[REVIEW]: Miet: an R package for region of interest analysis from magnetic reasonance images

whedon commented 5 years ago

Submitting author: @benoit-combes (Benoit Combès) Repository: https://gitlab.inria.fr/miet/miet Version: v0.2 Editor: @arokem Reviewer: @janfreyberg, @neuroimaginador Archive: 10.5281/zenodo.3626693

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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

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

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arokem know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @janfreyberg

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 repository url?
[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 (@benoit-combes) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @neuroimaginador

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 repository url?
[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 (@benoit-combes) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

whedon commented 5 years ago

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

:star: Important :star:

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whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 4 years ago

@arokem can you check progress here?

arokem commented 4 years ago

@janfreyberg : I see that you've checked off a couple of items. Any progress on the other items?

@neuroimaginador : have you had a chance to take a look?

janfreyberg commented 4 years ago

Hi @arokem - apologies for the delay! I've been away with work.

I've ticked the bits I was able to verify and will raise a few issues on their repo now.

benoit-combes commented 4 years ago

@janfreyberg @neuroimaginador. Thanks for agreing to review my work and for your first inputs. If I can do anything that may help you in the reviewing process, please let me know.

benoit-combes commented 4 years ago

@janfreyberg @neuroimaginador. Dear reviewers, I just realized that a directory was missing from the miet repository. This lack simply causes the function documentation not to be available using the regular package installation procedure. I corrected this lack by adding the missing directory so that the doc is not available using the regular "?" command. I hope this lack did not disturb too much your work. If I can do anything that may help you in the reviewing process, please let me know.

janfreyberg commented 4 years ago

Thanks @benoit-combes - I've left a few comments about the documentation. I think aside from a fix / answer to the issues on your gitlab issue, I didn't feel able to tick off "state of the field" - would you be able to add this to the paper, even if it's just "Currently you have to read array data manually and program all the table creations yourself" or something along those lines.

benoit-combes commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

benoit-combes commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

benoit-combes commented 4 years ago

@janfreyberg. Thanks for these valuable points. I tried to address them with my last pushes. Concerning the point you raised in your comment, I added to the joss paper (end of section 1):

"Such an analysis needs to iterate over all MR volumes to read them and to extract the relevant statistics. To the best of our knowledge, there is no dedicated framework to ease such tasks, which may result in lengthy technical analysis codes. Miet (acronym of medical imaging extraction tools) is an R package attempting to fill that gap. More specifically, miet is designed to specify and extract tibbles (which is an improved data.frame structure) ready for data analysis from a specified folder hierarchy and a set of extraction formulas."

I commented my fixes for each of the other points in the issues you raised on gitlab.

I hope everythink is correct to you, if for any reason it is not the case, please let me know.

Thanks again for your inputs.

benoit-combes commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

janfreyberg commented 4 years ago

Great, thanks. This addresses all my concerns.

benoit-combes commented 4 years ago

Dear @arokem, may I ask you whether you get supplemental information about @neuroimaginador availability to review the work ? Thanks in advance.

arokem commented 4 years ago

Sorry about the delay here. Let me try to track this reviewer down, as they have not responded here.

neuroimaginador commented 4 years ago

Sorry about the delay, @arokem and @benoit-combes , I'm now reviewing the paper and the package. Just opened an issue regarding a potential enhancement by using a "testthat" folder structure as described in http://r-pkgs.had.co.nz/tests.html, which is a standard and completely automated way of testing, and required by CRAN submissions.

neuroimaginador commented 4 years ago

Thank you, @benoit-combes for addressing my issues, I'm more than satisfied with this package, since it may be very useful to get people from neuroimaging into R. I have already closed all my issues. Thanks.

benoit-combes commented 4 years ago

@neuroimaginador. Thanks for this relevant suggestion. I modified the testing strategy following your suggestion. I hope everythink is now ok to you, if for any reason it is not the case, please let me know.

benoit-combes commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

benoit-combes commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

benoit-combes commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

benoit-combes commented 4 years ago

Dear @arokem, I read again the paper and fixed a few grammar/spelling mistakes and ambiguous wordings. If I can do anything that may help you in the editing process, please let me know.

arokem commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1148/radiographics.14.2.8190954 may be missing for title: Magnetization transfer: theory and clinical applications in neuroradiology.

INVALID DOIs

- None

arokem commented 4 years ago

In addition to adding the missing DOI for this reference, I have added some proposed edits in a patch attached to https://gitlab.inria.fr/miet/miet/issues/9

benoit-combes commented 4 years ago

@whedon generate pdf

benoit-combes commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1148/radiographics.14.2.8190954 may be missing for title: Magnetization transfer: theory and clinical applications in neuroradiology.

INVALID DOIs

- None

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

benoit-combes commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1148/radiographics.14.2.8190954 may be missing for title: Magnetization transfer: theory and clinical applications in neuroradiology.

INVALID DOIs

- None

benoit-combes commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

benoit-combes commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- https://pubs.rsna.org/doi/10.1148/radiographics.14.2.8190954 is INVALID because of 'https://doi.org/' prefix

benoit-combes commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

benoit-combes commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1148/radiographics.14.2.8190954 is INVALID because of 'https://doi.org/' prefix

benoit-combes commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

benoit-combes commented 4 years ago

@whedon check reference

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