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[REVIEW]: mixComp: An R package for estimating complexity of a mixture #4354

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editorialbot opened this issue Apr 27, 2022 · 89 comments
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editorialbot commented Apr 27, 2022

Submitting author: @yuliadm (Yulia)
Repository: https://github.com/yuliadm/mixComp
Branch with paper.md (empty if default branch):
Version: v0.1.3
Editor: @jbytecode
Reviewers: @Athene-ai, @zhiiiyang
Archive: 10.5281/zenodo.6660840

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/cfa75cededd35ccadce21d2048a68617"><img src="https://joss.theoj.org/papers/cfa75cededd35ccadce21d2048a68617/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/cfa75cededd35ccadce21d2048a68617/status.svg)](https://joss.theoj.org/papers/cfa75cededd35ccadce21d2048a68617)

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

@Athene-ai & @zhiiiyang, 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 @jbytecode 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 @Athene-ai

📝 Checklist for @zhiiiyang

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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

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.13 s (166.4 files/s, 96385.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             2            364              8           4581
R                               13            979           1604           2333
Markdown                         3            415              0           1166
TeX                              1             45              1            493
Rmd                              1            186            380            150
YAML                             2              2              4             31
-------------------------------------------------------------------------------
SUM:                            22           1991           1997           8754
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1002

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

OK DOIs

- 10.2307/3318593 is OK
- 10.1016/j.csda.2009.05.013 is OK
- 10.1016/j.csda.2006.06.006 is OK
- 10.1023/A:1003839420071 is OK
- 10.1002/9780470316801 is OK
- 10.2307/2291601 is OK
- 10.18637/jss.v011.i08 is OK
- 10.1016/j.csda.2006.08.014 is OK
- 10.18637/jss.v028.i04 is OK
- 10.1198/016214506000000555 is OK
- 10.2307/2347385 is OK
- 10.1007/978-1-4612-4432-5 is OK
- 10.32614/rj-2016-021 is OK
- 10.1007/978-0-387-75692-9_5 is OK
- 10.1016/j.csda.2014.10.021 is OK
- 10.1016/j.csda.2020.107014 is OK
- 10.1016/j.jspi.2019.04.006 is OK
- 10.2307/2341080 is OK
- 10.1080/01621459.1994.10476467 is OK
- 10.1080/00401706.1992.10484955 is OK
- 10.1111/1467-9868.00095 is OK
- 10.18637/jss.v051.i12 is OK
- 10.2307/3315623 is OK
- 10.1016/j.patrec.2004.07.007 is OK
- 10.1214/aoms/1177697626 is OK
- 10.1214/aoms/1177703862 is OK
- 10.1111/j.2517-6161.1977.tb01600.x is OK
- 10.1214/aos/1176346059 is OK
- 10.1214/aos/1176346245 is OK
- 10.2307/2531224 is OK
- 10.1002/0471721182 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@jbytecode
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@Athene-ai, please create your checklist typing: @editorialbot generate my checklist

@zhiiiyang, please create your checklist typing: @editorialbot generate my checklist

@zhiiiyang
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zhiiiyang commented Apr 27, 2022

Review checklist for @zhiiiyang

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/yuliadm/mixComp?
  • 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 (@yuliadm) 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?

@jbytecode
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jbytecode commented Apr 27, 2022

Dear @Athene-ai and @zhiiiyang

Thank you for accepting our invitation. You have just created your checklist. Please follow the instructions at the top of this page. Whenever you finish a review task, you can check the corresponding item on.

You can always interact with the other reviewers, the author(s), and the editor (me). You can also create issues in the target repository but please mention this thread so we can follow up what is going on outside of the main thread.

Please do not hesitate to ask me anything and ping me when you need help.

Thank you!

@zhiiiyang
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@jbytecode @yuliadm I have completed my review. Please see all the comments above. #4354 (comment)

@yuliadm has completed some requests in the dev branch and will merge them into the main branch once all requests in yuliadm/mixComp#2 are addressed. @Athene-ai, you might want to review the dev branch for the latest commits if the merge hasn't been completed by that time.

@Athene-ai
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Athene-ai commented May 9, 2022

@zhiiiyang many thanks for the advise 😉

@jbytecode
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@zhiiiyang - thank you for your review. However there are still unchecked task items and it seems your review is not complete. Please do not modify the checklist entry (just click the checkboxes) and post your reviewing report as posts in this issue.

@jbytecode
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@Athene-ai - could you please update your status and tell us how is your review going? Thank you in advance.

@zhiiiyang
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@jbytecode, I see. I just check off the checklist and posted all my comments below in a separate post.

Additional comments

  • Please add the unit tests Please add unit tests yuliadm/mixComp#1
  • Please reorganize the files into the corresponding folders. See more details Miscellaneous requests yuliadm/mixComp#2
  • Please add community guidelines Miscellaneous requests yuliadm/mixComp#2
  • Since the R package only has commits from Yulia. May I ask for the contributions of the other three co-authors?
  • Can authors comment on another R package, rebmix, compared to mixComp?
  • Please reduce unnecessary progress output to simplify printed output. Regarding the progress output  yuliadm/mixComp#3
  • For someone who doesn't know the MLE.function for certain, is there a convenient way to compare across different distributions and select the optimal one?
  • In readme.md, it said that nonparamHankel might not produce correct results. In https://github.com/yuliadm/mixComp#the-children-dataset, it used both functions paramHankel and paramHankel.scaled to conclude that the cluster is equal to 2. If we can't make results without having consistent results from both functions, should it be set as default? What if these two functions return different results?
  • Is the plot over different complexity j only available for nonparamHankel? Can we have that implemented for results from hellinger.cont or hellinger.disc

@jbytecode
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@yuliadm - please follow the suggestions, apply them, and report here when all of the stuff is complete .

@zhiiiyang - please review the authors' corrections (if exists) and report your final thougths.

thank you in advance.

@jbytecode
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@Athene-ai - could you please update your status? Thank you in advance!

@Athene-ai
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Hi @jbytecode !

I am finishing my review and next week I will upload it

@Athene-ai
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Athene-ai commented May 20, 2022

Review checklist for @Athene-ai

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/yuliadm/mixComp?
  • 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 (@yuliadm) 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?

@Athene-ai
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@jbytecode I just check off the checklist and posted all my comments below in a separate post.

@jbytecode
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@Athene-ai do you have any suggestions, comments,or improvements?

@jbytecode
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@Athene-ai - please suggest corrections and make comments. Whenever the authors apply them check off the corresponding item. After finishing the review please provide a summary and your decision. thank you.

@jbytecode
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@editorialbot check references

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

OK DOIs

- 10.2307/3318593 is OK
- 10.1016/j.csda.2009.05.013 is OK
- 10.1016/j.csda.2006.06.006 is OK
- 10.1023/A:1003839420071 is OK
- 10.1002/9780470316801 is OK
- 10.2307/2291601 is OK
- 10.18637/jss.v011.i08 is OK
- 10.1016/j.csda.2006.08.014 is OK
- 10.18637/jss.v028.i04 is OK
- 10.1198/016214506000000555 is OK
- 10.2307/2347385 is OK
- 10.1007/978-1-4612-4432-5 is OK
- 10.32614/rj-2016-021 is OK
- 10.1007/978-0-387-75692-9_5 is OK
- 10.1016/j.csda.2014.10.021 is OK
- 10.1016/j.csda.2020.107014 is OK
- 10.1016/j.jspi.2019.04.006 is OK
- 10.2307/2341080 is OK
- 10.1080/01621459.1994.10476467 is OK
- 10.1080/00401706.1992.10484955 is OK
- 10.1111/1467-9868.00095 is OK
- 10.18637/jss.v051.i12 is OK
- 10.2307/3315623 is OK
- 10.1016/j.patrec.2004.07.007 is OK
- 10.1214/aoms/1177697626 is OK
- 10.1214/aoms/1177703862 is OK
- 10.1111/j.2517-6161.1977.tb01600.x is OK
- 10.1214/aos/1176346059 is OK
- 10.1214/aos/1176346245 is OK
- 10.2307/2531224 is OK
- 10.1002/0471721182 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@jbytecode
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@editorialbot generate pdf

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

@jbytecode
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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.2307/3318593 is OK
- 10.1016/j.csda.2009.05.013 is OK
- 10.1016/j.csda.2006.06.006 is OK
- 10.1023/A:1003839420071 is OK
- 10.1002/9780470316801 is OK
- 10.2307/2291601 is OK
- 10.18637/jss.v011.i08 is OK
- 10.1016/j.csda.2006.08.014 is OK
- 10.18637/jss.v028.i04 is OK
- 10.1198/016214506000000555 is OK
- 10.2307/2347385 is OK
- 10.1007/978-1-4612-4432-5 is OK
- 10.32614/rj-2016-021 is OK
- 10.1007/978-0-387-75692-9_5 is OK
- 10.1016/j.csda.2014.10.021 is OK
- 10.1016/j.csda.2020.107014 is OK
- 10.1016/j.jspi.2019.04.006 is OK
- 10.2307/2341080 is OK
- 10.1080/01621459.1994.10476467 is OK
- 10.1080/00401706.1992.10484955 is OK
- 10.1111/1467-9868.00095 is OK
- 10.18637/jss.v051.i12 is OK
- 10.2307/3315623 is OK
- 10.1016/j.patrec.2004.07.007 is OK
- 10.1214/aoms/1177697626 is OK
- 10.1214/aoms/1177703862 is OK
- 10.1111/j.2517-6161.1977.tb01600.x is OK
- 10.1214/aos/1176346059 is OK
- 10.1214/aos/1176346245 is OK
- 10.2307/2531224 is OK
- 10.1002/0471721182 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

Check final proof 👉 openjournals/joss-papers#3301

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3301, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 25, 2022
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arfon commented Jun 26, 2022

@yuliadm – I made some slight changes to your paper to match the current preferred format for denoting equal authorship and corresponding authorship: yuliadm/mixComp#8

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arfon commented Jun 26, 2022

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.2307/3318593 is OK
- 10.1016/j.csda.2009.05.013 is OK
- 10.1016/j.csda.2006.06.006 is OK
- 10.1023/A:1003839420071 is OK
- 10.1002/9780470316801 is OK
- 10.2307/2291601 is OK
- 10.18637/jss.v011.i08 is OK
- 10.1016/j.csda.2006.08.014 is OK
- 10.18637/jss.v028.i04 is OK
- 10.1198/016214506000000555 is OK
- 10.2307/2347385 is OK
- 10.1007/978-1-4612-4432-5 is OK
- 10.32614/rj-2016-021 is OK
- 10.1007/978-0-387-75692-9_5 is OK
- 10.1016/j.csda.2014.10.021 is OK
- 10.1016/j.csda.2020.107014 is OK
- 10.1016/j.jspi.2019.04.006 is OK
- 10.2307/2341080 is OK
- 10.1080/01621459.1994.10476467 is OK
- 10.1080/00401706.1992.10484955 is OK
- 10.1111/1467-9868.00095 is OK
- 10.18637/jss.v051.i12 is OK
- 10.2307/3315623 is OK
- 10.1016/j.patrec.2004.07.007 is OK
- 10.1214/aoms/1177697626 is OK
- 10.1214/aoms/1177703862 is OK
- 10.1111/j.2517-6161.1977.tb01600.x is OK
- 10.1214/aos/1176346059 is OK
- 10.1214/aos/1176346245 is OK
- 10.2307/2531224 is OK
- 10.1002/0471721182 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

Check final proof 👉 openjournals/joss-papers#3308

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3308, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@arfon
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arfon commented Jun 26, 2022

Hrm, the formatting for Lilian Mueller is now a little weird with the updated formatting. @yuliadm – is there any particular need to specify/highlight that author as a 'contributor'?

@yuliadm
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yuliadm commented Jun 26, 2022

@arfon no specific reason, equal contribution would be OK! So I fixed it!

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arfon commented Jun 26, 2022

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.2307/3318593 is OK
- 10.1016/j.csda.2009.05.013 is OK
- 10.1016/j.csda.2006.06.006 is OK
- 10.1023/A:1003839420071 is OK
- 10.1002/9780470316801 is OK
- 10.2307/2291601 is OK
- 10.18637/jss.v011.i08 is OK
- 10.1016/j.csda.2006.08.014 is OK
- 10.18637/jss.v028.i04 is OK
- 10.1198/016214506000000555 is OK
- 10.2307/2347385 is OK
- 10.1007/978-1-4612-4432-5 is OK
- 10.32614/rj-2016-021 is OK
- 10.1007/978-0-387-75692-9_5 is OK
- 10.1016/j.csda.2014.10.021 is OK
- 10.1016/j.csda.2020.107014 is OK
- 10.1016/j.jspi.2019.04.006 is OK
- 10.2307/2341080 is OK
- 10.1080/01621459.1994.10476467 is OK
- 10.1080/00401706.1992.10484955 is OK
- 10.1111/1467-9868.00095 is OK
- 10.18637/jss.v051.i12 is OK
- 10.2307/3315623 is OK
- 10.1016/j.patrec.2004.07.007 is OK
- 10.1214/aoms/1177697626 is OK
- 10.1214/aoms/1177703862 is OK
- 10.1111/j.2517-6161.1977.tb01600.x is OK
- 10.1214/aos/1176346059 is OK
- 10.1214/aos/1176346245 is OK
- 10.2307/2531224 is OK
- 10.1002/0471721182 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

Check final proof 👉 openjournals/joss-papers#3309

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3309, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@arfon
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arfon commented Jun 26, 2022

@editorialbot accept

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

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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04354 joss-papers#3310
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04354
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Jun 26, 2022
@arfon
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arfon commented Jun 26, 2022

@Athene-ai, @zhiiiyang – many thanks for your reviews here and to @jbytecode 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 ✨

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

@arfon arfon closed this as completed Jun 26, 2022
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🎉🎉🎉 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.04354/status.svg)](https://doi.org/10.21105/joss.04354)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04354">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04354/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04354/status.svg
   :target: https://doi.org/10.21105/joss.04354

This is how it will look in your documentation:

DOI

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The 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:

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yuliadm commented Jun 28, 2022

@jbytecode , @zhiiiyang , @Athene-ai , @arfon
Thank you all so much!!!

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