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[PRE REVIEW]: dsmmR: Estimation and Simulation of Drifting Semi-Markov Models #5107

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editorialbot opened this issue Jan 27, 2023 · 54 comments
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pre-review R TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning waitlisted Submissions in the JOSS backlog due to reduced service mode.

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editorialbot commented Jan 27, 2023

Submitting author: @Mavrogiannis-Ioannis (Ioannis Mavrogiannis)
Repository: https://github.com/Mavrogiannis-Ioannis/dsmmR
Branch with paper.md (empty if default branch):
Version: v1.0.1
Editor: @Bisaloo
Reviewers: @Athene-ai, @RomainAzais
Managing EiC: Arfon Smith

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status

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HTML: <a href="https://joss.theoj.org/papers/55311848a971690d7ba82e421e350ac5"><img src="https://joss.theoj.org/papers/55311848a971690d7ba82e421e350ac5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/55311848a971690d7ba82e421e350ac5/status.svg)](https://joss.theoj.org/papers/55311848a971690d7ba82e421e350ac5)

Author instructions

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

@Mavrogiannis-Ioannis if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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:

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@editorialbot editorialbot added pre-review Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Jan 27, 2023
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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

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (721.9 files/s, 257897.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                                8             87           2749           1879
Markdown                         5            225              0            742
TeX                              1             22              0            104
YAML                             2             12              6             56
Rmd                              1             50            120             21
-------------------------------------------------------------------------------
SUM:                            17            396           2875           2802
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 901

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

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

OK DOIs

- None

MISSING DOIs

- 10.32614/rj-2018-050 may be a valid DOI for title: SMM: An R Package for Estimation and Simulation of Discrete-time semi-Markov Models.
- 10.1007/s11009-018-9682-8 may be a valid DOI for title: Reliability and survival analysis for drifting Markov models: modeling and estimation
- 10.21203/rs.3.rs-1414798/v1 may be a valid DOI for title: Learning the arm-leg coordination in breaststroke swimming: Identifying exploration of movement dynamics with drifting Markov Models

INVALID DOIs

- doi:10.2202/1544-6115.1326 is INVALID (failed connection)

@arfon arfon added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jan 27, 2023
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arfon commented Jan 27, 2023

@Mavrogiannis-Ioannis - 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!

@Mavrogiannis-Ioannis
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Thank you for your comment @arfon , I will wait. Should I suggest an editor for this paper from the list?

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@editorialbot commands

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Hello @Mavrogiannis-Ioannis, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (402.3 files/s, 143698.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                                8             87           2752           1878
Markdown                         5            232              0            751
TeX                              1             19              0             88
YAML                             2             12              6             56
Rmd                              1             49            121             21
-------------------------------------------------------------------------------
SUM:                            17            399           2879           2794
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 901

@Mavrogiannis-Ioannis
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@editorialbot check references

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@editorialbot generate my checklist

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Checklists can only be created once the review has started in the review issue

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

OK DOIs

- None

MISSING DOIs

- 10.2202/1544-6115.1326 may be a valid DOI for title: Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences
- 10.1007/s11009-018-9682-8 may be a valid DOI for title: Reliability and survival analysis for drifting Markov models: modeling and estimation

INVALID DOIs

- None

@Mavrogiannis-Ioannis
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@editorialbot check references

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

OK DOIs

- None

MISSING DOIs

- 10.2202/1544-6115.1326 may be a valid DOI for title: Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences
- 10.1007/s11009-018-9682-8 may be a valid DOI for title: Reliability and survival analysis for drifting Markov models: modeling and estimation

INVALID DOIs

- None

@Mavrogiannis-Ioannis
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@editorialbot check references

1 similar comment
@Mavrogiannis-Ioannis
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@editorialbot check references

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

OK DOIs

- None

MISSING DOIs

- 10.2202/1544-6115.1326 may be a valid DOI for title: Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences
- 10.1007/s11009-018-9682-8 may be a valid DOI for title: Reliability and survival analysis for drifting Markov models: modeling and estimation

INVALID DOIs

- None

@Mavrogiannis-Ioannis
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@editorialbot check references

1 similar comment
@Mavrogiannis-Ioannis
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@editorialbot check references

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

OK DOIs

- 10.2202/1544-6115.1326 is OK
- 10.1007/s11009-018-9682-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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arfon commented Mar 2, 2023

@editorialbot invite @Bisaloo as editor

👋 @Bisaloo would you be willing to edit this submission for JOSS?

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Assigned! @Bisaloo is now the editor

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Bisaloo commented Mar 6, 2023

Hi @Mavrogiannis-Ioannis 👋, I'll be your topic editor for this submission.

The first step in this pre-review is to find at least 2 reviewers. If you have any suggestions for potential reviewers, please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list). I'll already start looking in my own network in the meantime.

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Bisaloo commented Mar 8, 2023

Hi @dincerti 👋, would you be interested in reviewing this R package and the associated paper for the Journal of Open Source Software (JOSS)?

dsmmR: Estimation and Simulation of Drifting Semi-Markov Models

Given your experience as an author and maintainer of the hesim R package, I believe you could bring us very valuable insights.

You can have a look at our review criteria and review checklist to get an idea of what is expected.

If you are not available to review this submission, do you have any recommendation for suitable reviewers?

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Bisaloo commented Mar 13, 2023

Hi @chjackson 👋, would you be interested in reviewing this R package and the associated paper for the Journal of Open Source Software (JOSS)?

dsmmR: Estimation and Simulation of Drifting Semi-Markov Models

I found you via your work on the msm R package and I believe your expertise would be valuable here.

You can have a look at our review criteria and review checklist to get an idea of what is expected.

If you are not available to review this submission, do you have any recommendation for suitable reviewers?

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@Bisaloo Sorry to decline this, I'm very busy at the moment. Not sure that I know anyone with expertise particularly suited to this style of model, other than the authors of the packages cited in the paper.

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Bisaloo commented Mar 15, 2023

Hi @KZARCA @pierucci 👋 👋, would one of you be interested in reviewing this R package and the associated paper for the Journal of Open Source Software (JOSS)?

dsmmR: Estimation and Simulation of Drifting Semi-Markov Models

As the main contributors to the heemod R package, I believe you are particularly well-placed to review this submission.

You can have a look at our review criteria and review checklist to get an idea of what is expected.

If you are not available to review this submission, do you have any recommendation for suitable reviewers?

@KZARCA
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KZARCA commented Mar 15, 2023

Hi @Bisaloo, I'm sorry, this package is not within my area of expertise. Best regards

@dincerti
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Hi @dincerti 👋, would you be interested in reviewing this R package and the associated paper for the Journal of Open Source Software (JOSS)?

dsmmR: Estimation and Simulation of Drifting Semi-Markov Models

Given your experience as an author and maintainer of the hesim R package, I believe you could bring us very valuable insights.

You can have a look at our review criteria and review checklist to get an idea of what is expected.

If you are not available to review this submission, do you have any recommendation for suitable reviewers?

Hi, apologies for the delayed response. I am afraid I also do not have the time to review this package at the moment.

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Bisaloo commented Mar 20, 2023

Hi @m-clark 👋, would you be interested in reviewing this R package and the associated paper for the Journal of Open Source Software (JOSS)?

dsmmR: Estimation and Simulation of Drifting Semi-Markov Models

Your very interesting 'Model Estimation by Example' book made me think of you for this submission.

You can have a look at our review criteria and review checklist to get an idea of what is expected.

If you are not available to review this submission, do you have any recommendation for suitable reviewers?

@m-clark
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m-clark commented Mar 28, 2023 via email

@Mavrogiannis-Ioannis
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Hello everyone,

Thank you for taking the time to comment about your availability and to search about potential reviewers.
In the case that you have time and you need to know more, the authors are more than willing to answer to your questions.

Kind regards,
Ioannis

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Bisaloo commented Mar 28, 2023

Hi @Mavrogiannis-Ioannis, do you have recommendations for reviewers out of your own network? I'm not sure who else could be suitable right now. I'll keep thinking on my end as well.

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Bisaloo commented Apr 24, 2023

Hi @Mavrogiannis-Ioannis 👋, I hope you doing well. In the absence of an answer to my question about reviewer suggestion by May 8th, even if it's to say that you cannot think of anyone, I'm going to have to reject this submission.

@Mavrogiannis-Ioannis
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Hello @Bisaloo, sorry for my absence. I hope you are doing well and that life has been kind to you.

If we could reach some reviewers like @ellessenne, @Athene-ai, @dsurujon, which are the reviewers of the smmR package, it would be excellent.

Ioannis

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Athene-ai commented Apr 24, 2023 via email

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Hi,

I am afraid but I won't be able to review this submission this time.
Sorry!

Alessandro

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Bisaloo commented Apr 28, 2023

Thanks for your quick answers @Mavrogiannis-Ioannis @Athene-ai @ellessenne! I'll try to reach dsurujon by email.

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Bisaloo commented Apr 28, 2023

@editorialbot add @Athene-ai as reviewer

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@Athene-ai added to the reviewers list!

@dsurujon
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Hi, unfortunately I have to decline at this time. Best of luck all!

@Mavrogiannis-Ioannis
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Hello again @Bisaloo, we need one more reviewer for the process to start; is this correct?
Thank you

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Bisaloo commented May 16, 2023

Hi @Mavrogiannis-Ioannis, yes, this is correct. I'm still struggling to find another appropriate & available reviewer. Would you have other suggestions please?

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Bisaloo commented Jun 19, 2023

@editorialbot add @RomainAzais as reviewer

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@RomainAzais added to the reviewers list!

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Bisaloo commented Jun 19, 2023

@RomainAzais has informed me that he contributed a chapter to a book edited by submission authors.

While this is not completely defined in our conflict of interest policies, I have decided to officially waive it since this is akin to contribute to a special edition in a journal, and does not create a relationship that we deem likely to impact the quality and honesty of the review.

Since we now have two reviewers for this submission, I will close this pre-review issue and create the actual review issue, where our conversations will take place from now on.

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Bisaloo commented Jun 19, 2023

@editorialbot start review

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OK, I've started the review over in #5572.

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