Joss-reviews: [REVIEW]: ivporbit:An R package to estimate the instrumental variables probit model

[whedon]

Submitting author: @zedtaha (zaghdoudi Taha)
Repository: https://github.com/zedtaha/ivprobit-1.0
Version: v1.0
Editor: @leeper
Reviewer: @justinesarey
Archive: 10.5281/zenodo.1183253

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### Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

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 (v1.0)?
• [x] Authorship: Has the submitting author (@zedtaha) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

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)?
• [ ] 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

• [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)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @justinesarey it looks like you're currently assigned as the reviewer for this paper :tada:.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00523/joss.00523/10.21105.joss.00523.pdf

[leeper]

Hi @justinesarey just a quick nudge on this review!

[justinesarey]

Hi Thomas,

Got it; I should be able to respond soon.

-JE

--

Dr. Justin Esarey
Associate Professor of Political Science
Rice University
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Fax: [phone]
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On Sun, Feb 4, 2018 at 10:37 AM, Thomas J. Leeper [e-mail]
wrote:

Hi @justinesarey https://github.com/justinesarey just a quick nudge on
this review!

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[justinesarey]

I have completed this review. The software appears to work as advertised (at least, it matches results on identical data in Stata 15.1 -- an encouraging sign!). However, the documentation provided in R (when installed using install.packages("ivprobit", dep=T)) makes the software challenging to figure out. The basic issue is that the important information in the help files don't correspond to CRAN practices. Among other issues, (a) the example model should be included in the ivprobit help file and not the overall package help file; (b) the ivprobit and ivprobit.formula sub-methods should be subsumed into a single ivprobit help function (c) there should be actual details of, e.g., what arguments get passed to ivprobit in the ivprobit help file (d) the ivprob function should be hidden or should redirect attention to the main ivprobit function (d) the example data set shouldn't be duplicated three times. I strongly suggest the authors take a look at existing R packages and closely duplicate the structure of their help files.

[leeper]

Thanks, @justinesarey! Very helpful.

@zedtaha, can you address Justin's points here and the incomplete items from the review checklist above? Please ping me here when you've had a chance to respond to all of these points.

[zedtaha]

@leeper OK I will give Justin back. Thanks

[zedtaha]

Hi @justinesarey i updated the ivprobit R package close to your comment points. Hope its OK ;)

[zedtaha]

Hi @leeper i updated my code close to justin points and hope its ok ;) best

[justinesarey]

Is this updated on CRAN as well? I'd like to run
update.packages("ivprobit") and check out the new help files.

-JE

--

Dr. Justin Esarey
Associate Professor of Political Science
Rice University
Voice: [phone]
Fax: [phone]
E-mail: [e-mail][email protected]
Web: www.justinesarey.com

On Wed, Feb 21, 2018 at 8:52 AM, Taha Zaghdoudi [e-mail]
wrote:

Hi @leeper https://github.com/leeper i updated my code close to justin
points and hope its ok ;) best

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[zedtaha]

@justinesarey no just on the git but I ll do it now

[justinesarey]

Thanks! I'll take a look once the new package propagates to the CRAN mirror.

-JE

--

Dr. Justin Esarey
Associate Professor of Political Science
Rice University
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On Wed, Feb 21, 2018 at 9:22 AM, Taha Zaghdoudi [e-mail]
wrote:

@justinesarey https://github.com/justinesarey no just on the git but I
ll do it now

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[zedtaha]

Hi @justinesarey pckage on CRAN

[leeper]

@zedtaha Great. Can you please create a DOI for your repository by archiving through zenodo, figshare, or a similar service - and then put the DOI in your README file and as a comment here?

[zedtaha]

Hi @leeper done ;) DOI in Readme. Best

[leeper]

@zedtaha Can you please update the archive so it contains the current version of the software? Looks like the most recent version is from 2014.

[leeper]

@whedon set 10.5281/zenodo.1109725 as archive

[whedon]

OK. 10.5281/zenodo.1109725 is the archive.

[zedtaha]

@leeper archive updated

[zedtaha]

@leeper i delated the old licence

[zedtaha]

@leeper the updated archive https://doi.org/10.5281/zenodo.1183253

[leeper]

@zedtaha Great. Once you accept and merge this Pull Request, then your paper will be accepted at JOSS!

[leeper]

@whedon set 10.5281/zenodo.1183253 as archive

[whedon]

OK. 10.5281/zenodo.1183253 is the archive.

[leeper]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[leeper]

@arfon This one's over to you!

[arfon]

@justinesarey - many thanks for your review here and to @leeper for editing this submission ✨

@zedtaha - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00523 ⚡️🚀💥

[whedon]

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[zedtaha]

@leeper @justinesarey thank you for your comments and review @arfon thank you too JOSS and best

[justinesarey]

Just FYI: the title of the package is listed as “ivporbit” but I’m pretty
sure the author meant “ivprobit.” Perhaps that can be changed?

-JE

On Fri, Feb 23, 2018 at 8:44 AM Arfon Smith [e-mail]
wrote:

@justinesarey https://github.com/justinesarey - many thanks for your
review here and to @leeper https://github.com/leeper for editing this
submission ✨

@zedtaha https://github.com/zedtaha - your paper is now accepted into
JOSS and your DOI is https://doi.org/10.21105/joss.00523 ⚡️🚀💥

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>

Dr. Justin Esarey
Associate Professor of Political Science
Rice University
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Fax: [phone]
E-mail: [email protected]
Web: www.justinesarey.com
[Sent from Gmail Mobile]

[arfon]

Just FYI: the title of the package is listed as “ivporbit” but I’m pretty sure the author meant “ivprobit.” Perhaps that can be changed?

Good catch. I've just updated this.

[leeper]

Thanks, @justinesarey, for that but especially for your review!