111/j.1541-0420.2012.01824.x is OK
- 10.1093/biomet/asv064 is OK
- 10.1002/env.2194 is OK
- 10.1111/biom.12059 is OK
- 10.1016/j.spasta.2019.100392 is OK
- 10.1111/2041-210x.12782 is OK
- 10.1007/bf01386213 is OK
- 10.32614/RJ-2018-009 is OK
- 10.18637/jss.v033.i01 is OK
- 10.1007/bf02985802 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-02-27T13:22:13Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

elbeejay · 2023-02-27T13:23:38Z

@editorialbot set 10.5281/zenodo.7679406 as archive

editorialbot · 2023-02-27T13:23:41Z

Done! Archive is now 10.5281/zenodo.7679406

elbeejay · 2023-02-27T13:25:35Z

@skiptoniam thank you for doing that. A release on CRAN is not a requirement for JOSS, just a suggestion and a reminder I like for include as some R packages submitted to JOSS are already hosted on JOSS (and could be updated to match the JOSS version of record).

At this time I will be recommending ppmData for publication in JOSS. Sometime over the next week or so an editor-in-chief will review the paper and this issue to do a final check before officially publishing your article in JOSS.

elbeejay · 2023-02-27T13:25:50Z

@editorialbot recommend-accept

editorialbot · 2023-02-27T13:25:51Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-02-27T13:26:55Z

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

a_i) - \lambda_i\} \numberthis 
                   ^
unexpected "\\"
expecting "&", "\\\\", white space or "\\end"

editorialbot · 2023-02-27T13:27:37Z

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

OK DOIs

- 10.1890/10-1251.1 is OK
- 10.1111/1467-842X.00128 is OK
- 10.1016/j.ecolmodel.2005.03.026 is OK
- 10.1890/07-2153.1 is OK
- 10.1111/1365-2656.12071 is OK
- 10.1111/2041-210X.12352 is OK
- 10.1214/13-aoas667 is OK
- 10.1111/2041-210X.12242 is OK
- 10.1111/j.2041-210X.2011.00141.x is OK
- 10.1371/journal.pone.0079168 is OK
- 10.1214/10-AOAS331 is OK
- 10.1111/j.1467-9876.2011.01023.x is OK
- 10.2307/2347614 is OK
- 10.1111/anzs.12337 is OK
- 10.1111/j.1467-9876.2009.00701.x is OK
- 10.1111/j.1541-0420.2012.01824.x is OK
- 10.1093/biomet/asv064 is OK
- 10.1002/env.2194 is OK
- 10.1111/biom.12059 is OK
- 10.1016/j.spasta.2019.100392 is OK
- 10.1111/2041-210x.12782 is OK
- 10.1007/bf01386213 is OK
- 10.32614/RJ-2018-009 is OK
- 10.18637/jss.v033.i01 is OK
- 10.1007/bf02985802 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-02-27T13:27:48Z

👋 @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4000, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kthyng · 2023-02-27T15:40:29Z

archive looks good ✅
I might have missed this, but is the version up to date?

kthyng · 2023-02-27T15:43:28Z

paper looks good ✅

Once we verify the version, this is good to go!

skiptoniam · 2023-02-28T01:24:43Z

@elbeejay thanks for all your hard work on this.
@kthyng yes this is the most recent version. If you need me to reload the files or check it, then I can.

kthyng · 2023-03-01T15:06:30Z

@editorialbot accept

editorialbot · 2023-03-01T15:06:32Z

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

editorialbot · 2023-03-01T15:07:37Z

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

a_i) - \lambda_i\} \numberthis 
                   ^
unexpected "\\"
expecting "&", "\\\\", white space or "\\end"

editorialbot · 2023-03-01T15:08:41Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-03-01T15:08:42Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-03-01T15:08:43Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04771 joss-papers#4010
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04771
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2023-03-01T15:14:23Z

I see the complaint about the latex generation, but the final paper looks good!

Congrats on your new publication @skiptoniam! Many thanks to editor @elbeejay and reviewers @OwenWard and @mhesselbarth for your time, hard work, and expertise!!

editorialbot · 2023-03-01T15:14:36Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04771/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04771/status.svg
   :target: https://doi.org/10.21105/joss.04771

This is how it will look in your documentation:

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editorialbot added C++ R review TeX Track: 6 (ESE) Earth Sciences and Ecology labels Sep 19, 2022

editorialbot assigned elbeejay Sep 19, 2022

editorialbot mentioned this issue Sep 19, 2022

[PRE REVIEW]: The ppmData R-package for setting up spatial point process models #4646

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Feb 27, 2023

editorialbot added accepted published Papers published in JOSS labels Mar 1, 2023

kthyng closed this as completed Mar 1, 2023

editorialbot mentioned this issue Feb 17, 2024

[PRE REVIEW]: pivmet: an R package proposing pivotal methods for consensus clustering and mixture modelling #6363

Closed

[REVIEW]: The ppmData R-package for setting up spatial point process models #4771

[REVIEW]: The ppmData R-package for setting up spatial point process models #4771

Comments

editorialbot commented Sep 19, 2022 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Sep 19, 2022

editorialbot commented Sep 19, 2022

editorialbot commented Sep 19, 2022

editorialbot commented Sep 19, 2022

elbeejay commented Sep 19, 2022

elbeejay commented Sep 19, 2022

editorialbot commented Sep 19, 2022

elbeejay commented Sep 19, 2022

editorialbot commented Sep 19, 2022

editorialbot commented Sep 19, 2022

mhesselbarth commented Sep 21, 2022 • edited

Review checklist for @mhesselbarth

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

mhesselbarth commented Sep 21, 2022

OwenWard commented Oct 4, 2022 • edited

Review checklist for @OwenWard

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

elbeejay commented Feb 24, 2023 • edited

skiptoniam commented Feb 27, 2023

elbeejay commented Feb 27, 2023

elbeejay commented Feb 27, 2023

editorialbot commented Feb 27, 2023

editorialbot commented Feb 27, 2023

elbeejay commented Feb 27, 2023

editorialbot commented Feb 27, 2023

elbeejay commented Feb 27, 2023

elbeejay commented Feb 27, 2023

editorialbot commented Feb 27, 2023

editorialbot commented Feb 27, 2023

editorialbot commented Feb 27, 2023

editorialbot commented Feb 27, 2023

kthyng commented Feb 27, 2023

kthyng commented Feb 27, 2023

skiptoniam commented Feb 28, 2023

kthyng commented Mar 1, 2023

editorialbot commented Mar 1, 2023

editorialbot commented Mar 1, 2023

editorialbot commented Mar 1, 2023

editorialbot commented Mar 1, 2023

editorialbot commented Mar 1, 2023

kthyng commented Mar 1, 2023

editorialbot commented Mar 1, 2023

editorialbot commented Sep 19, 2022 •

edited

mhesselbarth commented Sep 21, 2022 •

edited

OwenWard commented Oct 4, 2022 •

edited

elbeejay commented Feb 24, 2023 •

edited