[REVIEW]: gibbonNetR: an R Package for the Use of Convolutional Neural Networks and TransferLearning on Acoustic Data

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@DenaJGibbon@faroit<!--end-editor-- Reviewers: @Desjonqu, @steffilazerte Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/40a9136ac136e187df2bbff0bb1afd11"><img src="https://joss.theoj.org/papers/40a9136ac136e187df2bbff0bb1afd11/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/40a9136ac136e187df2bbff0bb1afd11/status.svg)](https://joss.theoj.org/papers/40a9136ac136e187df2bbff0bb1afd11)

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

@Desjonqu & @steffilazerte, 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 @faroit 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 @steffilazerte

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (703.6 files/s, 157934.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               19            477            840           2404
HTML                             1             88              5            805
TeX                              1             39              0            418
Markdown                         3            120              0            340
Rmd                              1             72             90            115
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            26            797            939           4100
-------------------------------------------------------------------------------

Commit count by author:

   107  DenaJGibbon
     4  Dena J. Clink

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1857

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1093/biosci/biy147 is OK
- 10.1111/2041-210X.13101 is OK
- 10.1016/j.ecolind.2015.02.023 is OK
- 10.1038/nature14539 is OK
- 10.1371/journal.pcbi.1010372 is OK
- 10.7717/peerj.13152 is OK
- 10.1371/journal.pone.0283396 is OK
- 10.18637/jss.v091.i01 is OK
- 10.18637/jss.v028.i05 is OK
- 10.1016/j.ecolind.2021.107419 is OK
- 10.5281/zenodo.4092393 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: AMMonitor: Remote monitoring of biodiversity in an...
- No DOI given, and none found for title: Python and R for the Modern Data Scientist
- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: TensorFlow: Large-Scale Machine Learning on Hetero...
- No DOI given, and none found for title: reticulate: Interface to ’Python’
- No DOI given, and none found for title: luz: Higher Level ’API’ for ’torch’
- No DOI given, and none found for title: Deep Learning with PyTorch
- No DOI given, and none found for title: Deep Learning
- No DOI given, and none found for title: A survey on deep transfer learning
- No DOI given, and none found for title: A survey of transfer learning
- No DOI given, and none found for title: Convolutional networks for images, speech, and tim...
- No DOI given, and none found for title: Recent advances in convolutional neural networks
- No DOI given, and none found for title: Very deep convolutional networks for large-scale i...
- No DOI given, and none found for title: Characterizing soundscapes across diverse ecosyste...
- No DOI given, and none found for title: Caret package
- No DOI given, and none found for title: umap: Uniform Manifold Approximation and Projectio...
- No DOI given, and none found for title: soundClass: An automatic sound classification tool...

❌ MISSING DOIs

- 10.3389/fevo.2023.1071640 may be a valid DOI for title: A workflow for the automated detection and classif...
- 10.1080/09524622.2015.1133320 may be a valid DOI for title: Assessment of error rates in acoustic monitoring w...
- 10.1163/2214-8647_dnp_e612900 may be a valid DOI for title: Keras
- 10.1109/cvpr.2009.5206848 may be a valid DOI for title: Imagenet: A large-scale hierarchical image databas...
- 10.1201/9781003275923 may be a valid DOI for title: Deep Learning and Scientific Computing with R torc...
- 10.1145/3065386 may be a valid DOI for title: Imagenet classification with deep convolutional ne...
- 10.1109/cvpr.2016.90 may be a valid DOI for title: Deep residual learning for image recognition
- 10.1016/j.ecoinf.2023.102457 may be a valid DOI for title: Mel-frequency cepstral coefficients outperform emb...
- 10.1038/s41598-023-49989-z may be a valid DOI for title: Global birdsong embeddings enable superior transfe...
- 10.1371/journal.pone.0246564 may be a valid DOI for title: Not by the light of the moon: investigating circad...
- 10.1111/btp.13205 may be a valid DOI for title: Evidence for acoustic niche partitioning depends o...

❌ INVALID DOIs

- https://doi.org/10.1016/j.ecoinf.2022.101688 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.apacoust.2022.108939 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.ecoinf.2023.102457 is INVALID because of 'https://doi.org/' prefix

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

faroit commented 1 month ago

👋 @Desjonqu @steffilazerte thanks again for agreeing to review this submission. Let me know if you need any help starting the review process here.

One additional thing I would like to ask you is to not use this issue thread for discussions but instead open github issues on https://github.com/DenaJGibbon/gibbonNetR and link back to this thread here for easier reference.

Please complete your review in the next 4-5 weeks 🙏

faroit commented 3 weeks ago

@Desjonqu @steffilazerte can you please give us an update about the status of your review? Let me know if you need help or have further questions.

steffilazerte commented 3 weeks ago

Hi @faroit, Hi @DenaJGibbon, I have no update to report other than that this review is on my to-do list and will be done within the requested time frame. Thanks!

Desjonqu commented 3 weeks ago

Hi @faroit, same here. I'll be probably working on this on November 6-7th, I'll try earlier but not sure it will happen.

steffilazerte commented 2 weeks ago

Review checklist for @steffilazerte

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/DenaJGibbon/gibbonNetR?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@DenaJGibbon) 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.
[ ] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[ ] 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

[ ] 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).
[ ] 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?
[ ] 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?
[ ] 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)?
[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?

steffilazerte commented 2 weeks ago

Hi @DenaJGibbon! This is my review for your package.

It's exciting to see a new bioacoustics R package. It's been a while since I worked in song analysis, but I do find it fascinating! Most of my current experience is in R package development in the natural sciences, so many of my comments will reflect that background. I don't have a background in machine learning and am a bit out of touch with the acoustical software world so some of my questions may reflect this lack of understanding. Also @faroit, this is just a reminder that I won't be able to evaluate those technical details.

Generally, I think this package has the potential to be a valuable tool for bioacoustic analyses. There are two main areas which I think could use some modifications. First, is the documentation. This is a complex package and to be truly useful, I think there needs to be more clarity and explanations about how to use the functions and what a typical workflow might look like. Second, the R package itself could use some of polish with respect to following best practices for R package development (nothing that can't be fixed). The paper is generally well written, and I really appreciated the beginning. However, I think focused a bit too much on technical details rather than why this package is awesome and what it can be used to achieve.

Below I list the issues and specific aspects to fix. I tried to put most of my comments into separate issues in the repository, feel free to ask for clarification if anything isn't clear or you have follow up questions. Good luck!

Specific Details

[ ] Consider adding a pkgdown docs site (https://github.com/DenaJGibbon/gibbonNetR/issues/4)
[ ] Clarify and expand on the documentation (https://github.com/DenaJGibbon/gibbonNetR/issues/5)
[ ] Address issues in the README (https://github.com/DenaJGibbon/gibbonNetR/issues/6)
[ ] Incorporate R best practices (https://github.com/DenaJGibbon/gibbonNetR/issues/7)
[ ] Fix package check notes/warnings/errors (https://github.com/DenaJGibbon/gibbonNetR/issues/9)
[ ] Consider changes to the Manuscript (https://github.com/DenaJGibbon/gibbonNetR/issues/8)
[ ] Add the missing community contribution guidelines (see the rOpenSci Dev guide for some ideas)
[ ] @faroit, I'm not sure if they require more explicit animal research statements as the package does include vocalisations recorded from animals?

DenaJGibbon commented 1 week ago

Thank you so much for your detailed comments, @steffilazerte ! They will be very helpful for improving the package and the manuscript. We will get going on the revisions!

DenaJGibbon commented 4 days ago

Hello @Desjonqu. I wanted to let you know I am still working on the suggested revisions from @steffilazerte. I will try to push the updates by early next week. Thanks to both of you!

Desjonqu commented 1 day ago

Thanks for letting me know. Tell me when you're ready.

openjournals / joss-reviews