[REVIEW]: PCRedux: A Quantitative PCR Machine Learning Toolkit #4407

editorialbot · 2022-05-20T08:26:03Z

Submitting author: @devSJR (Stefan Rödiger)
Repository: https://github.com/PCRuniversum/PCRedux
Branch with paper.md (empty if default branch):
Version: 1.1-2
Editor: @csoneson
Reviewers: @jaybee84, @markziemann
Archive: 10.5281/zenodo.7009124

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/860ed94423d2d9908209c37ed8aec46b"><img src="https://joss.theoj.org/papers/860ed94423d2d9908209c37ed8aec46b/status.svg"></a>
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

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-05-20T08:26:04Z

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 · 2022-05-20T08:26:08Z

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
-------------------------------------------------------------------------------
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 · 2022-05-20T08:26:10Z

Wordcount for paper.md is 2249

editorialbot · 2022-05-20T08:26:15Z

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 · 2022-05-20T08:27:22Z

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

csoneson · 2022-05-20T08:30:16Z

👋🏼 @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 · 2022-05-20T13:10:49Z

@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 · 2022-05-20T13:17:42Z

@editorialbot generate pdf

devSJR · 2022-05-20T13:18:45Z

@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 · 2022-05-20T13:18:53Z

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

devSJR · 2022-05-20T13:55:07Z

@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 · 2022-05-20T13:55:14Z

@editorialbot generate pdf

editorialbot · 2022-05-20T13:56:34Z

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

csoneson · 2022-06-05T07:24:54Z

👋🏻 @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 · 2022-06-06T03:25:17Z

Review checklist for @jaybee84

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 https://github.com/PCRuniversum/PCRedux?
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 (@devSJR) 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, who the target audience is, and its relation to other work?
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?

devSJR · 2022-06-07T06:54:01Z

@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 · 2022-06-07T11:58:43Z

Review checklist for @markziemann

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 https://github.com/PCRuniversum/PCRedux?
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 (@devSJR) 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, who the target audience is, and its relation to other work?
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?

markziemann · 2022-06-07T15:17:14Z

👋🏻 @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 · 2022-06-07T16:02:21Z

Thank you @markziemann 🙂

csoneson · 2022-06-19T21:19:16Z

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

jaybee84 · 2022-06-22T17:46:33Z

@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 · 2022-06-29T05:56:46Z

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!

devSJR · 2022-08-03T12:17:07Z

@editorialbot generate pdf

editorialbot · 2022-08-03T12:18:57Z

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

devSJR · 2022-08-19T09:07:14Z

Thanks @devSJR! I went through the paper again and I think this looks good - I sent another small PR with a couple of minor fixes. Regarding the attachment, I would suggest that you upload the current vignette to e.g. Zenodo or FigShare, and refer to that (you would get a DOI).

Once these things are sorted, the next steps are as follows:
* [ ]  Make a tagged release of the software, and list the version tag of the archived version here.

* [ ]  Archive the reviewed software in Zenodo or a similar service

* [ ]  Check that the archival deposit (e.g., in Zenodo) has the correct metadata. In particular, the title and author list should be identical to those of the paper. You can also add the authors' ORCID.

* [ ]  Please list the DOI of the archived version here.
I can then move forward with accepting the submission.

@csoneson, finally here are the missing bits.

version tag of the archived version: 1.1-2
DOI of the archived version 10.5281/zenodo.7009124
https://doi.org/10.5281/zenodo.7009124

csoneson · 2022-08-21T14:02:48Z

@editorialbot check references

editorialbot · 2022-08-21T14:03:14Z

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

OK DOIs

- 10.5281/zenodo.6957714 is OK
- 10.32614/RJ-2015-011 is OK
- 10.32614/RJ-2013-024 is OK
- 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 · 2022-08-21T14:03:35Z

@editorialbot set 10.5281/zenodo.7009124 as archive

editorialbot · 2022-08-21T14:03:37Z

Done! Archive is now 10.5281/zenodo.7009124

csoneson · 2022-08-21T14:03:56Z

@editorialbot set 1.1-2 as version

editorialbot · 2022-08-21T14:03:57Z

Done! version is now 1.1-2

csoneson · 2022-08-21T14:06:12Z

@devSJR Thanks! I'll hand over now to an associate EiC for the final steps. Thanks for submitting to JOSS!

csoneson · 2022-08-21T14:06:17Z

@editorialbot recommend-accept

editorialbot · 2022-08-21T14:06:18Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-08-21T14:06:44Z

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

OK DOIs

- 10.5281/zenodo.6957714 is OK
- 10.32614/RJ-2015-011 is OK
- 10.32614/RJ-2013-024 is OK
- 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

editorialbot · 2022-08-21T14:08:14Z

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3454, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon · 2022-08-21T14:57:49Z

@editorialbot accept

editorialbot · 2022-08-21T14:57:50Z

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

editorialbot · 2022-08-21T15:00:09Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-08-21T15:00:10Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.04407 joss-papers#3455
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04407
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2022-08-21T15:04:46Z

@jaybee84, @markziemann – many thanks for your reviews here and to @csoneson for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@devSJR – your paper is now accepted and published in JOSS ⚡🚀💥

editorialbot · 2022-08-21T15:04:47Z

🎉🎉🎉 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.04407/status.svg)](https://doi.org/10.21105/joss.04407)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04407">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04407/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04407/status.svg
   :target: https://doi.org/10.21105/joss.04407

This is how it will look in your documentation:

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devSJR · 2022-08-21T15:20:00Z

@arfon @jaybee84 @markziemann @csoneson

Thanks!

editorialbot added CSS JavaScript R review labels May 20, 2022

editorialbot assigned csoneson May 20, 2022

editorialbot mentioned this issue May 20, 2022

[PRE REVIEW]: PCRedux: A Quantitative PCR Machine Learning Toolkit #4390

Closed

This was referenced Jun 7, 2022

How to contribute? PCRuniversum/PCRedux#9

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README needs to be more descriptive PCRuniversum/PCRedux#10

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editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Aug 21, 2022

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arfon closed this as completed Aug 21, 2022

editorialbot mentioned this issue Oct 4, 2023

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This was referenced Aug 19, 2024

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[PRE REVIEW]: PeakPerformance - A tool for Bayesian inference-based fitting of LC-MS/MS peaks #7141

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[PRE REVIEW]: funkyheatmap: Visualising data frames with mixed data types #7590

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[REVIEW]: PCRedux: A Quantitative PCR Machine Learning Toolkit #4407

[REVIEW]: PCRedux: A Quantitative PCR Machine Learning Toolkit #4407

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Review checklist for @jaybee84

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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markziemann commented Jun 7, 2022 • edited Loading

Review checklist for @markziemann

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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