[REVIEW]: PCRedux: A Quantitative PCR Machine Learning Toolkit

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@devSJR@csoneson<!--end-editor-- Reviewers: @jaybee84, @markziemann Archive: 10.5281/zenodo.7009124

Status

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Markdown: [![status](https://joss.theoj.org/papers/860ed94423d2d9908209c37ed8aec46b/status.svg)](https://joss.theoj.org/papers/860ed94423d2d9908209c37ed8aec46b)

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

@jaybee84 & @markziemann, 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 @csoneson 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 @jaybee84

📝 Checklist for @markziemann

editorialbot commented 2 years 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:

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

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (1038.8 files/s, 170467.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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HTML                            23           1123            261           3692
CSS                              3            360             73           1961
TeX                              2            144             10           1890
R                               41            399           1086           1659
Markdown                         4             77              0            471
JavaScript                       5             59             27            287
SVG                              2              0              1            122
YAML                             3             11              0             52
Rmd                              1              1             18              0
-------------------------------------------------------------------------------
SUM:                            84           2174           1476          10134
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 2249

editorialbot commented 2 years ago

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

OK DOIs

- 10.3233/JCB-15025 is OK
- 10.1373/clinchem.2014.230656 is OK
- 10.1093/bioinformatics/btx528 is OK
- 10.1093/bioinformatics/btv205 is OK
- 10.1016/j.bdq.2018.08.001 is OK
- 10.1038/srep38951 is OK
- 10.1038/s41598-021-00827-0 is OK
- 10.3390/life11111163 is OK
- 10.1198/106186007X178663 is OK
- 10.1186/gb-2004-5-10-r80 is OK
- 10.1186/1471-2105-9-221 is OK
- 10.1093/bioinformatics/btn227 is OK
- 10.1016/j.bdq.2014.08.002 is OK
- 10.1016/j.ymeth.2009.12.006 is OK
- 10.18637/jss.v023.i03 is OK
- 10.18637/jss.v062.i07 is OK
- 10.18637/jss.v032.i03 is OK
- 10.1016/j.ymeth.2012.08.011 is OK
- 10.1016/j.bdq.2015.07.001 is OK
- 10.1261/rna.059063.116 is OK
- 10.1016/j.bdq.2017.11.002 is OK
- 10.1016/S0304-3940(02)01423-4 is OK
- 10.1093/clinchem/hvab052 is OK
- 10.1016/j.tibtech.2018.12.002 is OK
- 10.1186/1471-2105-15-138 is OK
- 10.1093/gigascience/giy077 is OK
- 10.1111/anzs.12200 is OK
- 10.3390/life11111163 is OK
- 10.18637/jss.v049.i09 is OK

MISSING DOIs

- 10.32614/rj-2011-002 may be a valid DOI for title: testthat: Get Started with Testing
- 10.32614/rj-2014-015 may be a valid DOI for title: Archiving Reproducible Research with R and Dataverse

INVALID DOIs

- None

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:

csoneson commented 2 years ago

👋🏼 @devSJR, @jaybee84, @markziemann - this is the review thread for the submission. All of our communications will happen here from now on.

Please check the post at the top of the issue for instructions on how to generate your own review checklist. 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 directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!

devSJR commented 2 years ago

@csoneson, editorialbot found two MISSING DOIs

10.32614/rj-2011-002 may be a valid DOI for title: testthat: Get Started with Testing
10.32614/rj-2014-015 may be a valid DOI for title: Archiving Reproducible Research with R and Dataverse

The bot is right. We cited the packages without the DOIs of the articles of the R Journal. We will correct this accordingly.

devSJR commented 2 years ago

@editorialbot generate pdf

devSJR commented 2 years ago

@csoneson, editorialbot found two MISSING DOIs
* 10.32614/rj-2011-002 may be a valid DOI for title: testthat: Get Started with Testing

* 10.32614/rj-2014-015 may be a valid DOI for title: Archiving Reproducible Research with R and Dataverse
The bot is right. We cited the packages without the DOIs of the articles of the R Journal. We will correct this accordingly.

Done

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:

devSJR commented 2 years ago

@csoneson, I have found a duplication of a citation (R Core Team). This is fixed now. I will not touch the paper anymore unless you request me to do so.

devSJR commented 2 years ago

@editorialbot generate pdf

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:

csoneson commented 2 years ago

👋🏻 @jaybee84, @markziemann - just wanted to check in on your reviews. Note that you each need to generate your own review checklist (see instructions above). Let me know if you have any questions!

jaybee84 commented 2 years ago

Review checklist for @jaybee84

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/PCRuniversum/PCRedux?
[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 (@devSJR) 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

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?

devSJR commented 2 years ago

@csoneson I noticed in the checklist under General checks the entry "License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?"

So far the LICENSE (MIT) was stated in the DESCRIPTION file. However, there was no LICENSE text. I have added the text from https://opensource.org/licenses/MIT

markziemann commented 2 years ago

Review checklist for @markziemann

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/PCRuniversum/PCRedux?
[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 (@devSJR) 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

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?

markziemann commented 2 years ago

👋🏻 @jaybee84, @markziemann - just wanted to check in on your reviews. Note that you each need to generate your own review checklist (see instructions above). Let me know if you have any questions!

@csoneson Checklist is complete. All good from my end. Great piece of work.

csoneson commented 2 years ago

Thank you @markziemann 🙂

csoneson commented 2 years ago

👋🏻 @jaybee84 - could you update us on the status of your review? Thanks!

jaybee84 commented 2 years ago

@csoneson Apologies for the delayed response due to conference related travel. I should be able to complete this review by the end of the week. Thanks for your patience.

csoneson commented 2 years ago

I should be able to complete this review by the end of the week. Thanks for your patience.

@jaybee84 - just a gentle reminder of your review here. Thanks!

csoneson commented 2 years ago

👋🏻 Just wanted to check in what's the state of the review/discussion here. Thanks!

devSJR commented 2 years ago

Hello @csoneson,

Thanks for asking.

We try to reproduce an error/solve a problem that @jaybee84 observed.

https://github.com/PCRuniversum/PCRedux/issues/11

Since we pass our CI, the one of CRAN and have no problems on the machines we tested, things are progressing slowly ATM.

Kind regards Stefan

jaybee84 commented 2 years ago

Thanks @devSJR @csoneson for your patience with this review. My review is complete and I am happy to recommend acceptance for this software.

csoneson commented 2 years ago

Thank you @jaybee84!

@devSJR - I will take a quick look through the submission as well, and get back to you shortly with the next steps.

devSJR commented 2 years ago

@jaybee84 thanks!

csoneson commented 2 years ago

@editorialbot generate pdf

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:

csoneson commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.3233/JCB-15025 is OK
- 10.1373/clinchem.2014.230656 is OK
- 10.1093/bioinformatics/btx528 is OK
- 10.1093/bioinformatics/btv205 is OK
- 10.1016/j.bdq.2018.08.001 is OK
- 10.1038/srep38951 is OK
- 10.1038/s41598-021-00827-0 is OK
- 10.3390/life11111163 is OK
- 10.1198/106186007X178663 is OK
- 10.1186/gb-2004-5-10-r80 is OK
- 10.1186/1471-2105-9-221 is OK
- 10.1093/bioinformatics/btn227 is OK
- 10.1016/j.bdq.2014.08.002 is OK
- 10.1016/j.ymeth.2009.12.006 is OK
- 10.32614/rj-2011-002 is OK
- 10.18637/jss.v023.i03 is OK
- 10.18637/jss.v062.i07 is OK
- 10.18637/jss.v032.i03 is OK
- 10.1016/j.ymeth.2012.08.011 is OK
- 10.1016/j.bdq.2015.07.001 is OK
- 10.1261/rna.059063.116 is OK
- 10.1016/j.bdq.2017.11.002 is OK
- 10.1016/S0304-3940(02)01423-4 is OK
- 10.1093/clinchem/hvab052 is OK
- 10.1016/j.tibtech.2018.12.002 is OK
- 10.1186/1471-2105-15-138 is OK
- 10.32614/rj-2014-015 is OK
- 10.1093/gigascience/giy077 is OK
- 10.1111/anzs.12200 is OK
- 10.3390/life11111163 is OK
- 10.18637/jss.v049.i09 is OK

MISSING DOIs

- None

INVALID DOIs

- None

csoneson commented 2 years ago

👋🏻 @devSJR - I've sent a small PR to fix some inconsistencies in the references in the paper. Moreover, at the moment the paper is a bit too long - a JOSS paper should be between 250 and 1,000 words (see the guidelines), while this one is over 2,000 words. Could you try to cut this down a bit to get closer to the guidelines? I think you can remove some redundancy in both the Summary and Statement of Need sections, and perhaps some details can be referred to the package documentation. From my quick look, I would also suggest to move a brief (non-technical) explanation of what a "positive" and "negative" curve are a bit earlier in the paper, to make this easier to follow for a reader.

devSJR commented 2 years ago

Dear @csoneson,

Thanks for the feedback. We will shorten the paper ASAP and merge the bibliography.

Kind regards

devSJR commented 2 years ago

@editorialbot generate pdf

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:

devSJR commented 2 years ago

@editorialbot generate pdf

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:

devSJR commented 2 years ago

@editorialbot generate pdf

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:

devSJR commented 2 years ago

@editorialbot generate pdf

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:

devSJR commented 2 years ago

@editorialbot generate pdf

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:

devSJR commented 2 years ago

@editorialbot generate pdf

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:

devSJR commented 2 years ago

@editorialbot generate pdf

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:

devSJR commented 2 years ago

@editorialbot generate pdf

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:

devSJR commented 2 years ago

Dear @csoneson,

we have improved the paper as requested.

Is it possible to add the vignette of the PCRedux package presented here (v. 1.1-2) as an attachment to a JOSS article? The reason for this is that the article will not change, while the vignette (which describes all the data, functions etc.) is part of an evolving system. We refer the reader to some information in the vignette in the article. We would like to make sure that these references are correct in the future.

Yours sincerely

@devSJR @anspiess @michbur

openjournals / joss-reviews