[PRE REVIEW]: Multivariate Covariance Generalized Linear Models in Python: The mcglm library

[editorialbot]

Submitting author: !--author-handle-->@jeancmaia<!--end-author-handle-- (Jean Carlos Maia) Repository: https://github.com/jeancmaia/mcglm Branch with paper.md (empty if default branch): main Version: 0.2.1 Editor: !--editor-->@AJQuinn<!--end-editor-- Reviewers: @Spaak, @bkrayfield Managing EiC: George K. Thiruvathukal

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b0cf48e0bc9265d2ad754b1d33475936"><img src="https://joss.theoj.org/papers/b0cf48e0bc9265d2ad754b1d33475936/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b0cf48e0bc9265d2ad754b1d33475936/status.svg)](https://joss.theoj.org/papers/b0cf48e0bc9265d2ad754b1d33475936)

Author instructions

Thanks for submitting your paper to JOSS @jeancmaia. Currently, there isn't a JOSS editor assigned to your paper.

@jeancmaia if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, 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

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "," (COMMA) [#<BibTeX::Bibliography data=[26]>, "@", #<BibTeX::Entry >, {:title=>["The Minimum Sum of Absolute Errors Regression: A State of the Art Survey."], :author=>["Narula, Subhash C., and John F. Wellington."], :year=>["1982"]}, ",", "month", "="]

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.69 s (314.1 files/s, 27712.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          10            584            640           3674
CSS                              4             36             12           1838
R                                1             76             74           1515
Jupyter Notebook                 4              0           7572            836
TeX                              1            103              0            814
JavaScript                       6             80             88            633
Markdown                         2             47              0            221
JSON                           184              0              0            184
YAML                             2              6              4             41
TOML                             1              5              0             25
make                             1              4              7              9
reStructuredText                 1              6              7              7
-------------------------------------------------------------------------------
SUM:                           217            947           8404           9797
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1740

[editorialbot]

Failed to discover a Statement of need section in paper

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[jeancmaia]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[arfon]

@jeancmaia – thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

[gkthiruvathukal]

@jeancmaia Thank you for your submission to JOSS. We are currently facing a backlog of submissions in this track. Can you please follow up by looking at the list of editors to help me identify an editor that closely matches the topic of your submission? When you reach this page, please scroll down to Topic Editors. Please note that I am not asking you to suggest reviewers at this stage. Please simply list the GitHub IDs of prospective topic editors without using the @. Please reply to this thread by listing up to three GitHub IDs only (one per line).

Once I have this information, I can move the submission out of waitlist status.

[jeancmaia]

melissawm jbytecode fabian-s

[AJQuinn]

Hi @gkthiruvathukal - I was skimming through the backlog and saw this review waitlisted. I'd be happy to edit if it's still waiting for editorial capacity? I've worked with a few regression packages so it could be a good fit.

[arfon]

Just following up here with @AJQuinn – feel free to take this one (I'll go ahead and assign you now).

[arfon]

@editorialbot assign @AJQuinn as editor

[editorialbot]

Assigned! @AJQuinn is now the editor

[arfon]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

PyGModels: A Python package for exploring Probabilistic Graphical Models with Graph Theoretical Structures Submitting author: @D-K-E Handling editor: @dfm (Active) Reviewers: @eigenfoo, @ankurankan Similarity score: 0.8399

BGGM: Bayesian Gaussian Graphical Models in R Submitting author: @donaldRwilliams Handling editor: @akeshavan (Retired) Reviewers: @jayrobwilliams, @paulgovan Similarity score: 0.8384

GGLasso - a Python package for General Graphical Lasso computation Submitting author: @fabian-sp Handling editor: @gkthiruvathukal (Active) Reviewers: @papachristoumarios, @jameschapman19 Similarity score: 0.8369

gmr: Gaussian Mixture Regression Submitting author: @AlexanderFabisch Handling editor: @mikldk (Retired) Reviewers: @inakleinbottle, @soodoku Similarity score: 0.8368

VBLinLogit: Variational Bayesian linear and logistic regression Submitting author: @jdrugo Handling editor: @usethedata (Retired) Reviewers: @ManuelaS, @usethedata Similarity score: 0.8335

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

[arfon]

@AJQuinn – these recommendations might be useful ☝️

[AJQuinn]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.7287/PEERJ.PREPRINTS.1686V1 is OK
- 10.18637/jss.v076.i01 is OK
- 10.18637/jss.v084.i04 is OK
- 10.1016/j.spl.2011.03.006 is OK
- 10.1093/biomet/61.3.439 is OK
- 10.1088/1742-6596/855/1/012060 is OK
- 10.1093/biomet/61.3.439 is OK
- 10.1007/978-3-642-11760-2_2 is OK
- 10.1007/978-3-642-21551-3_24 is OK
- 10.1214/aos/1176345451 is OK
- 10.1002/9781118445112.stat07536 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.18637/jss.v084.i04 is OK
- 10.1111/rssc.12145 is OK

MISSING DOIs

- 10.1007/s10182-015-0250-z may be a valid DOI for title: Discrete dispersion models and their tweedie asymptotics.
- 10.1080/00401706.1999.10485652 may be a valid DOI for title: The theory of dispersion models.
- 10.1111/j.1467-9469.2004.00375.x may be a valid DOI for title: Parameter Orthogonality and Bias Adjustment for Estimating Functions
- 10.1214/12-ejs721 may be a valid DOI for title: Gaussian Copula Marginal Regression
- 10.1016/j.jmva.2013.05.001 may be a valid DOI for title: Factor Copula Models for Multivariate Data
- 10.2307/2841583 may be a valid DOI for title: Regression towards mediocrity in hereditary stature.
- 10.2307/2333849 may be a valid DOI for title: Studies in the History of Probability and Statistics. XV: The Historical Development of the Gauss Linear Model
- 10.25080/majora-92bf1922-011 may be a valid DOI for title: Statsmodels: Econometric and Statistical Modeling with Python
- 10.1214/14-aoas769 may be a valid DOI for title: Longitudinal Mixed Membership Trajectory Models for Disability Survey Data
- 10.1214/15-aoas816 may be a valid DOI for title: Covariance Pattern Mixture Models for the Analysis of Multivariate Heterogeneous Longitudinal Data
- 10.1214/15-aoas821 may be a valid DOI for title: Assessing Phenotypic Correlation through the Multivariate Phylogenetic Latent Liability Model
- 10.1214/15-aoas813 may be a valid DOI for title: Multi-species Distribution Modeling Using Penalized Mixture of Tegressions
- 10.1214/15-aoas823 may be a valid DOI for title: Bayesian Structured Additive Distributional Regression with an Application to Regional Income Inequality in Germany
- 10.1111/rssc.12090 may be a valid DOI for title: Bayesian Structured Additive Distributional Regression for Multivariate Responses
- 10.1111/rssa.12089 may be a valid DOI for title: Multilevel Multivariate Modelling of Legislative Count Data, with a Hidden Markov Chain
- 10.2139/ssrn.2550507 may be a valid DOI for title: A Multivariate Tweedie Lifetime Model: Censoring and Truncation
- 10.1093/ije/dyu262 may be a valid DOI for title: Joint Modelling of Repeated Measurement and Time-to-event Data: An Introductory Tutorial
- 10.1177/0962280206075305 may be a valid DOI for title: Random-effects Models for Multivariate Repeated Measures
- 10.1214/12-ejs721 may be a valid DOI for title: Gaussian Copula Marginal Regression
- 10.1016/j.jmva.2013.05.001 may be a valid DOI for title: Factor Copula Models for Multivariate Data
- 10.1111/j.1467-9469.2004.00375.x may be a valid DOI for title: Parameter Orthogonality and Bias Adjustment for Estimating Functions
- 10.1007/s10182-015-0250-z may be a valid DOI for title: Discrete Dispersion Models and Their Tweedie Asymptotics
- 10.1093/biomet/ast023 may be a valid DOI for title: A General Modelling Framework for Multivariate Disease Mapping
- 10.1214/12-ejs721 may be a valid DOI for title: Gaussian Copula Marginal Regression
- 10.1214/11-bjps171 may be a valid DOI for title: Construction of Multivariate Dispersion Models
- 10.1006/jmva.1999.1885 may be a valid DOI for title: Multivariate Dispersion Models
- 10.1080/00401706.1999.10485652 may be a valid DOI for title: The Theory of Dispersion Models
- 10.1214/aos/1193342389 may be a valid DOI for title: Asymptotically Efficient Estimation of Covariance Matrices with Linear Structure
- 10.1093/biomet/87.2.425 may be a valid DOI for title: Maximum Likelihood Estimation of Generalised Linear Models for Multivariate Normal Covariance Matrix
- 10.1111/j.1541-0420.2007.00803.x may be a valid DOI for title: Biometrical Modeling of Twin and Family Data Using Standard Mixed Model Software
- 10.1002/1097-0258(20000915/30)19:17/18<2555::aid-sim587>3.0.co;2-# may be a valid DOI for title: Bayesian modelling of inseparable space-time variation in disease risk
- 10.1111/j.1420-9101.2009.01915.x may be a valid DOI for title: General Quantitative Genetic Methods for Comparative Biology: Phylogenies, Taxonomies and Multi-trait Models for Continuous and Categorical Characters
- 10.1111/biom.12118 may be a valid DOI for title: Fast Forward Selection for Generalized Estimating Equations with a Large Number of Predictor Variables
- 10.1002/sim.4300 may be a valid DOI for title: Working Covariance Model Selection for Generalized Estimating Equations
- 10.2307/2533686 may be a valid DOI for title: Analysis of Serially Correlated Data Using Quasi-Least Squares
- 10.1111/aje.12260 may be a valid DOI for title: Decline in Hunter Offtake of Blue Duikers in Bioko Island, Equatorial Guinea

INVALID DOIs

- 110.1002/sim.4300 is INVALID
- 10.1080/01621459.1996.10476677. is INVALID
- https://doi.org/10.2307/2344614 is INVALID because of 'https://doi.org/' prefix

[AJQuinn]

Hi @jeancmaia - I'll be your editor during the review processing. First job is to find some reviewers to take a look over the toolbox and paper.

Could you take a look at the DOIs in the paper - there are few missing/invalid in our automated checking tool. I think two things may be going on. There are a lot more references in your bib than are referenced in the paper, and many of the references don't include an explicit doi within the paper info.

eg within https://github.com/jeancmaia/mcglm/blob/main/paper.bib

@article{Jorgensen:2016,
    author={J{\o}rgensen, B. and Kokonendji, C.},
    title={Discrete Dispersion Models and Their Tweedie Asymptotics},
    journal={AStA Advances in Statistical Analysis},
    volume = {100},
    number = {},
    pages={43--78},
    year={2016},
}

should include doi line

doi = {10.1007/s10182-015-0250-z}

you can rerun the reference check to see any changes with the relevant editorialbot line above

[AJQuinn]

👋 Hello - @eigenfoo, @inakleinbottle, @soodoku and @ejolly would any of you be willing to review this submission for JOSS? The code repository and paper details are further up in this thread.

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html - please check them out for more information and please feel free to ask questions in this thread.

Cheers!

[soodoku]

hey @AJQuinn, thanks for getting in touch. Unfortunately, I can't take it on. Is there a way to opt out of the JOSS pool of reviewers?

[AJQuinn]

Hi @soodoku - no problem, thanks for letting me know. I believe you can deselect an ' Available to review' checkbox on your reviewer profile page here: https://reviewers.joss.theoj.org/ Let me know if you run into problems with this. Thanks for your past reviews!

[jeancmaia]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.7287/PEERJ.PREPRINTS.1686V1 is OK
- 10.48550/arXiv.1809.10756 is OK
- 10.48550/arXiv.1810.09538 is OK
- 10.18637/jss.v076.i01 is OK
- 10.18637/jss.v084.i04 is OK
- 10.48550/arXiv.1409.7482 is OK
- 10.1111/j.2517-6161.1987.tb01685.x is OK
- 10.1002/1097-0258(20000730)19:14<1952::AID-SIM474>3.0.CO;2-K is OK
- 10.1214/12-EJS721 is OK
- 10.1016/j.jmva.2013.05.001 is OK
- 10.2307/2344614 is OK
- 10.1007/978-3-642-21551-3_24 is OK
- 10.1214/ss/1177013604 is OK
- 10.1214/aos/1176345451 is OK
- 10.1002/9781118445112.stat07536 is OK
- 10.2307/2841583 is OK
- 10.2307/2333849 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.18637/jss.v084.i04 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1177/0962280212445834 is OK
- 10.1214/12-EJS721 is OK
- 10.1016/j.jmva.2013.05.001 is OK
- 10.1093/biomet/73.1.13 is OK
- 10.1111/rssc.12145 is OK
- 10.1515/ijb-2017-0001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[AJQuinn]

Fantastic - thanks @jeancmaia

[AJQuinn]

👋 Hello - @Spaak would you be willing to review this submission for JOSS? The code repository and paper details are further up in this thread.

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html - please check them out for more information and please feel free to ask questions in this thread.

Cheers!

[AJQuinn]

👋 Hello - @wmvanvliet @tpurcell90 would you be willing to review this submission for JOSS? The code repository and paper details are further up in this thread.

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html - please check them out for more information and please feel free to ask questions in this thread.

Cheers!

[AJQuinn]

👋 Hello - @vankesteren would you be willing to review this submission for JOSS? The code repository and paper details are further up in this thread.

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html - please check them out for more information and please feel free to ask questions in this thread.

Cheers!

[tpurcell90]

Normally I would, but I am moving to the USA from Europe later this month so I can't confirm that I will be able to actually do the tests in a timely manner

[Spaak]

@AJQuinn Yes, happy to review.

[AJQuinn]

Great - thank you @Spaak!

@tpurcell90 - no problem, thanks for letting me know. All the best for the move.

[AJQuinn]

@editorialbot add @Spaak as reviewer

[editorialbot]

@Spaak added to the reviewers list!

[AJQuinn]

👋 Hello - @arunmano121 @bkrayfield would either of you be willing to review this submission for JOSS? The code repository and paper details are further up in this thread.

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html - please check them out for more information and please feel free to ask questions in this thread.

Cheers!

[bkrayfield]

@AJQuinn - Yes, happy to do it.

[arunmano121]

@AJQuinn - my apologies, I am unable to review at this time due to upcoming travel.

Best regards, Arun Manohar

-- Sent from my phone

On Nov 8, 2023, at 8:27 AM, bkrayfield @.***> wrote:



@AJQuinnhttps://github.com/AJQuinn - Yes, happy to do it.

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/5818#issuecomment-1802240716, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATAHAZU57YWJOHG77PXPRGLYDOXHVAVCNFSM6AAAAAA4PXPH5SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBSGI2DANZRGY. You are receiving this because you were mentioned.Message ID: @.***>

[AJQuinn]

Thank you @bkrayfield,

No problem @arunmano121 - thanks for letting me know.

[AJQuinn]

@editorialbot add @bkrayfield as reviewer

[editorialbot]

@bkrayfield added to the reviewers list!

[AJQuinn]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6037.