[PRE REVIEW]: spatPomp: An R package for spatiotemporal partially observed Markov process models

[editorialbot]

Submitting author: !--author-handle-->@ionides<!--end-author-handle-- (Edward Ionides) Repository: https://github.com/kidusasfaw/spatPomp Branch with paper.md (empty if default branch): joss Version: 0.35.1 Editor: !--editor-->@gkthiruvathukal<!--end-editor-- Reviewers: @bbolker, @johnlees Managing EiC: Chris Vernon

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

@ionides 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.

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (2057.3 files/s, 279158.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               71           1002           2227           6840
C                               12            272             99           1041
Markdown                         5            188              0            746
XML                              1              0              0            258
make                             3             66              0            189
YAML                             4             27              6            137
TeX                              1             16              0            119
C/C++ Header                     1              8             13             44
-------------------------------------------------------------------------------
SUM:                            98           1579           2345           9374
-------------------------------------------------------------------------------

Commit count by author:

   283  Kidus Asfaw
    92  Ed Ionides
    30  Edward Ionides
    25  Aaron A. King
    11  joonhap
     7  allistho
     2  Jesse Wheeler PC
     1  Aaron A King
     1  Edward L Ionides
     1  Haogao Gu
     1  Jifan Li
     1  Kidus
     1  Ning Ning

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1206

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

:warning: An error happened when generating the pdf.

[crvernon]

@editorialbot invite @RMeli as editor

👋 @RMeli can you take this on one as editor?

[editorialbot]

Invitation to edit this submission sent!

[crvernon]

@xuanxu can you take a look at the paper compile action error on this one to see if we can get it working? Thank you so much!

[ionides]

@editorialbot generate pdf

Dear JOSS editors,

Apologies for submitting a paper.md which failed to compile. I tested it successfully on my computer via:

docker run --rm -it -v $PWD:/data -u $(id -u):$(id -g) openjournals/inara -o pdf,crossref paper.md

From the error message at https://github.com/openjournals/joss-papers/actions/runs/9349651694/job/25731446811 it seemed possible that the problem with the JOSS GitHub action was related to the date format. On comparing with the example.md provided by JOSS, I noticed a difference in the date formatting. I have now changed the date format, and pushed a new version to the joss branch of https://github.com/kidusasfaw/spatPomp

It was unclear to me whether there is a way to run exactly the JOSS GitHub action to further test paper.md. Reviewing the website, it seems like the editorialbot may be able to do this. I'm experimenting with an editorialbot command in this email to see if that helps.

Thanks, Ed

Edward L. Ionides Associate Chair for Undergraduate Studies and Professor, Department of Statistics, University of Michigan 1085 South University, Ann Arbor, MI 48109-1107 email: @.*** phone: 734 615 3332 office: 453 West Hall

On Mon, Jun 3, 2024 at 10:19 AM Chris Vernon @.***> wrote:

@editorialbot https://github.com/editorialbot invite @RMeli https://github.com/RMeli as editor

👋 @RMeli https://github.com/RMeli can you take this on one as editor?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6827#issuecomment-2145325009, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABKAFT47I3BL4WEUOXFAG73ZFR3PHAVCNFSM6AAAAABIWLDXSSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBVGMZDKMBQHE . You are receiving this because you were mentioned.Message ID: @.***>

[editorialbot]

:warning: An error happened when generating the pdf. Problem with affiliations for Kidus Asfaw, perhaps the affiliations index need quoting?.

[ionides]

@editorialbot generate pdf

I've pushed a version quoting all affiliation numbers in paper.md

Edward L. Ionides Associate Chair for Undergraduate Studies and Professor, Department of Statistics, University of Michigan 1085 South University, Ann Arbor, MI 48109-1107 email: @.*** phone: 734 615 3332 office: 453 West Hall

On Mon, Jun 3, 2024 at 10:26 AM The Open Journals editorial robot < @.***> wrote:

⚠️ An error happened when generating the pdf https://github.com/openjournals/joss-papers/actions/runs/9351991353?check_suite_focus=true. Problem with affiliations for Kidus Asfaw, perhaps the affiliations index need quoting?.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6827#issuecomment-2145340590, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABKAFT6CSQXFCP7UOYQJAJLZFR4IFAVCNFSM6AAAAABIWLDXSSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBVGM2DANJZGA . You are receiving this because you were mentioned.Message ID: @.***>

[editorialbot]

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

[ionides]

Here are some referee suggestions:

Ben Bolker (bolker at mcmaster.ca) https://ms.mcmaster.ca/~bolker/ An expert on spatiotemporal population biology and statistical software. If he agrees to review, that would be great!

John Lees (jlees at ebi.ac.uk) https://www.infectiousdisease.cam.ac.uk/staff/dr-john-lees The corresponding author of a related open-source project, https://wellcomeopenresearch.org/articles/5-288/v2

Len Thomas (len.thomas at st-andrews.ac.uk) https://lenthomas.org/ Interested in partially observed Markov models in ecology, as well as statistical software.

[crvernon]

@editorialbot generate pdf I've pushed a version quoting all affiliation numbers in paper.md

Thanks @ionides!

[crvernon]

@xuanxu can you take a look at the paper compile action error on this one to see if we can get it working? Thank you so much!

✅ looks like this is resolved @xuanxu.

[RMeli]

@crvernon I'm sorry but I took over another submission that was more in line with my area of expertise.

[crvernon]

@editorialbot invite @gkthiruvathukal as editor

:wave: @gkthiruvathukal do you have the bandwidth to take this one on as editor?

[editorialbot]

Invitation to edit this submission sent!

[gkthiruvathukal]

@editorialbot assign me as editor

[editorialbot]

Assigned! @gkthiruvathukal is now the editor

[gkthiruvathukal]

@crvernon I'll start review next week.

[gkthiruvathukal]

@ionides Thanks for your reviewer suggestions; however, I need GitHub IDs to invite them. Can you please provide?

[gkthiruvathukal]

@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:

[gkthiruvathukal]

@editorialbot commands

[editorialbot]

Hello @gkthiruvathukal, here are the things you can ask me to do:

# List all available commands
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# Add to this issue's reviewers list
@editorialbot add @username as reviewer

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

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@editorialbot remind @reviewer in 2 weeks

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

# Set a value for version
@editorialbot set v1.0.0 as version

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

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@editorialbot create post-review checklist

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[gkthiruvathukal]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (2101.8 files/s, 282545.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               71           1002           2227           6840
C                               12            272             99           1041
Markdown                         5            188              0            746
make                             3             66              0            189
YAML                             4             27              6            137
TeX                              1             16              0            119
C/C++ Header                     1              8             13             44
-------------------------------------------------------------------------------
SUM:                            97           1579           2345           9116
-------------------------------------------------------------------------------

Commit count by author:

   283  Kidus Asfaw
    94  Ed Ionides
    30  Edward Ionides
    25  Aaron A. King
    11  joonhap
     7  allistho
     2  Jesse Wheeler PC
     1  Aaron A King
     1  Edward L Ionides
     1  Haogao Gu
     1  Jifan Li
     1  Kidus
     1  Ning Ning

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1208

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[gkthiruvathukal]

@editorialbot list reviewers

[editorialbot]

Please log in the JOSS Reviewers site to search through the list of current reviewers.

[gkthiruvathukal]

@crvernon or @arfon: What editorialbot command will give me the list of similar papers and identify potential reviewers? It seems not to have been triggered for this submission's pre-review, and the "commands" command gives no insight on this. I think we need an issue to make sure this is easy to find.

Somehow, I thought "generate pdf" would trigger this. It does not.

[crvernon]

@crvernon or @arfon: What editorialbot command will give me the list of similar papers and identify potential reviewers? It seems not to have been triggered for this submission's pre-review, and the "commands" command gives no insight on this. I think we need an issue to make sure this is easy to find.

Somehow, I thought "generate pdf" would trigger this. It does not.

:wave: @gkthiruvathukal - Let me make sure that there is a command to actually do this outside of what gets executed when the Pre-Review thread starts. I'll do so now and come back with an answer. Thanks!

[ionides]

Hi @gkthiruvathukal,

Here are the GitHub IDs for the potential referees I suggested.

Ben Bolker is bbolker at GitHub, Len Thomas is lenthomas, John Lees is johnlees.

Best, Ed

[crvernon]

@crvernon or @arfon: What editorialbot command will give me the list of similar papers and identify potential reviewers? It seems not to have been triggered for this submission's pre-review, and the "commands" command gives no insight on this. I think we need an issue to make sure this is easy to find. Somehow, I thought "generate pdf" would trigger this. It does not.

👋 @gkthiruvathukal - Let me make sure that there is a command to actually do this outside of what gets executed when the Pre-Review thread starts. I'll do so now and come back with an answer. Thanks!

@gkthiruvathukal - this is not a bot command and was / is an experimental feature. We are looking into getting it setup as an actual command we can evoke via the editorialbot.

[gkthiruvathukal]

@crvernon Let's hope for @editorialbot suggest-reviewers. It would be great if we can get the usernames, when clicked, to trigger an @editorialbot invite <username> as reviewer.

[gkthiruvathukal]

@crvernon: Signaling @arfon as he and I chatted about this long ago during one of our amazing calls! The fact that we have this pre-review feature is the result of an amazing pairing with Arfon. I wanted to code it but he went ahead with the implementation (ok with that!)

I would really like to eliminate the tedium of having to generate ad hoc invitation requests as well. Perhaps we can have the invite semantics be to generate a comment asking whether the prospective reviewer would be willing to edit this submission. It would be really amazing if they could just click a yes/no checkbox and be self-assigned.

I wonder whether I should open an issue, if only to articulate the thinking, which is based on many years of EIC service in IEEE publications. Most publications have workflows with few (if any) manual steps. AEICs (like you) and Editors (like me) should be able to have personalized templates for various requests, e.g. inviting reviewers, nudging reviewers, and checklists for acceptance.

Meanwhile, I'm going to go with @ionides's suggestions!

[crvernon]

Thanks @gkthiruvathukal, I think opening an issue is a good idea along with articulating your thoughts above in the development channel on our internal Slack forum. Lots of value to glean from you on these!

[gkthiruvathukal]

@bbolker, @lenthomas, and @johnlees: Are you available to contribute a review for this JOSS submission? I need at least two reviewers to proceed.

[bbolker]

I think I can do it (what's the time frame?)

[gkthiruvathukal]

Hi @bbolker. We work with our reviewers' availability and constraints. Would a few weeks be sufficient?

[bbolker]

OK

[gkthiruvathukal]

@editorialbot add @bbolker as reviewer

[editorialbot]

@bbolker added to the reviewers list!

[johnlees]

I am happy to review, if I can be given a deadline of Aug 2nd

[gkthiruvathukal]

@johnlees I can easily accommodate your schedule! I'm going to assume yes. As a general rule, we always work with our reviewers and their schedules. Thank you for saying yes!

[gkthiruvathukal]

@editorialbot add @johnlees as reviewer

[editorialbot]

@johnlees added to the reviewers list!

[gkthiruvathukal]

@editorialbot start review