[REVIEW]: Frites: A Python package for functional connectivity analysis and group-level statistics of neurophysiological data

[whedon]

Submitting author: @EtienneCmb (Etienne Combrisson)
Repository: https://github.com/brainets/frites
Branch with paper.md (empty if default branch): paper
Version: v0.4.3
Editor: @meg-simula
Reviewers: @madvn, @travisbthomp
Archive: 10.5281/zenodo.7278278

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@madvn & @travisbthomp, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @madvn

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@EtienneCmb) 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

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 and who the target audience is?
• 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?

Review checklist for @travisbthomp

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@EtienneCmb) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @madvn, @travisbthomp it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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[whedon]

PDF failed to compile for issue #3842 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.16 s (1281.4 files/s, 115986.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         109           2415           5772           7325
SVG                              1              0              0            710
reStructuredText                85            635            726            590
TeX                              1             25              0            221
YAML                             6             45              5            181
CSS                              1             15              3             49
HTML                             2              2              3             28
DOS Batch                        1              8              1             26
make                             2              8             11             23
-------------------------------------------------------------------------------
SUM:                           208           3153           6521           9153
-------------------------------------------------------------------------------


Statistical information for the repository 'cf89deaa1b9fbcf1596c55f5' was
gathered on 2021/10/22.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
EtienneCmb                     387         24295           8358           99.59
Ruggero Basanisi                 2             9              8            0.05
brovelli.a                      11            71             45            0.35

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
EtienneCmb                15464           63.7         11.0               19.01
Ruggero Basanisi              8           88.9          9.5               50.00
brovelli.a                   40           56.3          7.1               35.00

[meg-simula]

👋🏼 @EtienneCmb @madvn @travisbthomp this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also 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. 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. Also note that the current paper is in the branch 'paper', so use e.g.

-> @whedon generate pdf from branch paper
-> @whedon check references from branch paper

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

[meg-simula]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[meg-simula]

@whedon check references from branch paper

[whedon]

Attempting to check references... from custom branch paper

[whedon]

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

[whedon]

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

OK DOIs

- 10.1002/hbm.23471 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1145/2833157.2833162 is OK
- 10.1371/journal.pcbi.1008302 is OK
- 10.21105/joss.01081 is OK

MISSING DOIs

- 10.5334/jors.148 may be a valid DOI for title: xarray: ND labeled arrays and datasets in Python
- 10.1523/jneurosci.4892-14.2015 may be a valid DOI for title: Characterization of Cortical Networks and Corticocortical Functional Connectivity Mediating Arbitrary Visuomotor Mapping
- 10.1101/2021.08.14.456339 may be a valid DOI for title: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data

INVALID DOIs

- None

[brovelli]

We checked the 3 MISSING DOIs on https://dx.doi.org/ and they all appear to be correct.

[whedon]

👋 @travisbthomp, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @madvn, please update us on how your review is going (this is an automated reminder).

[madvn]

Sorry about the delay, I will get to it this weekend.

[travisbthomp]

Getting around to this now with other deadlines mostly behind me.

[travisbthomp]

@EtienneCmb I am running some of the examples from the documentation. I noticed the following (likely unintentional) output from plot_stim_spec_network.py

plot_stim_spec_network.py:211: SyntaxWarning: "is" with a literal. Did you mean "=="?
if direction is 'x->y':
plot_stim_spec_network.py:213: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif direction is 'y->x':
plot_stim_spec_network.py:215: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif direction is 'x.y':
plot_stim_spec_network.py:260: SyntaxWarning: "is" with a literal. Did you mean "=="?
if direction is 'x->y':
plot_stim_spec_network.py:262: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif direction is 'y->x':
plot_stim_spec_network.py:264: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif direction is 'x.y':

[travisbthomp]

@EtienneCmb

All Issues in this comment have now been addressed. Nov 29, 2021

Resolution: Updated to frites 0.4.1 and re-checked the scripts below

1. The second figure generated by plot_wf_mi_cc.py does not match the second figure in the corresponding documentation. (see https://brainets.github.io/frites/auto_examples/mi/plot_wf_mi_cc.html)

2. The example plot_est_custom.py does not work for me and generates the following error (see https://brainets.github.io/frites/auto_examples/estimators/plot_est_custom.html)

Traceback (most recent call last):
File "plot_est_custom.py", line 12, in
from frites.estimator import CustomEstimator
ImportError: cannot import name 'CustomEstimator' from 'frites.estimator'

3. The example plot_est_comparison.py does not faithfully recreate figure two (see https://brainets.github.io/frites/auto_examples/estimators/plot_est_comparison.html)

4. The example plot_ccf.py does not work for me and generates the following error (see
   https://brainets.github.io/frites/auto_examples/conn/plot_ccf.html)

Traceback (most recent call last):
File "plot_ccf.py", line 11, in
from frites.conn import conn_ccf
ImportError: cannot import name 'conn_ccf' from 'frites.conn'

5. The example plot_ar_instantaneous.py: The 3rd figure in the documentation (see https://brainets.github.io/frites/auto_examples/armodel/plot_ar_instantaneous.html) should be updated to match the figure generated by the code (different subplot titles, etc)

Update note: removed some other comments regarding plot mismatches as I noticed the data was generated using random values.

[madvn]

Hello all, I am just getting to this as well. Sorry about the delay.

Looks like a very interesting toolbox. I think the idea of feature-specific functional networks using mutual information can be used widely in not just neuroscientific settings but also sociology or even, more topically, epidemiology. I've updated my checklist based on a quick look at the repo and installing the package. I also took a quick look at the paper and have some notes for the authors based on the following requirements while I work my way through the rest of the checklist.

- [ ] **Summary:** Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?

You have a summary but please revise it to address the "for a diverse, non-specialist audience" part of the requirement. Add a note about the breadth of usability of these tools in other domains besides neuroscience.

- [ ] **State of the field:** Do the authors describe how this software compares to other commonly-used packages?

Please place your tool in the space of other information theory tools such as infotheory, IDTXL etc. as well as network neuroscience tools such as Brain connectivity toolbox etc. I do believe there are unique aspects to your package, such as combining information-theoretic measures with network neuroscience to find feature-specific functional networks (I'm not aware of other tools that does this -- I will look it up. If you are aware of others, please include those.

- [ ] **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]( https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html#citation_syntax)?

Please update references based on additional paper that you will cite to address the above points.

[EtienneCmb]

Dear @travisbthomp,

plot_stim_spec_network.py:211: SyntaxWarning: "is" with a literal. Did you mean "=="?

I fixed this morning the warning message by replacing 'is' with '=='

The second figure generated by plot_wf_mi_cc.py does not match the second figure in the corresponding documentation.

Indeed, as you saw, we are mainly using random data for illustrating the functions

The example plot_est_custom.py does not work for me and generates the following error
The example plot_ccf.py does not work for me and generates the following error

Indeed, both examples were using the develop branch. This morning I pushed the version 0.4.1 of Frites to Pypi, it should works now once updated.

[travisbthomp]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

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

[travisbthomp]

Suggestions for paper

After reviewing the paper I would like to make a few comments in the spirit of the review guidelines above.

Summary

Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?

The description of the high level functionality is not quite clear. "Frites provides such an integrated framework" for what? Is Frites limited to "discovery of cognitive brain networks from multi-channel neurophysiological datasets"? What types of networks? Conversely, I think that the documentation text is quite approachable and nice!

Frites is a Python toolbox for assessing information-based measures on human and animal
neurophysiological data (M/EEG, Intracranial). The toolbox also includes directed and undirected
connectivity metrics such as group-level statistics on measures of information (information-theory,
machine-learning and measures of distance).

In short, the current summary seems obfuscated and potentially difficult to read for a "non-specialist audience".

Statement of need

Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?

The paper does indeed have a section titled 'Statement of Need'. However, this section does not establish a clear need for the software nor does it "clearly state what problems the software is designed to solve and who the target audience is". At least, it does not do these things in a way that can be appreciated by an non-expert in the area, such as myself, who is not currently aware of the state of the art approaches, what problems they could solve better, and why Frites fills any of these gaps.

I would suggest revisiting this write up with the journal guidelines in mind.

State of the field

Do the authors describe how this software compares to other commonly-used packages?

I cannot find where this has been done in a manner that is decipherable to a non-expert. I would suggest an approach which clearly states the central problem Frites aims to solve and endeavors a comparative discussion to other available tools; what are the advantages of Frites over other packages? If there are no other packages, simply state that Frites is the first of its kind.

Quality of writing

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

The authors do not struggle with the tenets of structural composition. The central message of the statement of need is not currently clear, but this is not an issue with the sentence-by-sentence structure/language/quality per se.

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 did not see any issues with the references and all provided DOI links correct redirected to the appropriate paper.

[editorialbot]

👋 @openjournals/sbcs-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#3676, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[EtienneCmb]

@meg-simula I checked the final proof, everything seems correct :)

[meg-simula]

Great! Now, we are just waiting for one of editors-in-chief to take a look at it - no need to take further action from your side.

[oliviaguest]

@editorialbot recommend-accept

[oliviaguest]

@editorialbot recommend-accept

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1002/hbm.23471 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.5334/jors.148 is OK
- 10.1145/2833157.2833162 is OK
- 10.7551/mitpress/11442.001.0001 is OK
- 10.1523/jneurosci.4892-14.2015 is OK
- 10.1371/journal.pcbi.1008302 is OK
- 10.1016/j.neuroimage.2022.119347 is OK
- 10.21105/joss.01081 is OK
- 10.1523/JNEUROSCI.1672-16.2016 is OK
- 10.1016/j.jneumeth.2007.03.024 is OK
- 10.1016/j.neuroimage.2009.10.003 is OK
- 10.21105/joss.01609 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/sbcs-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#3696, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[oliviaguest]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

👋 @openjournals/sbcs-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#3698, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[editorialbot]

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

OK DOIs

- 10.1002/hbm.23471 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.5334/jors.148 is OK
- 10.1145/2833157.2833162 is OK
- 10.7551/mitpress/11442.001.0001 is OK
- 10.1523/jneurosci.4892-14.2015 is OK
- 10.1371/journal.pcbi.1008302 is OK
- 10.1016/j.neuroimage.2022.119347 is OK
- 10.21105/joss.01081 is OK
- 10.1523/JNEUROSCI.1672-16.2016 is OK
- 10.1016/j.jneumeth.2007.03.024 is OK
- 10.1016/j.neuroimage.2009.10.003 is OK
- 10.21105/joss.01609 is OK

MISSING DOIs

- Errored finding suggestions for "Scikit learn : Machine Learning in Python", please try later

INVALID DOIs

- None

[oliviaguest]

@editorialbot recommend-accept

[oliviaguest]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

👋 @openjournals/sbcs-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#3713, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[oliviaguest]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1002/hbm.23471 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.5334/jors.148 is OK
- 10.1145/2833157.2833162 is OK
- 10.7551/mitpress/11442.001.0001 is OK
- 10.1523/jneurosci.4892-14.2015 is OK
- 10.1371/journal.pcbi.1008302 is OK
- 10.1016/j.neuroimage.2022.119347 is OK
- 10.21105/joss.01081 is OK
- 10.1523/JNEUROSCI.1672-16.2016 is OK
- 10.1016/j.jneumeth.2007.03.024 is OK
- 10.1016/j.neuroimage.2009.10.003 is OK
- 10.21105/joss.01609 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

🐦🐦🐦 👉 Tweet 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.03842 joss-papers#3714
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03842
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...

[oliviaguest]

@EtienneCmb yay! congratulations! 🎉

Big thanks to @meg-simula for editing and the reviewers: @madvn, @travisbthomp! ❤️

[editorialbot]

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

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[EtienneCmb]

Great, thank you @oliviaguest and @meg-simula . Many thanks to the reviewers @madvn and @travisbthomp :)

[madvn]

@EtienneCmb , quick note, (maybe you've already planned this) you could put the pdf from here on arxiv for more visibility if you want.