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[PRE REVIEW]: spatPomp: An R package for spatiotemporal partially observed Markov process models #6827

Open editorialbot opened 1 month ago

editorialbot commented 1 month ago

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: Pending Managing EiC: Chris Vernon

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status

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HTML: <a href="https://joss.theoj.org/papers/45c57a035b559a99d543550bd5e54fe6"><img src="https://joss.theoj.org/papers/45c57a035b559a99d543550bd5e54fe6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/45c57a035b559a99d543550bd5e54fe6/status.svg)](https://joss.theoj.org/papers/45c57a035b559a99d543550bd5e54fe6)

Author instructions

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.

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 commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1206

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

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

editorialbot commented 1 month ago

:warning: An error happened when generating the pdf.

crvernon commented 1 month ago

@editorialbot invite @RMeli as editor

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

editorialbot commented 1 month ago

Invitation to edit this submission sent!

crvernon commented 1 month ago

@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 commented 1 month ago

@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 commented 1 month ago

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

ionides commented 1 month ago

@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 commented 1 month ago

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

ionides commented 1 month ago

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 commented 1 month ago

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

Thanks @ionides!

crvernon commented 1 month ago

@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 commented 1 month ago

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

crvernon commented 1 month ago

@editorialbot invite @gkthiruvathukal as editor

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

editorialbot commented 1 month ago

Invitation to edit this submission sent!

gkthiruvathukal commented 1 month ago

@editorialbot assign me as editor

editorialbot commented 1 month ago

Assigned! @gkthiruvathukal is now the editor

gkthiruvathukal commented 1 month ago

@crvernon I'll start review next week.

gkthiruvathukal commented 3 weeks ago

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

gkthiruvathukal commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

gkthiruvathukal commented 3 weeks ago

@editorialbot commands

editorialbot commented 3 weeks ago

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


# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

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

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@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

# Set a value for repository
@editorialbot set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@editorialbot set 10.5281/zenodo.6861996 as archive

# Mention the EiCs for the correct track
@editorialbot ping track-eic

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

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

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Flag submission with questionable scope
@editorialbot query scope

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

# Creates a post-review checklist with editor and authors tasks
@editorialbot create post-review checklist

# Open the review issue
@editorialbot start review
gkthiruvathukal commented 3 weeks ago

@editorialbot check repository

editorialbot commented 3 weeks ago

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 commented 3 weeks ago

Paper file info:

📄 Wordcount for paper.md is 1208

✅ The paper includes a Statement of need section

editorialbot commented 3 weeks ago

License info:

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

gkthiruvathukal commented 3 weeks ago

@editorialbot list reviewers

editorialbot commented 3 weeks ago

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

gkthiruvathukal commented 3 weeks ago

@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 commented 3 weeks ago

@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 commented 3 weeks ago

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 commented 3 weeks ago

@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 commented 3 weeks ago

@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 commented 3 weeks ago

@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 commented 3 weeks ago

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!