Joss-reviews: [REVIEW]: walkr: MCMC Sampling from Non-Negative Convex Polytopes

[whedon]

Submitting author: @andyyao95 (Andy Yao)
Repository: https://github.com/andyyao95/walkr
Version: v0.3.4
Editor: @karthik
Reviewer: @dgrtwo
Archive: 10.5281/zenodo.400944

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/71b0689984d98a4ecc39b5e906ba0c71/status.svg)](http://joss.theoj.org/papers/71b0689984d98a4ecc39b5e906ba0c71)

Reviewers and authors: Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue
in the target repository and link to those issues (especially acceptance-blockers)
in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice
versa will create corresponding breadcrumb trails in the link target.)

Reviewer questions

Conflict of interest

• [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

  General checks

• [x] Repository: Is the source code for this software available at the repository url?

• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

• [x] Version: Does the release version given match the GitHub release (v0.3.3)?

  Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?

• [x] Functionality: Have the functional claims of the software been confirmed?

• [x] Performance: Have any performance claims of the software been confirmed?

  Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?

• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g. API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
  

  Software paper

Paper PDF: 10.21105.joss.00061.pdf

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] References: Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?

[arfon]

Hi @andyyao95. Currently the paper doesn't compile properly as you're not actually citing any of the references in the paper. Could you actually cite the entries in your paper.bib (e.g. [@kannan]) in the body of the paper?

[andyyao95]

Hi Arfon,

Thank you so much, I used the reference for a longer version of the paper
instead (my bad). I just updated the paper.bib and paper.md to properly
cite all the references.

Let me know if you have any other questions. Thanks!

Andy

On Mon, Sep 12, 2016 at 12:54 AM, Arfon Smith [email protected]
wrote:

Hi @andyyao95 https://github.com/andyyao95. Currently the paper doesn't
compile properly as you're not actually citing any of the references in the
paper. Could you actually cite the entries in your paper.bib (e.g. [
@kannan https://github.com/kannan]) in the body of the paper?

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[arfon]

/ cc @openjournals/joss-reviewers - would anyone be willing to review this submission?

If you would like to review this submission then please comment on this thread so that others know you're doing a review (so as not to duplicate effort). Something as simple as :hand: I am reviewing this will suffice.

Reviewer instructions

• Please work through the checklist at the start of this issue.
• If you need any further guidance/clarification take a look at the reviewer guidelines here http://joss.theoj.org/about#reviewer_guidelines
• Please make a publication recommendation at the end of your review

Any questions, please ask for help by commenting on this issue! 🚀

[arfon]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the reviewer of this submission
@whedon assign @username as reviewer

# List the GitHub usernames of the JOSS editors
@whedon list editors

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

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Open the review issue
@whedon start review

:construction: Important :construction:

This is all quite new. Please make sure you check the top of the issue after running a @whedon command (you might also need to refresh the page to see the issue update).

[arfon]

@whedon assign @jakevdp as editor

[whedon]

OK, the editor is @jakevdp

[jakevdp]

I contacted Neal Thomas, author of R2OpenBUGS, to see if he's interested in reviewing.

[jakevdp]

Neal was not interested, nor were a couple other R/Bayesian folks. Still reaching out to some...

[karthik]

@jakevdp You might ask @dgrtwo if he's interested and has the time.

[jakevdp]

Hi folks,
I'm completely striking out finding a reviewer for this. To be entirely honest, I accepted this thinking it was a Python package. I'm finding I don't have enough ties to the Rstats community to find an appropriate person/someone who knows me well enough to not blow me off.

Is there a way to re-assign this to another editor? I'm frankly out of ideas.

[arfon]

@karthik - would you be able to take this one?

[karthik]

Sure. Assign it to me. Will handle on Friday when I'm back. 

On Thu, Sep 29, 2016 at 6:36 PM +0200, "Arfon Smith" [email protected] wrote:

@karthik - would you be able to take this one?

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You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub, or mute the thread.

[arfon]

@whedon assign @karthik as editor

[whedon]

OK, the editor is @karthik

[karthik]

Quick update that I am still working to find reivewers for this submission.

[arfon]

Quick update that I am still working to find reviewers for this submission.

Any update on this @karthik?

[andyyao95]

Hi @karthik,

I am wondering if there is any update from the reviewers. Please let me know if anything can be done on my end to faciliate the process.

Thanks!
Andy

[karthik]

Hi @andyyao95, Apologies for the delay but two folks I contacted declined the invitation to review. I'm still seeking out other reviewers. If you have any suggestions for people I should contact, please mention it in this thread or drop me a note (karthik.ram at berkeley edu).

[dgrtwo]

I volunteer to review this. I'll have it done by Saturday.

I'm sorry the process has taken so long!

[andyyao95]

@karthik @dgrtwo Thank you two so much! I look forward to hearing back from you guys.

Best,
Andy

[andyyao95]

Hi @dgrtwo .

I just wanted to check with you where the package is in the reviewing process. Thanks a ton!

Best,
Andy

[karthik]

@whedon assign @dgrtwo as reviewer

[whedon]

OK, the reviewer is @dgrtwo

[karthik]

@dgrtwo Hi Dave, can you update this thread when you get a chance? Thanks!

[arfon]

@dgrtwo Hi Dave, can you update this thread when you get a chance? Thanks!

Friendly new year reminder @dgrtwo 😁

[arfon]

:wave: @dgrtwo - are you still able to review this submission for JOSS? If not, we can look for another reviewer.

[maelle]

@arfon just noticed this from the CRANberries feed https://cran.r-project.org/web/packages/walkr/index.html

[maelle]

The reason for removal from CRAN is "Archived on 2017-02-16 as check problems were not corrected despite reminders."

[andyyao95]

@arfon @masalmon Hi. Very sorry about this. There was a minor error in compiling the package vignette on CRAN. I missed the reminder as it was in another email.

I've updated the package (same content, small vignette fix). I'll let you guys know when CRAN updates it. Thanks!

[maelle]

@andyyao95 great I had just copied this here in case you were MIA :wink: cool that you could solve the error!

[andyyao95]

It's back on CRAN now. (also updated on github.) Thank you guys for your patience. Let me know if anything else is needed in the review process.

Looking forward to hearing back, and have a nice day!

[arfon]

:wave: @dgrtwo - are you still able to review this submission?

@andyyao95 - I think we might need to find an alternative reviewer here.

[dgrtwo]

@arfon Sorry, this completely slipped my mind again :( I'll do it immediately.

[dgrtwo]

After review I'm recommending acceptance; my only issues (about GitHub/CRAN differences and DOIs) were resolved in this issue. My other note is that the version is now 0.3.4 (I don't know where that should change in the submission).

Overall this is a great package and I've been impressed as I've played with the mathematical sampling. I particularly like the detail and figures in the vignette and am impressed with the test coverage. paper.md covers the software's uses well.

I greatly appreciate your patience in this unusually long process, as well as Andy's quick response to feedback!

Reviewer questions

Conflict of interest

• [X] As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

  General checks

• [X] Repository: Is the source code for this software available at the repository url?

• [X] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

• [X] Version: Does the release version given match the GitHub release (v0.3.3)?

  Functionality

• [X] Installation: Does installation proceed as outlined in the documentation?

• [X] Functionality: Have the functional claims of the software been confirmed?

• [X] Performance: Have any performance claims of the software been confirmed?

  Documentation

• [X] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?

• [X] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [X] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [X] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g. API method documentation)?
• [X] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [X] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
  

  Software paper

Paper PDF: 10.21105.joss.00061.pdf

• [X] Authors: Does the paper.md file include a list of authors with their affiliations?
• [X] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [X] References: Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?

[arfon]

I greatly appreciate your patience in this unusually long process, as well as Andy's quick response to feedback!

👍 thanks @dgrtwo!

@andyyao95 - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[karthik]

Thanks @dgrtwo!

@arfon Getting caught up here but glad the review is in.

[andyyao95]

Hi @arfon. Here it is: https://doi.org/10.5281/zenodo.400944

Let me know if this is okay! Thanks for all the help.

[arfon]

@whedon set 10.5281/zenodo.400944 as archive

[whedon]

OK. 10.5281/zenodo.400944 is the archive.

[arfon]

Many thanks for the review @dgrtwo and for editing this one @karthik ✨

@andyyao95 - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00061 ⚡️ 🚀 💥

[andyyao95]

Hi @arfon @dgrtwo and @karthik, thanks so much for the help in the process. Really appreciate everything and glad that the review was successful.

[davidkane9]

Thanks to all involved!

Question: When I look at http://joss.theoj.org/papers/10.21105/joss.00061,
the Paper:
PDF link »
https://github.com/openjournals/joss-papers/raw/master/joss.00061/10.21105.joss.00061.pdf
does not link to a copy of the paper. Instead it links to a one page
summary. Is that correct?

[arfon]

@davidkane9 - https://github.com/openjournals/joss-papers/raw/master/joss.00061/10.21105.joss.00061.pdf _is_ the full JOSS paper. Please take a look at the author guidelines here.

[davidkane9]

Ah, yes. Read that so long ago that I had forgotten it!

;-)

On Mon, Mar 20, 2017 at 9:23 AM, Arfon Smith [e-mail]
wrote:

@davidkane9 https://github.com/davidkane9 - https://github.com/
openjournals/joss-papers/raw/master/joss.00061/10.21105.joss.00061.pdf
is the full JOSS paper. Please take a look at the author guidelines here
http://joss.theoj.org/about#author_guidelines.

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