[REVIEW]: PhaseTypeR: an R package for phase-type distributions in population genetics

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@rivasiker@majensen<!--end-editor-- Reviewers: @tkchafin, @nhejazi Archive: 10.5281/zenodo.7656038

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6be8cd15efabd25b38a5231f8185a376"><img src="https://joss.theoj.org/papers/6be8cd15efabd25b38a5231f8185a376/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/6be8cd15efabd25b38a5231f8185a376/status.svg)](https://joss.theoj.org/papers/6be8cd15efabd25b38a5231f8185a376)

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

@tkchafin & @nhejazi, 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 @majensen 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 @tkchafin

📝 Checklist for @nhejazi

editorialbot commented 1 year 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 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.12 s (864.8 files/s, 178124.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            41           2137            480          11061
R                               31            587           1083           1807
Rmd                              4            670            977            910
Markdown                        13            216              0            771
CSS                              4             99             49            431
JavaScript                       5             68             39            290
TeX                              3             27              0            287
YAML                             6             31              6            206
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           108           3835           2635          15774
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 2396

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/978-1-4939-7049-0 is OK
- 10.1016/j.tpb.2019.02.001 is OK
- 10.18637/jss.v025.i07 is OK
- 10.1111/sjos.12505 is OK
- 10.1017/jpr.2019.60 is OK
- 10.15807/jorsj.59.72 is OK
- 10.1007/978-3-319-22264-6_7 is OK
- 10.1007/s00285-021-01689-w is OK
- 10.1007/978-0-387-78168-6 is OK
- 10.1093/schbul/syp004 is OK
- 10.1534/genetics.114.173898 is OK
- 10.1006/tpbi.1997.1307 is OK
- 10.1016/0304-4149(82)90011-4 is OK
- 10.1006/tpbi.1995.1025 is OK
- 10.4171/ECR/17-1/8 is OK
- 10.1017/jpr.2021.79 is OK
- 10.1016/j.tpb.2022.08.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

majensen commented 1 year ago

@tkchafin @nhejazi Can you let us know how this review is proceeding for you. Thanks

tkchafin commented 1 year ago

Review checklist for @tkchafin

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/rivasiker/PhaseTypeR?
[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 (@rivasiker) 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?

tkchafin commented 1 year ago

I've completed my review -- provided some very minor suggestions and flagged a few missing bits to meet the community guidelines as issues #8, #9, #10, and #11.

No issues were encountered installing or running any of the vignettes, other than some undocumented dependencies which were flagged in the aforementioned issues. Once the contributing, issue/ bug report, and dependencies have been documented I'll tick the last box on the checklist. Thanks and congrats to the authors on a well put together R package.

majensen commented 1 year ago

@nhejazi - how is the review for this work coming along? Thanks

nhejazi commented 1 year ago

I will have my review completed by the end of this week — apologies for the delay

rivasiker commented 1 year ago

I've completed my review -- provided some very minor suggestions and flagged a few missing bits to meet the community guidelines as issues #8, #9, #10, and #11.

No issues were encountered installing or running any of the vignettes, other than some undocumented dependencies which were flagged in the aforementioned issues. Once the contributing, issue/ bug report, and dependencies have been documented I'll tick the last box on the checklist. Thanks and congrats to the authors on a well put together R package.

We thank the reviewer for the very useful feedback and comments! We have incorporated the suggestions in the code and paper for the package.

rivasiker commented 1 year ago

@editorialbot generate pdf

tkchafin commented 1 year ago

Completed my checklist

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:

nhejazi commented 1 year ago

Review checklist for @nhejazi

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/rivasiker/PhaseTypeR?
[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 (@rivasiker) 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?

nhejazi commented 1 year ago

I've just completed my checklist. I encountered only the issues already reported by the other reviewer, which appear to have now been fixed on the joss-paper branch. The package is very well put together, and the paper is also succinct and informative -- congratulations to the authors on such a nice product.

majensen commented 1 year ago

Thanks @nhejazi - I will have my final look this week. Much appreciated!

majensen commented 1 year ago

@editorialbot check references

majensen commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/978-1-4939-7049-0 is OK
- 10.1016/j.tpb.2019.02.001 is OK
- 10.18637/jss.v025.i07 is OK
- 10.1111/sjos.12505 is OK
- 10.1017/jpr.2019.60 is OK
- 10.15807/jorsj.59.72 is OK
- 10.1007/978-3-319-22264-6_7 is OK
- 10.1007/s00285-021-01689-w is OK
- 10.1007/978-0-387-78168-6 is OK
- 10.1093/schbul/syp004 is OK
- 10.1534/genetics.114.173898 is OK
- 10.1006/tpbi.1997.1307 is OK
- 10.1016/0304-4149(82)90011-4 is OK
- 10.1006/tpbi.1995.1025 is OK
- 10.4171/ECR/17-1/8 is OK
- 10.1017/jpr.2021.79 is OK
- 10.1016/j.tpb.2022.08.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

majensen commented 1 year ago

@rivasiker all I can say is, I wish I'd had phase-type distributions and this nice package back in the late 90s! The paper reads very well, and I don't see any issues. Before recommending for publication, can you create a public archive of the codebase using Zenodo, FigShare, or similar? (see https://github.com/openjournals/joss-reviews/issues/1839#issuecomment-560048729 for a short tutorial if needed). Please let me know in this thread the DOI you get.

rivasiker commented 1 year ago

@majensen, thank you very much for your kind words! I have just created a release of the package in Zenodo with DOI: 10.5281/zenodo.7656038 (https://doi.org/10.5281/zenodo.7656038). Please, let me know if there is something else I should do.

majensen commented 1 year ago

@editorialbot set 10.5281/zenodo.7656038 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7656038

majensen commented 1 year ago

@editorialbot set v1.0.5-beta as version

editorialbot commented 1 year ago

Done! version is now v1.0.5-beta

majensen commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/978-1-4939-7049-0 is OK
- 10.1016/j.tpb.2019.02.001 is OK
- 10.18637/jss.v025.i07 is OK
- 10.1111/sjos.12505 is OK
- 10.1017/jpr.2019.60 is OK
- 10.15807/jorsj.59.72 is OK
- 10.1007/978-3-319-22264-6_7 is OK
- 10.1007/s00285-021-01689-w is OK
- 10.1007/978-0-387-78168-6 is OK
- 10.1093/schbul/syp004 is OK
- 10.1534/genetics.114.173898 is OK
- 10.1006/tpbi.1997.1307 is OK
- 10.1016/0304-4149(82)90011-4 is OK
- 10.1006/tpbi.1995.1025 is OK
- 10.4171/ECR/17-1/8 is OK
- 10.1017/jpr.2021.79 is OK
- 10.1016/j.tpb.2022.08.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

{\rm Cov}(T_{\text{left}},T_{\text{right
     ^
unexpected control sequence \rm
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

{\rm Cov}(T_{\text{left}},T_{\text{right
     ^
unexpected control sequence \rm
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

editorialbot commented 1 year ago

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3987, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

rivasiker commented 1 year ago

@majensen Looking at the final proof, I have noticed that Table 2 spans two pages. I think it could span just one by adjusting the width of the table columns. Additionally, the two warnings that appeared during the generation of the final proof could also be easily fixed. Should I go ahead and fix these two details? After doing so, should I re-generate the proof by running @editorialbot generate pdf?

majensen commented 1 year ago

@rivasiker Yes that would be great

rivasiker 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:

Kevin-Mattheus-Moerman commented 1 year ago

@rivasiker I am the AEiC for this track and here to help process the final steps towards acceptance of this work in JOSS. Below are some minor points that need your attention.

On the archive:

[ ] Ensure that the ZENODO listed license matches the software license, it currently says Other (Open), you may need to manually edit this.
[ ] Ensure that the ZENODO title matches the paper title
[ ] Ensure that the ZENODO author set matches those on the paper (including the order)

The paper seems in order. Note that you have no "Acknowledgements" section. This section is not required but if you do need it (e.g. to acknowledge funding) you can add one now if you like.

rivasiker 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:

rivasiker commented 1 year ago

@Kevin-Mattheus-Moerman, thank you for you pointing all of this out! I have updated the license information, title, and author list at the Zenodo archive, which can be found under the same DOI as before. Additionally, I have added a small "Acknowledgements" section. With this, the draft would be finalized.

Kevin-Mattheus-Moerman commented 1 year ago

@rivasiker the archive looks good now. I'll now proceed to accept this submission in JOSS.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3996
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05054
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 1 year ago

Congratulations on this publication @rivasiker !

Thanks for editing @majensen.

And a special thanks to the reviewers: @tkchafin and @nhejazi !

editorialbot commented 1 year ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05054/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.05054

This is how it will look in your documentation:

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