[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: v0.2.0 Editor: !--editor-->@likeajumprope<!--end-editor-- Reviewers: @matt-graham, @larryshamalama Managing EiC: Arfon Smith

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (677.9 files/s, 198333.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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R                                7            176            675           1922
Markdown                         4            200              0            762
TeX                              1             49              0            201
YAML                             2             20              7             84
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SUM:                            14            445            682           2969
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1415

[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

[editorialbot]

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

[arfon]

@danielturek - 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!

[editorialbot]

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⚠️ 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 considering asking the reviewers of these papers to review again for JOSS.

[danielturek]

@danielskatz Asked me to reference previous submission of this article in PR #5636 .

This submission was closed for additional updates to the manuscript, which have now been completed.

[arfon]

@editorialbot invite @jromanowska as editor

:wave: @jromanowska – would you be willing to edit this submission for JOSS?

[editorialbot]

Invitation to edit this submission sent!

[jromanowska]

@arfon - sorry, I'm not an expert in this topic! I hope you can find another editor to handle that one.

[likeajumprope]

I can take this one - I work with pyMC and Stan a lot

[likeajumprope]

@editorialbot assign @likeajumprope as editor

[editorialbot]

Assigned! @likeajumprope is now the editor

[likeajumprope]

Hi @danielturek - while I am looking for reviewers, do you maybe have some suggestions?

[danielturek]

@likeajumprope Yes, perhaps (GitHub usernames, taken from the list of JOSS reviewers):

• larryshamalama (possible in April 2024)
• thomaspinder
• tbrown122387
• Volkerschmid
• braniii

[likeajumprope]

👋 @larryshamalama @thomaspinder @tbrown122387 @Volkerschmid could you maybe help us out with reviewing this one?

[tbrown122387]

Hey @likeajumprope @danielturek: unfortunately I'm strapped for time at the moment, and I'm already reviewing another JOSS paper. I appreciate the invite though

[larryshamalama]

👋 @larryshamalama @thomaspinder @tbrown122387 @volkerschmid could you maybe help us out with reviewing this one?

Unfortunately, I am busy for the next month or so. If you are okay if I do this revision in early April, I would be happy to do it then.

[likeajumprope]

Hi @braniii, could you help with this one maybe?

[braniii]

Hi @likeajumprope, thx for the invitation. The project sounds very exciting, but unfortunately I have no experience in R and only basic knowledge of HMC. So it probably makes more sense to have someone else review it.

[likeajumprope]

Hi @likeajumprope, thx for the invitation. The project sounds very exciting, but unfortunately I have no experience in R and only basic knowledge of HMC. So it probably makes more sense to have someone else review it.

Thanks for letting me know!

[danielturek]

@likeajumprope Is there anything I can do to help the review process get started?

Thanks!

[likeajumprope]

@likeajumprope Is there anything I can do to help the review process get started?

Thanks!

The search for reviewers has been quite hard, both on an off github. Do you maybe have some more suggestions?

[danielturek]

@likeajumprope Perhaps either goldingn or njtierney ?

[arfon]

@likeajumprope – just checking to see if any of the automated recommendations from @editorialbot have been checked here too?https://github.com/openjournals/joss-reviews/issues/6237#issuecomment-1898206686

[oliviaguest]

@likeajumprope have you tried to email people who have ignored your tag on github? 😊

[danielturek]

Thanks for the suggestions @oliviaguest

@likeajumprope please let me know if I can help facilitate the process, I'm keen to see it move forward.

[likeajumprope]

Hi all, I sent out 4 additional invitations per email on Friday - hopefully we'll have some replies soon. It has been quite hard to find reviewers tbh.

[matt-graham]

I received an invite to review this by email. I'd be happy to do so, but just wanted to note I'm not an R expert. I do however know Hamiltonian Monte Carlo well so happy to review on that basis. I'm also currently reviewing another JOSS paper and will be not working over Easter so wouldn't be able to start on reviewing this till a couple of weeks.

[likeajumprope]

I received an invite to review this by email. I'd be happy to do so, but just wanted to note I'm not an R expert. I do however know Hamiltonian Monte Carlo well so happy to review on that basis. I'm also currently reviewing another JOSS paper and will be not working over Easter so wouldn't be able to start on reviewing this till a couple of weeks.

Yes that would be fine, thanks @matt-graham!

[likeajumprope]

@editorialbot add @matt-graham as reviewer

[editorialbot]

@matt-graham added to the reviewers list!

[danielturek]

@matt-graham Much obliged!

[likeajumprope]

I had two more rejections per email, but I also sent out three more requests today, so fingers crossed! Apologies this has been taking a while @danielturek

[likeajumprope]

just to give an update: I have been writing to 5 more potential reviewers behind the scenes, with no luck so far. Will continue and keep you posted

[danielturek]

@likeajumprope Thanks much for the update. Please let me know if I can assist, which I'd be happy to do.

[larryshamalama]

👋 @larryshamalama @thomaspinder @tbrown122387 @volkerschmid could you maybe help us out with reviewing this one?

Unfortunately, I am busy for the next month or so. If you are okay if I do this revision in early April, I would be happy to do it then.

@likeajumprope @danielturek I'm back from holidays and have a bit more capacity these days. If you are still looking for a reviewer, you can assign me

[danielturek]

@likeajumprope I'll please let you perform any official actions, but it seems like we have 2 willing reviewers (@matt-graham and @larryshamalama). Is that the number required?

[crvernon]

👋 @likeajumprope - just checking in to see if you saw the above. Let me know if you need anything to help get this one started. Thanks for all the work finding reviewers!

[danielturek]

@likeajumprope @danielskatz @crvernon @matt-graham @larryshamalama @editorialbot

Is there anything I can (please) do to help get this review process started?

I believe we have two reviewers identified (@matt-graham @larryshamalama).

[crvernon]

:wave: @danielturek I am the AEiC for this track of submissions. I am trying to get in touch with your editor now. If I cannot, I'll take your submission on myself. In the meantime, let's go ahead and get this review started.

[crvernon]

@editorialbot add @larryshamalama as reviewer

[editorialbot]

@larryshamalama added to the reviewers list!

[crvernon]

@editorialbot start review

👋 - Alright @danielturek, @matt-graham, and @larryshamalama - I am going to close this Pre-Review and kick off the full review which you should receive a notification for. Thanks!

And thank you @matt-graham and @larryshamalama for agreeing to review!

cc. @likeajumprope

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6745.

[danielturek]

@crvernon Thanks for taking this on.