[REVIEW]: ssdtools v2: An R package to fit Species Sensitivity Distributions

[editorialbot]

Submitting author: @joethorley (Joseph Thorley)
Repository: https://github.com/bcgov/ssdtools
Branch with paper.md (empty if default branch): joss-paper
Version: v2.0.0
Editor: @fabian-s
Reviewers: @flor14, @nanhung
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/71203219bdc07f83284fd827c3922f53/status.svg)](https://joss.theoj.org/papers/71203219bdc07f83284fd827c3922f53)

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

@flor14 & @nanhung, 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 @fabian-s 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 @flor14

📝 Checklist for @nanhung

[editorialbot]

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (3475.8 files/s, 233177.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                              132           1150           3401           7037
CSV                            114              0              0           1836
Markdown                        18            512              0           1139
Rmd                              8            669           1416            961
TeX                              2             53              0            502
C/C++ Header                    10            164            459            413
YAML                             7             38             11            304
C++                              4             15             54             97
SVG                              8              0              0             96
-------------------------------------------------------------------------------
SUM:                           303           2601           5341          12385
-------------------------------------------------------------------------------

Commit count by author:

  1439	Joe Thorley
   262	joethorley
    13	Nadine Hussein
     7	Sarah Lyons
     7	atillmanns
     5	stephhazlitt
     4	Nan-Hung Hsieh
     4	Rebecca Fisher
     3	cschwarz-stat-sfu-ca
     1	Angeline Tillmanns
     1	Hadley Wickham
     1	Seb Dalgarno
     1	Sergio Ibarra Espinosa
     1	Stephanie Hazlitt
     1	repo-mountie[bot]

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1510

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

[editorialbot]

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

✅ OK DOIs

- 10.1002/etc.5620190233 is OK
- 10.21105/joss.02848 is OK
- 10.1002/etc.4373 is OK
- 10.18637/jss.v064.i04 is OK
- 10.1007/978-0-387-98141-3 is OK
- 10.1007/b97636 is OK
- 10.1002/9780470094846 is OK
- 10.18637/jss.v070.i05 is OK
- 10.1002/etc.4925 is OK
- 10.25845/fm9b-7n28 is OK
- 10.25845/xtvt-yc51 is OK
- 10.23645/epacomptox.11971392.v2 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Improving Statistical Methods for Modeling Species...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Burrlioz 2.0 Manual
- No DOI given, and none found for title: Revised Method for Deriving Australian and New Zea...
- No DOI given, and none found for title: Manual on the methodological framework to derive e...
- No DOI given, and none found for title: Derivation of Water Quality Guidelines for the Pro...

❌ MISSING DOIs

- 10.32614/cran.package.ssddata may be a valid DOI for title: ssddata: Species Sensitivity Distribution Data
- 10.21105/joss.01082 may be a valid DOI for title: ssdtools: An R package to fit species sensitivity ...

❌ INVALID DOIs

- None

[editorialbot]

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

[fabian-s]

👋🏼 @joethorley @flor14 @nanhung this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7492 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@fabian-s) if you have any questions/concerns.

[fabian-s]

@joethorley while we wait for the reviews, could you check the "missing DOIs" the bot found in the comment above and add them to your refs if they are correct?

[flor14]

Review checklist for @flor14

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/bcgov/ssdtools?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@joethorley) 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?

The documentation is complete and detailed. I received this message when I tried to download the package from CRAN.

There is a binary version available but the
source version is later:
binary source needs_compilation
ssdtools 1.0.6 2.1.0 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel)

• 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)?

The package documentation created with pkgdown is very comprehensive, combining mathematical formulas with code examples that illustrate its use.

1. Issue: In almost all the vignettes there seems to be a bug in the formulas that are inside a grey box:

2. There are also issues with the rendering of images and formulas in the "Additional Technical Details" vignette.

3. The NEWS section mentions that some of the changes introduced have effects ("The following changes are major in the sense that they could alter previous hazard concentrations or break code".), either by adding arguments to the functions and/or altering the potential results of functions compared to the original version.
   It could be beneficial to briefly mention in the internal documentation of these specific functions that significant changes were made in version X of the package. This would help ensure that users of previous versions are aware of these modifications and prevent errors of interpretation when comparing new outputs with previous results or results of other articles using the same software.
   I know this information is also in the changelog, but not all the users will check it. This package was created for researchers who do not necessarily have a background in software development. It is more likely that users will consult the function 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?

Yes, the description is clear and easy to understand. The term "toxicological data" may not be very informative for a non-specialist audience. It might be interesting to include some minimal requirements about the type of data used to construct these curves, as the data selection can change the results. The documentation mentions ssdata as a source of datasets, but it is not the only possibility.

• 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?

1. This package has a very specific use, so there aren't many others to compare it with. However, in the context of this review, the change in an important dependency as fitdistrplus to TMB might deserve a bit more attention. The article mentions that this change promotes greater control over model specifications. How exactly does this change affect the user experience with the functions in ssdtools? Could a line be added to explain the existence of new functions or what specific changes to expect?
2. This comment is similar to the previous one but a bit more general regarding the Technical Details section. In some subsections, such as Multiple Distribution Functions and Plotting, the technical changes introduced are accompanied by the ssdtools functions they affect between brackets. On the other hand, other sections, like Model Averaging and Model Fitting, are more theoretical.
   The inclusion of formulas is important in a statistically oriented package like ssdtools. However, since this publication emphasizes software development, I would suggest adding a code example. This could minimally involve mentioning the functions affected by these changes (as done in other subsections) or including a few lines of code to demonstrate how the explained concepts translate into changes in the package's functionality.
   The ssdtools vignettes are very detailed and combine well code and the statistical theory, they could also be cited to avoid repeating information. My comment is more about linking the code with the theory/changes explicitly.

• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?

This update includes two significant changes in the versions of ssdtools. It might be helpful to organize the Technical Details section to indicate which changes were introduced in the first major version update and which were added in the second one.

• 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?

[joethorley]

@joethorley while we wait for the reviews, could you check the "missing DOIs" the bot found in the comment above and add them to your refs if they are correct?

@fabian-s I've added the two missing DOIs.

[joethorley]

@editorialbot generate pdf

[editorialbot]

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

[nanhung]

Review checklist for @nanhung

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/bcgov/ssdtools?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@joethorley) 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?

[flor14]

@fabian-s
My review is complete. I believe the package is truly valuable, and these updates position it as the most up-to-date and comprehensive software for fitting and calculating relevant concentrations from an SSD. I also appreciate the work put into the documentation, which is easy to follow and well-organized.

One aspect I’ve always appreciated about JOSS papers is that they provide insights into aspects of the software not covered in other sections of the documentation. Since this is the second article for ssdtools, I found myself considering what additional information could be included, especially given that there is already an existing article for this software. For a manuscript's second version, it could be valuable to include examples addressing changes in functions that result in breaking changes. Also, requesting a more detailed explanation of the reasons and the impacts of changes in dependencies could be informative in some cases.

I understand that this may go beyond the scope of this review as the process is now, so I focused on the points outlined in the checklist. Probably, you have already considered this when deciding to allow the publication of new versions and have taken these factors into account. I wanted to mention it since it influenced the comments I made in my review.

@joethorley Only two points of the review have not been marked as resolved. I added notes on a few other points, but there are suggestions or comments that I don't consider to affect the quality of the software/manuscript. I believe these are "stylistic" considerations that are up to you, so I marked them as solved.

[fabian-s]

@flor14 thank you so much for your timely, constructive and detailed review -- this is great! I second your recommendations, with one exception. i.e. "It might be helpful to organize the Technical Details section to indicate which changes were introduced in the first major version update and which were added in the second one." -- this level of historical detail seems less relevant to me, since the new paper is supposed to document the current state of the software.