[REVIEW]: {histoc} histocompatibility functions for organ transplantation

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@balima78@crvernon<!--end-editor-- Reviewers: @turgeonmaxime, @aj2duncan Archive: 10.5281/zenodo.7338242

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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

@turgeonmaxime & @aj2duncan, 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 @crvernon 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 @turgeonmaxime

📝 Checklist for @aj2duncan

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (685.6 files/s, 84476.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               23            394            826           2724
HTML                             1             62              5            233
YAML                             6             25              6            193
Markdown                         6             83              0            185
TeX                              1              9              0             87
Rmd                              3             65            105             42
JSON                             1              0              0              8
-------------------------------------------------------------------------------
SUM:                            41            638            942           3472
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1125

crvernon commented 2 years ago

👋 @balima78, @turgeonmaxime, @aj2duncan - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) 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. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/4807 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

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

OK DOIs

- 10.32932/pjnh.2020.07.070 is OK
- 10.1053/j.ajkd.2005.07.031 is OK
- 10.1097/TP.0000000000001326 is OK

MISSING DOIs

- None

INVALID DOIs

- None

turgeonmaxime commented 2 years ago

Review checklist for @turgeonmaxime

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/txopen/histoc?
[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 (@balima78) 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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?
[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: 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?
[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?

aj2duncan commented 2 years ago

Review checklist for @aj2duncan

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/txopen/histoc?
[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 (@balima78) 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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?
[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: 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?
[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?

crvernon commented 2 years ago

📣 Mid-week rally!

👋 @turgeonmaxime and @aj2duncan - Can you provide a status update to how things are going on your side of things? Thanks!

Keep up the good work!

turgeonmaxime commented 2 years ago

Thanks for the heads-up, I'll admit this review fell off my radar. I'll be taking a look over the next few days.

turgeonmaxime commented 2 years ago

@balima78 I've read the manuscript a couple of times. I think the statement of need needs to be expanded. For example, I can't find the answer to the following questions:

Who is the intended audience for the package? Physicians? Researchers in kidney transplant allocation policy? Biostatisticians? Health systems administrator?
What is the current state of software solutions for this problem?
How does histoc compare to current software?

In particular, the last sentence of the summary is as follows:

The goal of this package is to aid the evaluation and assessment of KAS in transplantation.

However, it is unclear to me how histoc achieves this goal. Answering the three questions above would help make this clearer and strengthen your claim.

aj2duncan commented 2 years ago

Hi @balima78,

I agree with @turgeonmaxime that the statement of need in the manuscript could have some additional info added. I would also suggest that you need to add some more detail to the guidelines for contribution.

Thanks.

balima78 commented 1 year ago

Thanks to @turgeonmaxime and @aj2duncan for your patience and your insights. We will try to address each one of your comments and upload a new version of our draft.

balima78 commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

balima78 commented 1 year ago

@turgeonmaxime and @aj2duncan, we review our paper to address your comments and questions.

thank you for your help.

turgeonmaxime commented 1 year ago

@balima78 Thanks for adding more details about the state of available software.

I did notice a few typos:

Line 7: Should be "as equitable as possible", instead of "equitably".
Line 36: "a vignette is available", instead of "it is available a vignette".
Line 41: "makes available", instead of "make available".
Subsection on Portugese Model: The numbered list didn't render properly. I think it's because there should be an empty line between the end of the paragraph and the beginning of the list.
Line 57: Should be "hypersensitized", instead of "hipersensitized".
Line 99: Should be "dialysis", instead of "dialisys".
Line 112: There is an extra bracket ] that should be remove.

balima78 commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

balima78 commented 1 year ago

thank you @turgeonmaxime, typos corrected.

turgeonmaxime commented 1 year ago

Thanks @balima78

@crvernon I can't really comment on the technical side of this package (i.e. kidney allocation systems), but I've completed the review, and I'm satisfied that it meets the checklist review criteria.

aj2duncan commented 1 year ago

Hi @balima78,

Thanks very much for those changes. I think you just need to make a couple of additions to your documentation/github and everything is complete. At the moment the paper has both a Statement of Need and details on Bug Reports and How to Contribute, I would suggest you add these to Github and/or your documentation as you see fit - just in case someone doesn't find the paper.

By the way, one of your tests is skipped when running testthat::test_local() as it is empty. Otherwise, this is a well written, tested and documented package.

balima78 commented 1 year ago

thank you @aj2duncan, I added the 'Bug report' to the package's README and website, as suggested.

crvernon commented 1 year ago

Thank you for your review @balima78 !

crvernon commented 1 year ago

@aj2duncan looks like the review is making good progress. Let me know when you have finished your review checklist. Thanks!

aj2duncan commented 1 year ago

@balima78, thanks for sorting that and apologies for the delay getting back to you.

@crvernon, that's me all done. Happy with all the items on the checklist.

crvernon commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

crvernon commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.32932/pjnh.2020.07.070 is OK
- 10.1053/j.ajkd.2005.07.031 is OK
- 10.1097/TP.0000000000001326 is OK

MISSING DOIs

- None

INVALID DOIs

- None

crvernon commented 1 year ago

@balima78 here are some items I would like you to address in the current draft of your paper:

[ ] GENERAL: please change package mentions using brackets (e.g., {histoc}) to backticks (e.g., `histoc`)
[ ] GENERAL: to increase readability, please use a format such as "...Eurotransplant (ET model, EuroTransplant, 2020)..." instead of groups of content with multiple back-to-back parenthesis like "...Eurotransplant (ET model) (EuroTransplat, 2020)...". This can be achieved using the following format in markdown "...Eurotransplant [ET model; @ET]..."
[ ] LINE 19: I don't believe there is a need to site you documentation for Lima & Reis, 2022 since the package in question is actually being described in this paper.
[ ] LINE 23: missing citation for the PT model
[ ] LINE 29: write out number less than 10, so..."By default two candidates.."
[ ] LINE 28: HLA acronym not described before this mention. Please do so here.
[ ] LINE 29: write out number less than 10, so..."By default two candidates.."
[ ] LINE 32: ABO acronym not described before this mention. Please do so here.
[ ] LINES 66-70: the variable/function name at the end of each sorting mechanism should have parenthesis similar to the following example in markdown: "...Senior Program [`SP`, 65+ years old candidates when the doner has 65+ years];..."
[ ] LINE 66: do you mean to state "...65+ year old candidates..."?
[ ] LINE 75: should "Tiers" be lower case in the middle of this sentence?
[ ] LINES 109-114: to remove redundancy, the following could be stated (my following summary is not in markdown so the links and formatting will need to be inserted): "We provide example datasets within histoc for 500 wait list transplant candidates and a pool of 70 doners both of which are described in our candidates' selection vignette. Additionally, an additional column in the output can be generated to calculate the estimated 5-year event probability for mortality and graft failure described by Molnar et al. (2018). This is available from the application TxScore and can be computed using the txscore() function."
[ ] LINE 116: should read "User provided input data used by this package regarding either candidate or donor information should match the exact format of the provided example data."
[ ] LINES 121-123: should simply read in markdown: Any bug reporting, feature requests, or other feedback will be welcomed by [submitting an issue](https://github.com/txopen/histoc/issues) in our repository. When reporting a bug, please ensure that a reproducible example of your code is included so that we may respond to your issue promptly.

balima78 commented 1 year ago

@editorialbot generate pdf

balima78 commented 1 year ago

@crvernon, thanks for your insigths. I corrected all itens but the one about ABO, because it is not an acronym (https://www.ncbi.nlm.nih.gov/books/NBK2267/)

crvernon commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

crvernon commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.32932/pjnh.2020.07.070 is OK
- 10.1053/j.ajkd.2005.07.031 is OK
- 10.1097/TP.0000000000001326 is OK

MISSING DOIs

- None

INVALID DOIs

- None

crvernon commented 1 year ago

@balima78 please see the PR above for some additional minor paper edits.

crvernon commented 1 year ago

@balima78 after we confirm that the above compiles in a way that suits you and the changes are brought into your main branch, we can move on to setting up the archive for a new release:

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do after the most recent paper changes have been made:

[x] Conduct a GitHub release of the current reviewed version of the software you now have on the main and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) to ensure it has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[x] List the DOI of the archived version here

txopen commented 1 year ago

@crvernon, please find here the requested DOI 10.5281/zenodo.7338242

balima78 commented 1 year ago

hi @crvernon , do we need to do anything else?

crvernon commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

crvernon commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.32932/pjnh.2020.07.070 is OK
- 10.1053/j.ajkd.2005.07.031 is OK
- 10.1097/TP.0000000000001326 is OK

MISSING DOIs

- None

INVALID DOIs

- None

crvernon commented 1 year ago

@editorialbot set v0.2.1 as version

editorialbot commented 1 year ago

Done! version is now v0.2.1

crvernon commented 1 year ago

@editorialbot set 10.5281/zenodo.7338242 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7338242

crvernon commented 1 year ago

@balima78 - thanks for putting together a really nice software product! Thanks to @turgeonmaxime and @aj2duncan for a constructive and timely review!

I am recommending that your submission be accepted. An EIC will review this shortly and confirm final publication if all goes well.

openjournals / joss-reviews