Joss-reviews: [PRE REVIEW]: simode: R Package for Statistical Inference of Ordinary Differential Equations using Separable Integral-Matching
Submitting author: @ramiyaari (Rami Yaari)
Repository: https://github.com/ramiyaari/simode/
Version: v1.1.6
Editor: @mjsottile
Reviewers: @cscherrer, @jgoldfar, @osorensen
Author instructions
Thanks for submitting your paper to JOSS @ramiyaari. Currently, there isn't an JOSS editor assigned to your paper.
@ramiyaari if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.
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whedon
All 96 comments
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
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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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This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:
You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.
whedon
on 29 Sep 2019
Attempting PDF compilation. Reticulating splines etc...
Failed to discover a valid open source license.
whedon
on 29 Sep 2019
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
whedon
on 29 Sep 2019
@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.
danielskatz
on 29 Sep 2019
@whedon generate pdf
ramiyaari
on 30 Sep 2019
Attempting PDF compilation. Reticulating splines etc...
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
...
l.466 \begin{equation}
Looks like we failed to compile the PDF
whedon
on 30 Sep 2019
@whedon generate pdf
ramiyaari
on 30 Sep 2019
Attempting PDF compilation. Reticulating splines etc...
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
whedon
on 30 Sep 2019
@whedon generate pdf
ramiyaari
on 30 Sep 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 30 Sep 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 30 Sep 2019
Attempting PDF compilation. Reticulating splines etc...
@danielskatz thanks for your comments
I believe I fixed all these issues
ramiyaari
on 30 Sep 2019
@whedon commands
ramiyaari
on 30 Sep 2019
Here are some things you can ask me to do:
# List Whedon's capabilities
@whedon commands
# List of editor GitHub usernames
@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
# Ask Whedon to check the references for missing DOIs
@whedon check references
Please update the software version to 1.1.6
Suggested Reviewers: Jgoldfar, trashbirdecology, MikeLydeamore, MaaniBeigy, llauriciu, matloff, ellessenne, osorensen, RomainAzais
ramiyaari
on 30 Sep 2019
@whedon set v1.1.6 as version
danielskatz
on 1 Oct 2019
OK. v1.1.6 is the version.
whedon
on 1 Oct 2019
I still don't see a readme or a license in the source repo.
danielskatz
on 1 Oct 2019
There is a README.txt and a LICENSE.txt file under inst/joss in the repo, together with paper.md
ramiyaari
on 1 Oct 2019
@danielskatz: There is a README.txt and a LICENSE.txt file under inst/joss in the repo, together with paper.md
ramiyaari
on 3 Oct 2019
These need to be at the top level of the repo
danielskatz
on 4 Oct 2019
OK, fixed it
ramiyaari
on 5 Oct 2019
👋 @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/
labarba
on 9 Oct 2019
Yes, I can take this submission as editor.
mjsottile
on 12 Oct 2019
@whedon assign @mjsottile as editor
labarba
on 12 Oct 2019
OK, the editor is @mjsottile
whedon
on 12 Oct 2019
👋@cscherrer would you be interested in reviewing this paper?
mjsottile
on 15 Oct 2019
@whedon add @cscherrer as reviewer
mjsottile
on 15 Oct 2019
OK, @cscherrer is now a reviewer
whedon
on 15 Oct 2019
@whedon assign @cscherrer as reviewer
mjsottile
on 15 Oct 2019
OK, the reviewer is @cscherrer
whedon
on 15 Oct 2019
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?
mjsottile
on 16 Oct 2019
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?
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jgoldfar
on 18 Oct 2019
Thanks @jgoldfar. That timeline should be fine in November.
mjsottile
on 30 Oct 2019
@whedon add @jgoldfar as reviewer
mjsottile
on 30 Oct 2019
OK, @jgoldfar is now a reviewer
whedon
on 30 Oct 2019
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.
mjsottile
on 30 Oct 2019
Yes, I am interested.
osorensen
on 30 Oct 2019
Yes, I am interested.
MaaniBeigy
on 30 Oct 2019
Yes, I am interested
On Wed, 30 Oct 2019, 07:33 Øystein Sørensen, notifications@github.com
wrote:
Yes, I am interested.
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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,
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MaaniBeigy
on 30 Oct 2019
Thanks @osorensen - I'll add you. @MaaniBeigy , I will hold off adding you unless we need an additional reviewer during the process.
mjsottile
on 30 Oct 2019
@whedon add @osorensen as reviewer
mjsottile
on 30 Oct 2019
OK, @osorensen is now a reviewer
whedon
on 30 Oct 2019
@whedon start review
mjsottile
on 30 Oct 2019
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1850. Feel free to close this issue now!
whedon
on 30 Oct 2019
@whedon generate pdf
ramiyaari
on 16 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 16 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 16 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 16 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 16 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 16 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 16 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 16 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 16 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 16 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 16 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 16 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 17 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ramiyaari
on 26 Nov 2019
Attempting PDF compilation. Reticulating splines etc...
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