[REVIEW]: presize: An R-package for precision-based sample size calculation in clinical research

[whedon]

Submitting author: @aghaynes (Alan G Haynes)
Repository: https://github.com/CTU-Bern/presize
Version: 0.2.3
Editor: @majensen
Reviewer: @amoeba, @TomKellyGenetics
Archive: 10.5281/zenodo.4680282

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Markdown: [![status](https://joss.theoj.org/papers/780db6ae34eb2317ef9b084012cce4de/status.svg)](https://joss.theoj.org/papers/780db6ae34eb2317ef9b084012cce4de)

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

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

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✨ 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 ✨

Review checklist for @amoeba

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 (@aghaynes) 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 @TomKellyGenetics

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 (@aghaynes) 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. @amoeba, @TomKellyGenetics it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.23 s (331.6 files/s, 51806.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            22           1109            281           3442
R                               34            606           1043           3296
CSS                              3             99             48            428
Markdown                         4            109              0            314
JavaScript                       3             64             32            256
YAML                             6             57             11            215
TeX                              1             17              0            165
Rmd                              1             34             70             11
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                            75           2095           1486           8138
-------------------------------------------------------------------------------


Statistical information for the repository 'e500a6278ac16dd2edc8b7be' was
gathered on 2021/03/17.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
aghaynes                         2           357              5          100.00

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
aghaynes                    352           98.6          0.0                9.09

[whedon]

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

OK DOIs

- 10.2307/2685779 is OK
- 10.1198/000313002317572736 is OK
- 10.1016/S0140-6736(86)90837-8 is OK
- 10.1136/bmj.b3985 is OK
- 10.1002/sim.1108 is OK
- 10.1214/ss/1009213286 is OK
- 10.1007/BF02294183 is OK
- 10.1177/0962280211415469 is OK
- 10.1148/radiology.143.1.7063747 is OK
- 10.2307/2530610 is OK
- 10.2307/2531551 is OK
- 10.1002/sim.4780040211 is OK
- 10.1002/(sici)1097-0258(19980430)17:8<873::aid-sim779>3.0.co;2-i is OK
- 10.1016/j.jclinepi.2011.10.019  is OK
- 10.1097/EDE.0000000000000876 is OK
- 10.1016/S0140-6736(10)60484-9 is OK
- 10.1016/0895-4356(91)90128-v is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[amoeba]

Hey @aghaynes & @majensen, I've completed my review at CTU-Bern/presize#61 and conditionally accept the submission conditional upon the items listed over there.

[whedon]

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

[whedon]

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

[TomKellyGenetics]

It's still on my list. Sorry, was meaning to do it this week but have been off sick for a few days. Will try to get it done soon.

[TomKellyGenetics]

Great job on developing a handy package and Shiny App. I agree this is deserving of publication with some corrections. The software seems to be of high quality and valuable to the community. The manuscript has some room for improvement. Sorry for the delayed review, I should have time to review in more details soon. I will post minor comments here and major issues on the package repository.

Installation from CRAN works for version 0.1.3 as expected. Installation from GitHub installs the development version 0.2.1 but the documentation is not available. I will review the development version on GitHub conditional on an updated release on CRAN to pending changes during review (as discussed in CTU-Bern/presize#61).

[aghaynes]

Thanks @TomKellyGenetics. As discussed elsewhere, I do indeed intend to submit the newest version to CRAN.
I hope to merge the PR today, pending some modifications for input validation. Note that we made substantial changes to the paper itself in the PR also.

[TomKellyGenetics]

@aghaynes thanks for letting us know. I will wait for the PR to be merged before checking the updated Shiny App and manuscript. I see you are working on a Docker image as well. Excellent idea. 👍

Regarding the "statement of need", as previously discussed with @majensen and senior editors this does not need to be an explicit section in the paper. Authors may merge this into the abstract/summary at their discretion. The statement of need is clear in the documentation (README).

[TomKellyGenetics]

Sorry I realise it is a holiday period in western countries (I'm based in Asia where it is not). Please do not feel obligated to respond to my review until you are ready. Enjoy your holidays. 😄

I will review the manuscript once the pull request above has been completed. Please let me know when it is ready.

[aghaynes]

Hi all,
I merged a new PR covering the reviews so far...

@whedon generate pdf

[TomKellyGenetics]

@whedon generate pdf

[whedon]

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

[TomKellyGenetics]

I've reported a bug here: CTU-Bern/presize#72

This completes my review. I recommend acceptance conditional on revisions in issues opened on the https://github.com/CTU-Bern/presize repository. Great work to develop a useful package.

[aghaynes]

I've addressed your comments @TomKellyGenetics. I guess it's back to you and @amoeba for 'final' acceptance...

[aghaynes]

@whedon generate pdf

[whedon]

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

[aghaynes]

OK, i think it's ready again...

There is one reference thats still a little odd (the one for trialsize), but i dont know how to fix that. I tried the [@author:year; other stuff] syntax, but that didnt compile properly (it didnt work for any of the references I tried it for). Happy to fix if you know how, @kyleniemeyer or @majensen

[majensen]

Hi @aghaynes - pull in CTU-Bern/presize#79 - should fix.

[aghaynes]

obvious really... thanks @majensen!

@whedon generate pdf

[majensen]

Another pair of eyes can do wonders!

[danielskatz]

@whedon generate pdf

a command to whedon needs to be on the first line of a comment

[whedon]

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

[kyleniemeyer]

@whedon accept

OK, this goods good to me now.

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.2307/2685779 is OK
- 10.1198/000313002317572736 is OK
- 10.1016/S0140-6736(86)90837-8 is OK
- 10.1136/bmj.b3985 is OK
- 10.1002/sim.1108 is OK
- 10.1214/ss/1009213286 is OK
- 10.1007/BF02294183 is OK
- 10.1177/0962280211415469 is OK
- 10.1148/radiology.143.1.7063747 is OK
- 10.2307/2530610 is OK
- 10.2307/2531551 is OK
- 10.1002/sim.4780040211 is OK
- 10.1002/(sici)1097-0258(19980430)17:8<873::aid-sim779>3.0.co;2-i is OK
- 10.1016/j.jclinepi.2011.10.019  is OK
- 10.1097/EDE.0000000000000876 is OK
- 10.1016/S0140-6736(10)60484-9 is OK
- 10.1016/0895-4356(91)90128-v is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2227

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2227, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03118 joss-papers#2228
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03118
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...

[kyleniemeyer]

Congrats @aghaynes on your article's publication in JOSS!

Many thanks to @amoeba and @TomKellyGenetics for reviewing this, and @majensen for editing it.

(FYI, the DOI seems to still not be resolving, but this is likely just a delay. Everything else on the JOSS side looks good.)

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03118/status.svg)](https://doi.org/10.21105/joss.03118)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03118">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03118/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03118/status.svg
   :target: https://doi.org/10.21105/joss.03118

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[majensen]

Great work @aghaynes @amoeba @TomKellyGenetics - you gave me an editorial hat trick this month! Whedon and I really appreciate all the effort.

[kyleniemeyer]

Looks like the DOI is still not resolving, which is likely a delay with CrossRef. In the meantime you can see the published article here: https://joss.theoj.org/papers/10.21105/joss.03118

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03118/status.svg)](https://doi.org/10.21105/joss.03118)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03118">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03118/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03118/status.svg
   :target: https://doi.org/10.21105/joss.03118

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[aghaynes]

Thanks for the help everyone!

[amoeba]

Congrats @aghaynes! It was a pleasure to review. And thanks @majensen and @TomKellyGenetics for the help.

[TomKellyGenetics]

Well done @aghaynes! Delighted to see this accepted. Best of luck for your future endeavours.