[REVIEW]: stemflow: A Python Package for Adaptive Spatio-Temporal Exploratory Model

[editorialbot]

Submitting author: @chenyangkang (Yangkang Chen)
Repository: https://github.com/chenyangkang/stemflow
Branch with paper.md (empty if default branch): main
Version: v1.1
Editor: @kthyng
Reviewers: @jedalong, @earth-chris
Archive: 10.6084/m9.figshare.24669132

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/50a385b3283faf346fc16484f50f6add/status.svg)](https://joss.theoj.org/papers/50a385b3283faf346fc16484f50f6add)

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

@jedalong & @earth-chris, 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 @diazrenata 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 @earth-chris

📝 Checklist for @jedalong

[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:

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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=0.09 s (541.8 files/s, 141108.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            698           1217           2253
TeX                              3            194              0           1336
Jupyter Notebook                 8              0           5006            953
Markdown                        15            112              0            260
YAML                             3             16             21            150
CSS                              1              3             14              7
-------------------------------------------------------------------------------
SUM:                            47           1023           6258           4959
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1132

[editorialbot]

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

OK DOIs

- 10.1609/aaai.v27i1.8484 is OK
- 10.1093/biosci/biy068 is OK
- 10.1146/annurev-ecolsys-102209-144636 is OK
- 10.1093/biosci/biab093 is OK
- 10.1016/j.biocon.2013.11.003 is OK
- 10.1016/j.biocon.2013.07.037 is OK
- 10.1111/j.2007.0906-7590.05171.x is OK
- 10.1111/ele.12048 is OK
- 10.2307/1941447 is OK
- 10.1145/356924.356930 is OK
- 10.1002/eap.2056 is OK
- 10.1111/2041-210X.14052 is OK
- 10.1002/ecs2.3994 is OK
- 10.2173/ebirdst.2021 is OK
- 10.1016/j.cub.2023.01.066 is OK
- 10.1016/j.biocon.2022.109523 is OK
- 10.1890/14-1826.1 is OK
- 10.1111/2041-210X.13559 is OK
- 10.21105/joss.04930 is OK
- 10.1002/ecm.1370 is OK
- 10.1101/2022.03.24.485545 is OK
- 10.1111/2041-210X.14101 is OK
- 10.1111/ecog.05877 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[diazrenata]

Hi @jedbrown & @earth-chris - happy new year! As you're ready, the review for this contribution will take place in this issue thread. The reviewer guidelines are available here.

Thank you for your time!

[jedbrown]

Hi 👋 looks like you meant to tag @jedalong.

[earth-chris]

Review checklist for @earth-chris

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/chenyangkang/stemflow?
• 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 (@chenyangkang) 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?

[earth-chris]

Hi @chenyangkang, I have concluded my review - thank you for the contribution! This is a valuable software package.

This software passes the majority of the checklist-based review guidelines, and the majority of my comments are related to improved documentation regarding the functionality of the package (see here).

I also created new issues regarding automated testing and community guidelines.

I don't believe any of the above issues merit withholding publication, and would be willing to check the boxes if @diazrenata is sufficiently satisfied (there are manual, not automated tests; a statement on contribution exists, but is minimal). But I at least wanted to flag them as minor issues.

[diazrenata]

@jedbrown My mistake! I apologize for the confusion.

[diazrenata]

Hi @jedalong - this issue is where review for the stemflow submission to JOSS will take place. As you're ready, the reviewer guidelines are available here.

[chenyangkang]

Hi @earth-chris, thank you for the comments on stemflow! I agree with all of your suggestions as they are helpful for introducing stemflow to the community.

Based on your suggestions, I did the following revisions:

1. Add documentation on spatiotemporal information decoding.
2. Add documentation on feature types and formatting.
3. Add documentation on different tasks (regression, classification and hurdle).
4. Add detailed comments and annotations to each example notebooks for better user guidance.

The details could be found in the issue.

I also added automated testing and contributor guidelines.

Again I want to thank you for reviewing stemflow and devote your time to the community. I hope these revisions response to your comments. Please let me know if you have any other concern.

[jedalong]

Hi @chenyangkang Here are my comments on the paper hopefully they are useful. I couldnt figure out how to do the checklist. I think the package is useful and the documentation is well delivered, but I have one comment about how the spatial binning is organized that you should at least think about in detail.

L10 - I think you need to explain what AdaSTEM is more explicitly at the beginning of the abstract similar to line 32 so the reader knows what this is.
L18 consider rephrasing this sentence.
L26 - consider rephrasing 'mine its merits'
L79 - rephrase 'mounting'
L85 - rephrase this entire sentence, not sure this is what you mean, confusing 'dependency conjugated with bias in data abundance'?
L89 - rephrase 'potentials'

My main issue with the structure of the code is the inability to leverage the existing spatial infrastructure in python. Using only tabular data and then using a cartesian gridding process is inadequate for global data (on a sphereical earth). The data is assumed to be in a cartesian plane (which latitude and longitude are not) and then divided into 'grids'.

In the mallard example you use 50 spatial and temporal blocks for the global distribution of mallards.
That is, if the data X have longitude ranging from (-180, 180), latitude ranging from (-90, 90), and whole year data (1, 366), each block will approximately contain data of 7.2 longitude (about 720km), 3.6 latitude (about 360km), and 7 days, which approximately catch the spatiotemporal scale of bird migration. These are rough estimates to get a sense of the scale.

One degree of longitude is always about 110km so 7.2 km is about 792 km. The big issue is that 1 degree of latitude varies from 110km at the equator to 0 km at the poles, so the area of your blocks varies greatly from equator to pole. Gridding data on the globe without accounting for the spherical geometry of the earth is problematic (your package is not alone in ignoring this major issue). Could you instead allow the users to pass in spatial objects or define bins based on actual geometry so that bins are more equally sized to reflect global distribution data.

To me it would be more approparite for a user to pass in a single parameter associated with the desired output spatial resolution of the grid size (e.g., grids with a size of 100km x 100km) and then the package would create the grid on the fly from a single parameter. You expecte 4 parameters for this same gridding process? I note that your package s does not force grid cells to be square in area, which is IMO unusual.

This issue is further demonstrated in the Tips section for using a different coordinate system where the user must pass in 1000 to 10000 m as the range for "latitude" and "longitude" values in another coordinate system that does not use latidtude and longitude but rather x and y.

I think it is probably associated with the tools used for modelling that do not expect spatial objects, but binning the data correctly based on spatial objects and then back transforming to the expected data structure migth be a more correct way to deal with the spherical geometry issue.

What is the difference between temporal_step and temporal_bin_interval? I didnt follow the whole 'sliding' window part of this are they bins/blocks or a moving window?

Documentation Notes:
Rephrase: stemflow have 4 important gridding parameters. Actually only two:
The maximum grid length, and the minimum grid length. It can be separately set by longitude and latitude, and that will be 4.

[diazrenata]

Hi @jedalong, thank you for your review! To get your checklist working, could you try adding a comment to this thread with this text (and this text only)?

@editorialbot generate my checklist

[chenyangkang]

Hi @jedalong, thank you for the valuable suggestions! I agree with most of your suggestions, and here are my responses:

1. Based on your suggestion, I implemented SphereAdaSTEM module for spherical indexing and gridding, to solve the distortion problem. The gridding parameters can now be input as real distance in km. For a demo visualization, see here.
   
   Related issue: [JOSS review] Add spherical indexing system chenyangkang/stemflow#24

2. Besides the 3D indexing, for 2D indexing:

• I implemented STEM module where user can input fixed grid size (1 parameter).
• For AdaSTEM, I reduces the parameters from 4 to 2 (2 is necessary because gird size of AdaSTEM is adapted to sample size by design).
  
  Related issue: [JOSS review] Improve cartesian indexing system chenyangkang/stemflow#23

3. You suggested that user should be able to input spatial object (I suppose you are referring to shapely and related), which I philosophically agree with you. However, after conducting some test here, I found that spatial object operation is much slower than the original numpy operation, which leverages vectorization. This could be an issue as stemflow is positioned for big data modeling, and also for other reasons (I discussed them in the issue thread). Some other methods were considered, like scikit-spatial, but it is simply a wrapper of numpy operation and I think that is not helpful in our circumstances. Consequently, I think I will keep the methodology unchanged. Please do let me know if you believe there are better solutions or tools that I missed.
   
   Related issue: [Feature] Speed boost? Using Geo indexing dependency chenyangkang/stemflow#30

4. All changes are reflected in home page, documentations, and notebooks. Documentations are modified based on your suggestions (for example, a sliding window illustration is added here). Paper is revised according to your suggestions.
   
   Related issues:

• [JOSS review] Documentation revision chenyangkang/stemflow#25
• [JOSS review] paper revision chenyangkang/stemflow#22

Again, thank you for your suggestions and contribution to stemflow and the community! Please feel free to open issues or reply if you have further concerns.

[jedalong]

Review checklist for @jedalong

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/chenyangkang/stemflow?
• 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 (@chenyangkang) 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?

[earth-chris]

hi @chenyangkang and @diazrenata, sorry for the delay but I'm just writing to confirm that I have checked the remaining boxes on my review. It looks like jedalong has too. Thanks for putting together a nice package, chenyangkang, and I look forward to working with stemflow.

[kthyng]

@editorialbot assign me as editor

I'm going to take over as editor!

Thanks for your review @earth-chris!

@jedalong I see your review list is checked off and the author opened some issues related to your comments which they have also subsequently closed. Can you look through the comments and issues to verify if your concerns have been addressed, and if you consider your review finished?

[editorialbot]

Assigned! @kthyng is now the editor

[kthyng]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a pull request)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

[kthyng]

@chenyangkang Please go through the bullet list above (you might copy-paste it so you can use it as a checklist) and let me know when you're finished with the actions.

[chenyangkang]

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

[chenyangkang]

Hi @kthyng, I have completed the checklist. The new version is v1.1, releasing on figshare with DOI: 10.6084/m9.figshare.24669132

Thanks!

[kthyng]

@editorialbot set v1.1 as version

[editorialbot]

Done! version is now v1.1

[kthyng]

@editorialbot set 10.6084/m9.figshare.24669132 as archive

[editorialbot]

Done! archive is now 10.6084/m9.figshare.24669132

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

@chenyangkang paper comments:

• line 47 typo espetially

[kthyng]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.18637/jss.v040.i01 is OK
- 10.1609/aaai.v27i1.8484 is OK
- 10.1093/biosci/biy068 is OK
- 10.1146/annurev-ecolsys-102209-144636 is OK
- 10.1093/biosci/biab093 is OK
- 10.1016/j.biocon.2013.11.003 is OK
- 10.1016/j.biocon.2013.07.037 is OK
- 10.1111/j.2007.0906-7590.05171.x is OK
- 10.1111/ele.12048 is OK
- 10.2307/1941447 is OK
- 10.1145/356924.356930 is OK
- 10.1002/eap.2056 is OK
- 10.1111/2041-210X.14052 is OK
- 10.1002/ecs2.3994 is OK
- 10.2173/ebirdst.2021 is OK
- 10.1016/j.cub.2023.01.066 is OK
- 10.1016/j.biocon.2022.109523 is OK
- 10.1890/14-1826.1 is OK
- 10.1111/2041-210X.13559 is OK
- 10.21105/joss.04930 is OK
- 10.1002/ecm.1370 is OK
- 10.1101/2022.03.24.485545 is OK
- 10.1111/2041-210X.14101 is OK
- 10.1111/ecog.05877 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[chenyangkang]

Hi @kthyng, typo fixed!

[chenyangkang]

@editorialbot generate pdf

[editorialbot]

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

[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: Chen
  given-names: Yangkang
- family-names: Gu
  given-names: Zhongru
- family-names: Zhan
  given-names: Xiangjiang
doi: 10.6084/m9.figshare.24669132
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Chen
    given-names: Yangkang
  - family-names: Gu
    given-names: Zhongru
  - family-names: Zhan
    given-names: Xiangjiang
  date-published: 2024-02-23
  doi: 10.21105/joss.06158
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6158
  title: "stemflow: A Python Package for Adaptive Spatio-Temporal
    Exploratory Model"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06158"
  volume: 9
title: "stemflow: A Python Package for Adaptive Spatio-Temporal
  Exploratory Model"

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 👉 Creating pull request for 10.21105.joss.06158 joss-papers#5042
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06158
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]

Congrats on your new publication @chenyangkang! Many thanks to early editor @diazrenata and to reviewers @jedalong @earth-chris for your time, hard work, and expertise!!

[editorialbot]

🎉🎉🎉 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.06158/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06158/status.svg
   :target: https://doi.org/10.21105/joss.06158

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[chenyangkang]

@kthyng @diazrenata thank you so much for your editorial effort and devotion to this great journal! ❤️ @earth-chris @jedalong Thank you for your valuable suggestions that make stemflow significantly better and more meaningful to the community. I deeply appreciate your time and advice!

Wish you all the best!

Yangkang

[kthyng]

Thank you @chenyangkang! If you are interested in contributing to JOSS, please consider signing up as a reviewer! https://reviewers.joss.theoj.org/](https://reviewers.joss.theoj.org/)

[chenyangkang]

Thanks @kthyng! I already did! Looking forward to contributing!