[PRE REVIEW]: nimbleHMC: An R package for Hamiltonian Monte Carlo sampling in nimble

[editorialbot]

Submitting author: !--author-handle-->@danielturek<!--end-author-handle-- (Daniel Turek) Repository: https://github.com/nimble-dev/nimbleHMC Branch with paper.md (empty if default branch): joss Version: v0.1.1 Editor: Pending Reviewers: Pending Managing EiC: Daniel S. Katz

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Markdown: [![status](https://joss.theoj.org/papers/42161f4e58dec5ecd3b4d60717242d5c/status.svg)](https://joss.theoj.org/papers/42161f4e58dec5ecd3b4d60717242d5c)

Author instructions

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

@danielturek 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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (945.3 files/s, 193093.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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Markdown                         5            243              0            955
R                                6             96            504            885
TeX                              2             47              0            223
YAML                             2             20              7             84
-------------------------------------------------------------------------------
SUM:                            15            406            511           2147
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for example_paper.md is 627

[editorialbot]

:warning: An error happened when generating the pdf.

[danielskatz]

👋 @danielturek - note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it.

The error here is Problem with ORCID (0000-0000-0000-0000) for Adrian Price-Whelan. Invalid ORCID (Theoj::Error) Please either add the correct ORCID or remove the line with the false one.

Please feel free to make changes to your .md file, then use the command @editorialbot generate pdf to make a new PDF. editorialbot commands need to be the first entry in a new comment.

Once you have done this, please check the references, using the command @editorialbot check references. If you find errors, fix them, then check again, and once the references are good, generate a final draft PDF for the process to continue.

[danielskatz]

In addition, because the amount of code is relatively low (less than 1000 LOC), I'm going to ask the JOSS editor to review the submission to discuss if it meets the substantial scholarly effort criterion for review by JOSS. You should hear back in a week or so.

[danielskatz]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[danielskatz]

@openjournals/dev - note that the check repository checked a different .md file than the generate pdf command used. Is there some logic that can be changed to fix this?

[danielturek]

@danielskatz I believe I have followed all the instructions, but the editorial bot checked joss/materials_from_joss/example_paper.md, which is not the path that I specified when submitting.

Rather, the manuscript source file is located at joss/paper/paper.md.

Please advise. If necessary, I could simply try removing the directory joss/materials_from_joss.

[danielskatz]

Yes, please go ahead and remove the extra directory

[danielskatz]

@openjournals/dev - note this problem. Is there a solution? A way to identify which paper is the JOSS paper when there are multiple .md files?

[danielturek]

@danielskatz Done. The only remaining *.md file is the manuscript file:

joss/paper/paper.md

Are you able to restart the automated review process?

[danielskatz]

@editorialbot check references

[danielskatz]

@editorialbot generate pdf

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.21105/joss.03844 may be a valid DOI for title: compareMCMCs: An R package for studying MCMC efficiency
- 10.1080/10618600.2016.1172487 may be a valid DOI for title: Programming with models: writing statistical algorithms for general model structures with NIMBLE
- 10.1214/16-ba1008 may be a valid DOI for title: Automated parameter blocking for efficient Markov chain Monte Carlo sampling
- 10.1002/ece3.6053 may be a valid DOI for title: One size does not fit all: Customizing MCMC methods for hierarchical models using NIMBLE
- 10.1080/10618600.2013.791193 may be a valid DOI for title: Automated factor slice sampling
- 10.2307/2937171 may be a valid DOI for title: Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies
- 10.1007/s10651-016-0353-z may be a valid DOI for title: Efficient Markov chain Monte Carlo sampling for hierarchical hidden Markov models

INVALID DOIs

- None

[danielskatz]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (837.4 files/s, 186343.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                                6             96            504            885
Markdown                         4            222              0            865
TeX                              1             42              0            168
YAML                             2             20              7             84
-------------------------------------------------------------------------------
SUM:                            13            380            511           2002
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2221

[editorialbot]

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

[danielskatz]

@danielturek - you can run all the commands I ran, just as I did. You can also add the needed DOIs, assuming they are right. And the paper is probably too long (normally papers are about 1000 words), but let's wait for the scope review to complete before you do work on cutting it, in case this review doesn't happen.

[danielturek]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.21105/joss.03844 is OK
- 10.1080/10618600.2016.1172487 is OK
- 10.18637/jss.v076.i01 is OK
- 10.1214/aos/1056562461 is OK
- 10.1214/16-BA1008 is OK
- 10.1002/ece3.6053 is OK
- 10.1080/10618600.2013.791193 is OK
- 10.2307/2937171 is OK
- 10.1007/s10651-016-0353-z is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielturek]

@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:

[danielturek]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (759.3 files/s, 169783.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                                6             96            504            885
Markdown                         4            223              0            869
TeX                              1             42              0            177
YAML                             2             20              7             84
-------------------------------------------------------------------------------
SUM:                            13            381            511           2015
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2235

[danielturek]

@danielskatz I will stay tuned for anything further.

[danielskatz]

@danielturek - this has passed the scope review, so please do go ahead and reduce the size of the paper somewhat, referring to the JOSS guidelines: https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain

[danielskatz]

👋 @richardjgowers - do you think you would be able to edit this JOSS submission?

[danielskatz]

@editorialbot invite @richardjgowers as editor

[editorialbot]

Invitation to edit this submission sent!

[danielturek]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (802.2 files/s, 170998.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                                6             96            504            885
Markdown                         4            197              0            759
TeX                              1             42              0            177
YAML                             2             20              7             84
-------------------------------------------------------------------------------
SUM:                            13            355            511           1905
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1383

[danielturek]

@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:

[danielturek]

@danielskatz I have reduced the word count to 1383.

[danielskatz]

👋 @richardjgowers - just checking again 👇

👋 @richardjgowers - do you think you would be able to edit this JOSS submission?

[danielturek]

@danielskatz @richardjgowers

Following a recent conversations with the development team, we will be making some changes to the nimbleHMC package in the next few weeks. This will include naming conventions for methods and arguments, and also providing an updated version of the algorithm.

I am writing to ask: should review be (temporarily) put on hold? Or, should we proceed, and I will make the relevant changes to the manuscript at the time of other revisions?

Thank you.

[danielskatz]

I'll put this on hold for now - let me know when we should restart it.

[danielturek]

👍

[danielskatz]

@danielturek - how are these changes coming along?

[danielturek]

@danielskatz This is still in the works - certainly not forgotten, but taking longer than usual (as things always do). I appreciate you checking in, and I presume there's not hard deadline on this? But please let me know if there's any sort of timeline that I should be aware of.

[danielskatz]

No, there's not a hard deadline, but at some point, particularly since there are no reviewers, it might be better to remove this and just have you resubmit later when you are ready, rather than keeping submissions in the JOSS system that make it harder to see what we do need to be working on.

[danielturek]

@danielskatz Thank you for explaining. If it's ok, let me give it a few more weeks to try and pull everything (and everyone) together on this.

[danielskatz]

@danielturek - any progress?

[danielturek]

@danielskatz I really appreciate your patience, and checking in. The fact is, we made significant progress and I was hopeful for unpausing the JOSS review. However, a user pointed out a shortcoming in our update which is going to require some developer effort to address.

Given this, would it be best to close this issue, and I will re-open a new review when the software is released and stable?

Thank you again for your patience and help.

[danielskatz]

Yes, let's do that. When you resubmit, please mention this issue (https://github.com/openjournals/joss-reviews/issues/5636)