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[REVIEW]: The ppmData R-package for setting up spatial point process models
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: Pending
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: [](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
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
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
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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
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SUM: 32 715 582 3100
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gitinspector failed to run statistical information for the repository
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@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
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)
Review checklist for @mhesselbarth
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/skiptoniam/ppmData?
- [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 (@skiptoniam) 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?
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.
Review checklist for @OwenWard
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/skiptoniam/ppmData?
- [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 (@skiptoniam) 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?
@mhesselbarth beat me to it with most of my initial comments. I would agree with all those issues, including the questions about the tests, external data, and the missing code of conduct, help file, license. Would it be possible to include a vignette going through the example with the snail data in a bit more detail? I think this would be useful for people who may be unfamiliar with these types of problems.
I would also suggest renaming the default branch from master to main.
Would it be possible to include a vignette going through the example with the snail data in a bit more detail? I think this would be useful for people who may be unfamiliar with these types of problems.
Is there any recommendations what to put into the README and into vignettes in general? I opened https://github.com/skiptoniam/ppmData/issues/26 related to this, but personally don't have any strong opinion if that should be in the README or an additionally vignette. But some more guidance would be great!
Is there any recommendations what to put into the README and into vignettes in general? I opened skiptoniam/ppmData#26 related to this, but personally don't have any strong opinion if that should be in the README or an additionally vignette. But some more guidance would be great!
For JOSS I don't think so, but https://r-pkgs.org/vignettes.html has some ideas about vignettes. My opinion would be that from the README you can tell if the package does what you want/need, and then if you are going to use it a vignette would give you the details to actually implement it.
I agree with the issue about the README, and would encourage (but not require) a vignette, so that it would hopefully lead to more people using the package.
For JOSS I don't think so, but https://r-pkgs.org/vignettes.html has some ideas about vignettes.
This is correct, as JOSS covers a wide array of programming languages we do not provide guidance on language-specific forms of documentation such as vignettes. Even for README files we provide only minimal suggestions as these can vary based on the language and community. Suggestions above are all appropriate as far as I can tell.
:wave: @OwenWard, please update us on how your review is going (this is an automated reminder).
:wave: @mhesselbarth, please update us on how your review is going (this is an automated reminder).
I still have to review the manuscript and go through the code in more detail, but its on my list for the end of this week!
@elbeejay It seems like there have been some recent updates on the JOSS branch for this repo, so maybe it would make sense for @mhesselbarth and I to wait until an update that they have been completed before we finish the review? They seem to be addressing some of the previously mentioned comments.
@OwenWard that definitely makes sense. @skiptoniam why don't you complete the changes you are working on and ping all of us (@OwenWard, @mhesselbarth, and @elbeejay) once you are ready for us to complete the review.
@elbeejay @mhesselbarth @OwenWard cool. I probably won't get to this until next week or the week after. But happy to do that.
Some comments considering the manuscript. Overall its written very well and does a good job explaining the package and method. Just some minor suggestions and comments:
-
Line 8/9: This is an appropriate statistical approach only if locations can be meaningful described by points (e.g., as for plants, nests).
-
Line 13/14: This is one common driver, but also other processes can be more important for the pattern (e.g., competition, neutral theory, etc.). Thus, I would suggest to reword using e.g., “such as”, “for example”, “besides others”.
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Line 15: I would suggest to use locations instead of sightings to be concise.
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Line 16: Maybe add one more sentence to the previous section to better link habitat conditions to inhomogeneous poisson process models. That should help the reader better to connect the two.
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Line 17-19: I think there is a "that" missing in the sentence.
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Line 36-42: Please reword and state only what the package is intended and capable of doing now. Personally, I think the initial intention part is a bit confusing. Also, as far as I understand it, the package can be used for any qualitative marks and not just species. Thus, I would reword the sentence and using species as one example of qualitative marks.
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Line 66: I understand why the Statement of Need is introduced so late because the reader needs some background about the point processes first. However, I think it might also make sense to move this part up, or at least refer to it earlier in the introduction. But if you decided to keep the structure as it is right now that would be also fine for me.
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Line 95-99: Please add some information on what kind of computer/laptop this benchmark is based on (number of cores, RAM, operating system, etc.).
-
Line 107-109: As also mentioned in skiptoniam/ppmData/issues/24. I would strongly suggest to add conversion methods for spatstat objects or at least explain somewhere in the Vignettes how to convert between spatstat and terra/sf given how popular the spatstat package is.
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Line 140/141: This sentence could use some more explanation. Why is the step required?
I will wait for @skiptoniam dealing with the open issues (which should tick most of the open boxes in the checklist) before I continue with my last round of reviews of the actual code and functionality.
Just wanted to follow up also with a bit more detail on my comments. I don't think there is any large enough for an issue which @mhesselbarth hasn't already covered but I'll list my comments again. These include the current updates in the joss_submission branch.
- Can you provide a reference for the external data? It might be easier to just include it in the package directly? then it would get a help file, etc
- There isn’t an appropriate license for JOSS included
- The tests which are included don’t currently test any of the methods of the package.
- There should be a section detailing how to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
- Given that the statement of need for this paper emphasizes the computational benefits, I think an experiment demonstrating the speedup should be included in the JOSS paper, even commented out, so that readers can confirm it for themselves. I think you could also demonstrate this in the Readme.
- I'm not sure of the role of the file
package.R? It also seems to be somehow linked to the documentation and comes up when you run?ppmData - There are some small typos in the ReadMe in the JOSS branch
- In the summary, “Quasi random sampling quadrature are form” and “thus reducing low errors”
- In the example the text mentions red points which are now green
- Also some small typos in the paper on top of those mentioned previously, nothing much
- Page 3 line 77, extra “is”
- Page 4 line 111-112 maybe missing “is”?
- Page 5 line 130 using “the” glm function maybe?
- The second reference in the bibliography has some missing latex
Otherwise, when all these points are addressed I'd like to take another quick look at the code.
@skiptoniam I wanted to follow up here and ask: how are the revisions coming along?
@elbeejay I've started them. I hope to have them finished by next week. I hope that is ok.
Sounds good @skiptoniam, had just been poking around the repository and didn't see any recent activity so I was getting worried.
@skiptoniam just wanted to check-in here and find out how the revisions are going. It looks like you've made a number of commits to the joss_submission branch so that is encouraging. Do you have a revised timeline for when you think you'll be ready to ask our reviewers to have another look?