[REVIEW]: pivmet: an R package proposing pivotal methods for consensus clustering and mixture modelling #6461

editorialbot · 2024-03-10T22:16:55Z

Submitting author: @LeoEgidi (LEONARDO EGIDI)
Repository: https://github.com/LeoEgidi/pivmet
Branch with paper.md (empty if default branch): master
Version: v0.6.0
Editor: @skanwal
Reviewers: @adriancorrendo, @larryshamalama
Archive: 10.5281/zenodo.11243277

Status

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Markdown: [![status](https://joss.theoj.org/papers/27410f99af44fd07417b87b8ec193ef5/status.svg)](https://joss.theoj.org/papers/27410f99af44fd07417b87b8ec193ef5)

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

@adriancorrendo & @larryshamalama, 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 @skanwal 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 @adriancorrendo

📝 Checklist for @larryshamalama

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

editorialbot · 2024-03-10T22:16:58Z

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editorialbot · 2024-03-10T22:17:38Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1098.3 files/s, 258564.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               14            441            941           2031
HTML                             2             70              5            983
TeX                              2             76              0            518
Markdown                         4            108              0            305
Rmd                              3            187            245            206
YAML                             1              1              1              3
-------------------------------------------------------------------------------
SUM:                            26            883           1192           4046
-------------------------------------------------------------------------------

Commit count by author:

   503	Leonardo Egidi
   168	LeoEgidi
     6	Leonardo

editorialbot · 2024-03-10T22:17:42Z

Paper file info:

📄 Wordcount for paper.md is 1196

✅ The paper includes a Statement of need section

editorialbot · 2024-03-10T22:17:44Z

License info:

🔴 Failed to discover a valid open source license

editorialbot · 2024-03-10T22:17:48Z

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

OK DOIs

- None

MISSING DOIs

- No DOI given, and none found for title: A conceptual introduction to Hamiltonian Monte Car...
- No DOI given, and none found for title: K-means seeding via MUS algorithm
- 10.1007/978-3-319-73906-9_7 may be a valid DOI for title: Maxima Units Search (MUS) algorithm: methodology a...
- 10.1007/s11222-017-9774-2 may be a valid DOI for title: Relabelling in Bayesian mixture models by pivotal ...
- No DOI given, and none found for title: Cluster ensembles - A knowledge reuse framework fo...
- 10.1109/tpami.2005.113 may be a valid DOI for title: Combining multiple clusterings using evidence accu...
- No DOI given, and none found for title: k-means++: The advantages of careful seeding
- No DOI given, and none found for title: Bayesian solutions to the label switching problem
- 10.1214/09-ba414 may be a valid DOI for title: Improved criteria for clustering based on the post...
- 10.1111/1467-9868.00265 may be a valid DOI for title: Dealing with label switching in mixture models
- 10.1080/03610926.2010.526741 may be a valid DOI for title: Bayesian mixture labeling and clustering
- 10.1214/088342305000000016 may be a valid DOI for title: Markov chain Monte Carlo methods and the label swi...
- 10.1198/jasa.2009.0237 may be a valid DOI for title: Bayesian mixture labeling by highest posterior den...
- 10.1198/016214501750333063 may be a valid DOI for title: Markov chain Monte Carlo estimation of classical a...
- 10.1198/0003130043286 may be a valid DOI for title: Difficulties in drawing inferences with finite-mix...
- 10.1080/00949655.2012.707201 may be a valid DOI for title: An online Bayesian mixture labelling method by min...
- 10.1198/jcgs.2010.09008 may be a valid DOI for title: An artificial allocations based solution to the la...
- No DOI given, and none found for title: label.switching: An R package for dealing with the...
- No DOI given, and none found for title: label.switching: Relabelling MCMC Outputs of Mixtu...
- No DOI given, and none found for title: bayesmix: Bayesian Mixture Models with JAGS
- 10.2307/2531224 may be a valid DOI for title: Statistical analysis of finite mixture distributio...
- No DOI given, and none found for title: Finite Mixture Models
- No DOI given, and none found for title: Comparing partitions
- 10.1080/10618600.2012.735624 may be a valid DOI for title: Label switching in Bayesian mixture models: Determ...
- 10.1007/978-0-387-38983-7 may be a valid DOI for title: Bayesian core: a practical approach to computation...
- 10.1016/s0169-7161(05)25016-2 may be a valid DOI for title: Bayesian modelling and inference on mixtures of di...
- 10.2307/2669477 may be a valid DOI for title: Computational and inferential difficulties with mi...
- 10.1007/s11222-009-9129-8 may be a valid DOI for title: Probabilistic relabelling strategies for the label...
- No DOI given, and none found for title: Bayesian inference for mixture models via Monte Ca...
- 10.1007/bf00143556 may be a valid DOI for title: Sampling from multimodal distributions using tempe...
- No DOI given, and none found for title: On Bayesian analysis of mixtures with an unknown n...
- 10.2307/2289993 may be a valid DOI for title: Density estimation with confidence sets exemplifie...
- No DOI given, and none found for title: foreign: Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’...
- No DOI given, and none found for title: MASS: Support Functions and Datasets for Venables ...
- No DOI given, and none found for title: mclust: Gaussian Mixture Modelling for Model-Based...
- No DOI given, and none found for title: pivmet: Pivotal Methods for Bayesian Relabelling a...
- No DOI given, and none found for title: RStan: the R interface to Stan
- No DOI given, and none found for title: rjags: Bayesian graphical models using MCMC
- No DOI given, and none found for title: runjags: An R package providing interface utilitie...
- 10.1214/08-aoas191 may be a valid DOI for title: A weakly informative default prior distribution fo...
- No DOI given, and none found for title: Prior distributions for variance parameters in hie...
- 10.1214/009053604000001147 may be a valid DOI for title: Spike and slab variable selection: frequentist and...
- 10.2307/1390653 may be a valid DOI for title: Markov chain sampling methods for Dirichlet proces...
- No DOI given, and none found for title: Bayesian density estimation by mixtures of normal ...
- 10.2307/2291069 may be a valid DOI for title: Bayesian density estimation and inference using mi...
- No DOI given, and none found for title: dirichletprocess: An R Package for Fitting Complex...
- No DOI given, and none found for title: A Bayesian analysis of some nonparametric problems
- 10.1007/s11634-018-0329-y may be a valid DOI for title: From here to infinity: sparse finite versus Dirich...
- 10.1007/s11222-014-9500-2 may be a valid DOI for title: Model-based clustering based on sparse finite Gaus...
- 10.1111/anzs.12350 may be a valid DOI for title: Spying on the prior of the number of data clusters...
- No DOI given, and none found for title: Model-based clustering, discriminant analysis, and...

INVALID DOIs

- None

editorialbot · 2024-03-10T22:18:30Z

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

adriancorrendo · 2024-03-11T04:02:28Z

Review checklist for @adriancorrendo

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/LeoEgidi/pivmet?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@LeoEgidi) 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
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

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?

arfon · 2024-03-24T08:56:12Z

@LeoEgidi – this may have been discussed already but what license is this software released under? JOSS requires software published here to have a file named LICENSE at the root of the repository with the whole text of an OSI-approved license.

LeoEgidi · 2024-03-26T14:25:26Z

@LeoEgidi – this may have been discussed already but what license is this software released under? JOSS requires software published here to have a file named LICENSE at the root of the repository with the whole text of an OSI-approved license.

Hi @arfon , the License, as documented by the description file, is GPL-2

LeoEgidi · 2024-03-26T14:26:22Z

I investigate a bit more

LeoEgidi · 2024-03-26T14:32:36Z

Ok, now I put a LICENSE file at the repository root as suggested

@LeoEgidi – this may have been discussed already but what license is this software released under? JOSS requires software published here to have a file named LICENSE at the root of the repository with the whole text of an OSI-approved license.

Hi @arfon , the License, as documented by the description file, is GPL-2

adriancorrendo · 2024-04-05T04:23:56Z

Hi @LeoEgidi .
How are you? Thanks for developing the pivmet package and submitting it for review here.

I've just created an issue on your repo with my review comments at LeoEgidi/pivmet#1 (comment)

Could you please take a look?

Thanks,
Adrian

LeoEgidi · 2024-04-08T10:34:42Z

Hi @adriancorrendo , thanks a lot for your comments, I took a first look. I'll try to get a deeper look this week, or at most next week. Should I reply your points here or directly in the repo? What do you prefer? Thanks a lot

adriancorrendo · 2024-04-11T17:50:59Z

Hi @adriancorrendo , thanks a lot for your comments, I took a first look. I'll try to get a deeper look this week, or at most next week. Should I reply your points here or directly in the repo? What do you prefer? Thanks a lot

Hi Leo, how are you?
You would need to answer on the issue I created in the package repo.
Once you address those comments, I'll start checking the remaining boxes until giving my full ok. That's what I did when I published my paper here.

Hope it helps!
Adrian

larryshamalama · 2024-04-16T20:39:33Z

Review checklist for @larryshamalama

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/LeoEgidi/pivmet?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@LeoEgidi) 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
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

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?

larryshamalama · 2024-04-16T22:33:25Z

Hi @LeoEgidi, thanks for the submission. Overall, looks good, but I do have some doubts with the paper. Some comments below align with @adriancorrendo's review.

Major comments/questions

A statement of need and State of the field: You define pivotal units in the first paragraph without diving into the details of the math; this is nice. Was this concept introduced in your 2018 paper or was it previously introduced? The main comment here is that I cannot find any "literature (software) review" of any packages that have any capabilities in finding pivotal units. If the concept was introduced in your 2018 paper, it makes sense that there is no software that specifically provides functionality for identifying pivotal units. It would be nice to either 1) if no other software can be used, identify what mixture modelling packages could potentially be helpful in identifying pivotal units or 2) summarize what this package contributes on top of other pivotal unit software.

Minor comments

I think that it would be good to include a quickstart akin to what is available in the README in the software paper itself.
Community guidelines seem to be missing. For instance, you can add a CONTRIBUTING.md file outlining how to ask questions (via GitHub issues or discussions) and how to contribute to the package via pull requests.
I found some typos in the article. I tried solving the ones I found in my PR. I may have missed some, please have a look again.

LeoEgidi · 2024-05-09T09:03:35Z

Hi @adriancorrendo , thanks a lot for your comments, I took a first look. I'll try to get a deeper look this week, or at most next week. Should I reply your points here or directly in the repo? What do you prefer? Thanks a lot

Hi Leo, how are you? You would need to answer on the issue I created in the package repo. Once you address those comments, I'll start checking the remaining boxes until giving my full ok. That's what I did when I published my paper here.

Hope it helps! Adrian

@arfon @adriancorrendo

I replied the comments from Adrian in the issue he created. Now time to work on the @larryshamalama comments

LeoEgidi · 2024-05-09T09:38:34Z

Hi @LeoEgidi, thanks for the submission. Overall, looks good, but I do have some doubts with the paper. Some comments below align with @adriancorrendo's review.

Major comments/questions

A statement of need and State of the field: You define pivotal units in the first paragraph without diving into the details of the math; this is nice. Was this concept introduced in your 2018 paper or was it previously introduced? The main comment here is that I cannot find any "literature (software) review" of any packages that have any capabilities in finding pivotal units. If the concept was introduced in your 2018 paper, it makes sense that there is no software that specifically provides functionality for identifying pivotal units. It would be nice to either 1) if no other software can be used, identify what mixture modelling packages could potentially be helpful in identifying pivotal units or 2) summarize what this package contributes on top of other pivotal unit software.

Thanks. In line with the comments from @adriancorrendo , we added a new paragraph at the end the "Statement of need" section to make an overview of other R packages related to pivmet. For this reason, we summarized why pivmet is so beneficial in the search of the pivotal units and how this package is naturally related to other existing packages, such as 'rstan', 'rjags' and 'bayesmix'.

Minor comments

I think that it would be good to include a quickstart akin to what is available in the README in the software paper itself.

Ok, If I well understood your point, in line with one of the comments from @adriancorrendo , we included now in the two examples in the paper, #Example 1 and #Example 2, some relevant lines of R code, basically the same included in the README file.

Community guidelines seem to be missing. For instance, you can add a CONTRIBUTING.md file outlining how to ask questions (via GitHub issues or discussions) and how to contribute to the package via pull requests.

Thanks, done. We added a new .md file "CODE OF CONDUCT" in the main repo to properly suggest the users how to contribute and report bugs.

I found some typos in the article. I tried solving the ones I found in my PR. I may have missed some, please have a look again.

Thanks, I read another time, and so far no other typos have been found. I merged the pull request.

LeoEgidi · 2024-05-09T09:41:25Z

@arfon @larryshamalama @adriancorrendo

Thanks a lot;)
I replied all your comments, for any doubt/clarification I am available

crvernon · 2024-05-13T12:41:15Z

👋 - @skanwal will you check in on this submission? It looks like the author and reviewers are making good progress. Thanks!

skanwal · 2024-05-14T23:34:35Z

Thanks so much @adriancorrendo and @larryshamalama.
The checklists look fairly complete to me. Are you happy for this submission to be accpeted? I wanted to confirm there are no outstanding tasks?

Also, thanks @LeoEgidi for staying on top of comments and updates.

editorialbot · 2024-06-12T11:27:55Z

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

OK DOIs

- 10.1007/978-3-319-73906-9_7 is OK
- 10.1007/s11222-017-9774-2 is OK
- 10.1162/153244303321897735 is OK
- 10.1109/TPAMI.2005.113 is OK
- 10.1007/978-3-642-03915-7_33 is OK
- 10.1214/09-BA414 is OK
- 10.1111/1467-9868.00265 is OK
- 10.1198/016214501750333063 is OK
- 10.18637/jss.v069.c01 is OK
- 10.1111/1467-9868.00095 is OK
- 10.1080/10618600.2000.10474879 is OK
- 10.1080/01621459.1995.10476550 is OK
- 10.1007/s11634-018-0329-y is OK
- 10.1007/s11222-014-9500-2 is OK

MISSING DOIs

- No DOI given, and none found for title: A conceptual introduction to Hamiltonian Monte Car...
- No DOI given, and none found for title: K-means seeding via MUS algorithm
- No DOI given, and none found for title: k-means++: The advantages of careful seeding
- 10.1080/03610926.2010.526741 may be a valid DOI for title: Bayesian mixture labeling and clustering
- 10.1214/088342305000000016 may be a valid DOI for title: Markov chain Monte Carlo methods and the label swi...
- 10.1198/jasa.2009.0237 may be a valid DOI for title: Bayesian mixture labeling by highest posterior den...
- 10.1198/0003130043286 may be a valid DOI for title: Difficulties in drawing inferences with finite-mix...
- 10.1080/00949655.2012.707201 may be a valid DOI for title: An online Bayesian mixture labelling method by min...
- 10.1198/jcgs.2010.09008 may be a valid DOI for title: An artificial allocations based solution to the la...
- 10.32614/cran.package.label.switching may be a valid DOI for title: label.switching: Relabelling MCMC Outputs of Mixtu...
- No DOI given, and none found for title: bayesmix: Bayesian Mixture Models with JAGS
- 10.2307/2531224 may be a valid DOI for title: Statistical analysis of finite mixture distributio...
- No DOI given, and none found for title: Finite Mixture Models
- No DOI given, and none found for title: Comparing partitions
- 10.1080/10618600.2012.735624 may be a valid DOI for title: Label switching in Bayesian mixture models: Determ...
- 10.1007/978-0-387-38983-7 may be a valid DOI for title: Bayesian core: a practical approach to computation...
- 10.1016/s0169-7161(05)25016-2 may be a valid DOI for title: Bayesian modelling and inference on mixtures of di...
- 10.2307/2669477 may be a valid DOI for title: Computational and inferential difficulties with mi...
- 10.1007/s11222-009-9129-8 may be a valid DOI for title: Probabilistic relabelling strategies for the label...
- No DOI given, and none found for title: Bayesian inference for mixture models via Monte Ca...
- 10.1007/bf00143556 may be a valid DOI for title: Sampling from multimodal distributions using tempe...
- 10.2307/2289993 may be a valid DOI for title: Density estimation with confidence sets exemplifie...
- No DOI given, and none found for title: foreign: Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’...
- No DOI given, and none found for title: MASS: Support Functions and Datasets for Venables ...
- No DOI given, and none found for title: mclust: Gaussian Mixture Modelling for Model-Based...
- No DOI given, and none found for title: pivmet: Pivotal Methods for Bayesian Relabelling a...
- No DOI given, and none found for title: RStan: the R interface to Stan
- No DOI given, and none found for title: rjags: Bayesian graphical models using MCMC
- No DOI given, and none found for title: runjags: An R package providing interface utilitie...
- 10.1214/08-aoas191 may be a valid DOI for title: A weakly informative default prior distribution fo...
- No DOI given, and none found for title: Prior distributions for variance parameters in hie...
- 10.1214/009053604000001147 may be a valid DOI for title: Spike and slab variable selection: frequentist and...
- No DOI given, and none found for title: Bayesian density estimation by mixtures of normal ...
- No DOI given, and none found for title: dirichletprocess: An R Package for Fitting Complex...
- No DOI given, and none found for title: A Bayesian analysis of some nonparametric problems
- 10.1111/anzs.12350 may be a valid DOI for title: Spying on the prior of the number of data clusters...
- No DOI given, and none found for title: Model-based clustering, discriminant analysis, and...

INVALID DOIs

- None

crvernon · 2024-06-12T12:07:30Z

@LeoEgidi thanks for making the changes. These last two changes should wrap things up:

LINE 13: Missing new line before paragraph.
Per the list of "Missing DOI" above, please remove any unused references from your paper.bib file

LeoEgidi · 2024-06-12T13:40:25Z

@editorialbot check references

editorialbot · 2024-06-12T13:40:54Z

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

OK DOIs

- 10.1007/s11222-017-9774-2 is OK
- 10.1162/153244303321897735 is OK
- 10.1111/1467-9868.00265 is OK
- 10.1198/016214501750333063 is OK
- 10.18637/jss.v069.c01 is OK
- 10.2307/2531224 is OK
- 10.1111/1467-9868.00095 is OK
- 10.1080/10618600.2000.10474879 is OK
- 10.1080/01621459.1995.10476550 is OK
- 10.1007/s11634-018-0329-y is OK
- 10.1007/s11222-014-9500-2 is OK

MISSING DOIs

- No DOI given, and none found for title: bayesmix: Bayesian Mixture Models with JAGS
- No DOI given, and none found for title: pivmet: Pivotal Methods for Bayesian Relabelling a...
- No DOI given, and none found for title: RStan: the R interface to Stan
- No DOI given, and none found for title: rjags: Bayesian graphical models using MCMC
- No DOI given, and none found for title: A Bayesian analysis of some nonparametric problems

INVALID DOIs

- None

LeoEgidi · 2024-06-12T13:43:59Z

@editorialbot generate pdf

editorialbot · 2024-06-12T13:45:23Z

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

LeoEgidi · 2024-06-12T13:52:13Z

Thanks @crvernon

@LeoEgidi thanks for making the changes. These last two changes should wrap things up:

LINE 13: Missing new line before paragraph.

DONE

Per the list of "Missing DOI" above, please remove any unused references from your paper.bib file

DONE

crvernon · 2024-06-12T14:19:11Z

@editorialbot generate pdf

editorialbot · 2024-06-12T14:20:28Z

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

crvernon · 2024-06-12T14:27:03Z

@editorialbot check references

editorialbot · 2024-06-12T14:27:25Z

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

OK DOIs

- 10.1007/s11222-017-9774-2 is OK
- 10.1162/153244303321897735 is OK
- 10.1111/1467-9868.00265 is OK
- 10.1198/016214501750333063 is OK
- 10.18637/jss.v069.c01 is OK
- 10.2307/2531224 is OK
- 10.1111/1467-9868.00095 is OK
- 10.1080/10618600.2000.10474879 is OK
- 10.1080/01621459.1995.10476550 is OK
- 10.1007/s11634-018-0329-y is OK
- 10.1007/s11222-014-9500-2 is OK

MISSING DOIs

- No DOI given, and none found for title: bayesmix: Bayesian Mixture Models with JAGS
- No DOI given, and none found for title: pivmet: Pivotal Methods for Bayesian Relabelling a...
- No DOI given, and none found for title: RStan: the R interface to Stan
- No DOI given, and none found for title: rjags: Bayesian graphical models using MCMC
- No DOI given, and none found for title: A Bayesian analysis of some nonparametric problems

INVALID DOIs

- None

crvernon · 2024-06-12T14:28:11Z

@editorialbot accept

editorialbot · 2024-06-12T14:28:13Z

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

editorialbot · 2024-06-12T14:34:54Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Egidi
  given-names: Leonardo
  orcid: "https://orcid.org/0000-0003-3211-905X"
- family-names: Pappada
  given-names: Roberta
  orcid: "https://orcid.org/0000-0002-4852-0561"
- family-names: Pauli
  given-names: Francesco
  orcid: "https://orcid.org/0000-0002-7982-3514"
- family-names: Torelli
  given-names: Nicola
  orcid: "https://orcid.org/0000-0001-9523-5336"
contact:
- family-names: Egidi
  given-names: Leonardo
  orcid: "https://orcid.org/0000-0003-3211-905X"
doi: 10.5281/zenodo.11243277
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Egidi
    given-names: Leonardo
    orcid: "https://orcid.org/0000-0003-3211-905X"
  - family-names: Pappada
    given-names: Roberta
    orcid: "https://orcid.org/0000-0002-4852-0561"
  - family-names: Pauli
    given-names: Francesco
    orcid: "https://orcid.org/0000-0002-7982-3514"
  - family-names: Torelli
    given-names: Nicola
    orcid: "https://orcid.org/0000-0001-9523-5336"
  date-published: 2024-06-12
  doi: 10.21105/joss.06461
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6461
  title: "pivmet: an R package proposing pivotal methods for consensus
    clustering and mixture modelling"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06461"
  volume: 9
title: "pivmet: an `R` package proposing pivotal methods for consensus
  clustering and mixture modelling"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-06-12T14:34:57Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-06-12T14:34:58Z

🚨🚨🚨 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.06461 joss-papers#5493
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06461
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

LeoEgidi · 2024-06-12T14:50:42Z

GREAT!!!

Thanks everyone @arfon @crvernon @skanwal @larryshamalama @adriancorrendo

crvernon · 2024-06-12T14:52:43Z

👋 @LeoEgidi - I just noticed that you have backticks in the title around "R". Could you remove these as they cause a formatting error when we publish the paper on our website. Let me know when this is done and I'll reaccept. Thanks!

LeoEgidi · 2024-06-12T15:38:48Z

👋 @LeoEgidi - I just noticed that you have backticks in the title around "R". Could you remove these as they cause a formatting error when we publish the paper on our website. Let me know when this is done and I'll reaccept. Thanks!

DONE!

crvernon · 2024-06-12T15:54:10Z

@editorialbot reaccept

editorialbot · 2024-06-12T15:54:13Z

Rebuilding paper!

editorialbot · 2024-06-12T15:55:49Z

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#5496

crvernon · 2024-06-12T16:03:57Z

🥳 Congratulations on your new publication @LeoEgidi! Many thanks to @skanwal for editing and @adriancorrendo, and @larryshamalama for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

editorialbot · 2024-06-12T16:03:59Z

🎉🎉🎉 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.06461/status.svg)](https://doi.org/10.21105/joss.06461)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06461">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06461/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06461/status.svg
   :target: https://doi.org/10.21105/joss.06461

This is how it will look in your documentation:

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editorialbot added HTML R review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Mar 10, 2024

editorialbot assigned skanwal Mar 10, 2024

editorialbot mentioned this issue Mar 10, 2024

[PRE REVIEW]: pivmet: an R package proposing pivotal methods for consensus clustering and mixture modelling #6363

Closed

larryshamalama mentioned this issue Apr 16, 2024

Fix typos in paper.md LeoEgidi/pivmet#2

Merged

larryshamalama mentioned this issue Apr 16, 2024

Load corresponding packages in README's examples LeoEgidi/pivmet#3

Merged

editorialbot added accepted published Papers published in JOSS labels Jun 12, 2024

crvernon changed the title ~~[REVIEW]: pivmet: an R package proposing pivotal methods for consensus clustering and mixture modelling~~ [REVIEW]: pivmet: an R package proposing pivotal methods for consensus clustering and mixture modelling Jun 12, 2024

crvernon closed this as completed Jun 12, 2024

This was referenced Dec 17, 2024

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

Open

[PRE REVIEW]: fuzzyclara: Efficient Medoid-based Clustering Algorithms for Large and Fuzzy Data #7609

Open

[REVIEW]: pivmet: an R package proposing pivotal methods for consensus clustering and mixture modelling #6461

[REVIEW]: pivmet: an R package proposing pivotal methods for consensus clustering and mixture modelling #6461

Comments

editorialbot commented Mar 10, 2024 • edited Loading

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adriancorrendo commented Mar 11, 2024 • edited Loading

Review checklist for @adriancorrendo

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

arfon commented Mar 24, 2024

LeoEgidi commented Mar 26, 2024

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adriancorrendo commented Apr 5, 2024

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larryshamalama commented Apr 16, 2024 • edited Loading

Review checklist for @larryshamalama

Conflict of interest

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General checks

Functionality

Documentation

Software paper

larryshamalama commented Apr 16, 2024

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LeoEgidi commented May 9, 2024

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crvernon commented May 13, 2024

skanwal commented May 14, 2024

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