[PRE REVIEW]: simode: R Package for Statistical Inference of Ordinary Differential Equations using Separable Integral-Matching

[whedon]

Submitting author: @ramiyaari (Rami Yaari) Repository: https://github.com/ramiyaari/simode/ Version: v1.1.6 Editor: @mjsottile Reviewers: @cscherrer, @jgoldfar, @osorensen

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

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[whedon]

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

Failed to discover a valid open source license.

[whedon]

PDF failed to compile for issue #1772 with the following error:

Could not find bibliography file: simode.bib Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

[danielskatz]

@ramiyaari - I see some high-level issues here:

• no readme
• no license

Please see https://joss.readthedocs.io/en/latest/submitting.html#typical-paper-submission-flow

Also, in your paper, you say the bib is "bibliography: simode.bib" but it's actually "paper.bib" - please fix this, then enter @whedon generate pdf as a new comment in this issue to recompile.

[ramiyaari]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1772 with the following error:

Error producing PDF. ! LaTeX Error: Bad math environment delimiter.

See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ...

l.466 \begin{equation}

Looks like we failed to compile the PDF

[ramiyaari]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1772 with the following error:

Error producing PDF. ! Missing \endgroup inserted.

\endgroup l.482 \begin{eqnarray} Looks like we failed to compile the PDF

[ramiyaari]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[ramiyaari]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[ramiyaari]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[ramiyaari]

@danielskatz thanks for your comments I believe I fixed all these issues

[ramiyaari]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
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@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

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@whedon check references

[ramiyaari]

Please update the software version to 1.1.6 Suggested Reviewers: Jgoldfar, trashbirdecology, MikeLydeamore, MaaniBeigy, llauriciu, matloff, ellessenne, osorensen, RomainAzais

[danielskatz]

@whedon set v1.1.6 as version

[whedon]

OK. v1.1.6 is the version.

[danielskatz]

I still don't see a readme or a license in the source repo.

[ramiyaari]

There is a README.txt and a LICENSE.txt file under inst/joss in the repo, together with paper.md

[ramiyaari]

@danielskatz: There is a README.txt and a LICENSE.txt file under inst/joss in the repo, together with paper.md

[danielskatz]

These need to be at the top level of the repo

[ramiyaari]

OK, fixed it

[labarba]

👋 @mjsottile — Could you handle this submission as editor? simode: R Package for Statistical Inference of Ordinary Differential Equations using Separable Integral-Matching Repository: https://github.com/ramiyaari/simode/

[mjsottile]

Yes, I can take this submission as editor.

[labarba]

@whedon assign @mjsottile as editor

[whedon]

OK, the editor is @mjsottile

[mjsottile]

👋@cscherrer would you be interested in reviewing this paper?

[mjsottile]

@whedon add @cscherrer as reviewer

[whedon]

OK, @cscherrer is now a reviewer

[mjsottile]

@whedon assign @cscherrer as reviewer

[whedon]

OK, the reviewer is @cscherrer

[mjsottile]

Other possible reviewers from the spreadsheet: @jgoldfar - you appear to have knowledge of differential equations and R. @fabian-s - you appear to have knowledge of R and inference methods. Interested in taking this on to help review?

[jgoldfar]

I would be able to take this on at the beginning of November; I'd be happy to help if there is still a need for review.

On Oct 16, 2019, at 12:09 AM, Matthew Sottile notifications@github.com wrote:

Other possible reviewers from the spreadsheet: @jgoldfar https://github.com/jgoldfar - you appear to have knowledge of differential equations and R. @fabian-s https://github.com/fabian-s - you appear to have knowledge of R and inference methods. Interested in taking this on to help review?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1772?email_source=notifications&email_token=ABKORGJBHNLI3VV2BR544G3QO2HY7A5CNFSM4I3SPZ5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBK7HSA#issuecomment-542503880, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABKORGL2H4XEZAAD5Y3IJTDQO2HY7ANCNFSM4I3SPZ5A.

[mjsottile]

Thanks @jgoldfar. That timeline should be fine in November.

[mjsottile]

@whedon add @jgoldfar as reviewer

[whedon]

OK, @jgoldfar is now a reviewer

[mjsottile]

Hi, @trashbirdecology, @MikeLydeamore, @MaaniBeigy, @llauriciu, @matloff, @ellessenne, @osorensen, @RomainAzais - you were suggested as potential reviewers for this JOSS submission. Let me know if you're interested in reviewing this submission. I am looking for at least one reviewer to add before I start the review process.

[osorensen]

Yes, I am interested.

[MaaniBeigy]

Yes, I am interested.

[MaaniBeigy]

Yes, I am interested

On Wed, 30 Oct 2019, 07:33 Øystein Sørensen, notifications@github.com wrote:

Yes, I am interested.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1772?email_source=notifications&email_token=AI6QPJQF3GOSJPYQO62VO5LQREBQXA5CNFSM4I3SPZ5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECS3GGY#issuecomment-547730203, or unsubscribe https://github.com/notifications/unsubscribe-auth/AI6QPJQIJE2CV5K4PA43QOTQREBQXANCNFSM4I3SPZ5A .

[mjsottile]

Thanks @osorensen - I'll add you. @MaaniBeigy , I will hold off adding you unless we need an additional reviewer during the process.