Joss-reviews: [REVIEW]: `hopit`: An R Package for Analysis of Reporting Behavior Using Generalized Ordered Probit Models

[whedon]

Submitting author: @MaciejDanko (Maciej J. Dańko)
Repository: https://github.com/MaciejDanko/hopit
Version: v0.10.1.9000
Editor: @alexhanna
Reviewer: @soodoku, @mkearney
Archive: 10.5281/zenodo.3530634

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/73b926670df79a6cfa48cffa7d4775a6"><img src="http://joss.theoj.org/papers/73b926670df79a6cfa48cffa7d4775a6/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/73b926670df79a6cfa48cffa7d4775a6/status.svg)](http://joss.theoj.org/papers/73b926670df79a6cfa48cffa7d4775a6)

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) by leaving comments 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 instructions & questions

@soodoku & @mkearney, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @alexhanna know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @soodoku

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: v0.10.1.9000
• [x] Authorship: Has the submitting author (@MaciejDanko) 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)?
• [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

• [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)?

Review checklist for @mkearney

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: v0.10.1.9000
• [x] Authorship: Has the submitting author (@MaciejDanko) 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)?
• [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

• [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, a robot that can help you with some common editorial tasks. @soodoku, @mkearney it looks like you're currently assigned to review this paper :tada:.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[MaciejDanko]

@soodoku, I noticed that you haven't checked "functionality" in the functionality checklist.

I decided to improved the functionality of the package by adding generic functions (_print_, _summary_, _plot_) to _latentIndex_, _standardizeCoef_, _getLevels_, and _getCutPoints_. I also improved the code so the functions are easier to run (less 'initial' parameters) for a user. The vignette and readme were slightly modified to follow the code update.

The community guidelines are now both in the readme and the contributing files

I also put DOI everywhere where it was passible.

[soodoku]

thanks @MaciejDanko. cool improvements. hope to test it out v. soon and update the checklist!

[soodoku]

@MaciejDanko: went through the package and the health example to check functionality. things seem to pan out. i have put in an all-clear.

my only rec. would be = to prove to yourself that you are doing the right thing computationally, use either an off-the-shelf package or a toy example that you can reason through. otherwise, god speed!

[labarba]

@alexhanna — reviewer @mkearney seems to have gone MIA: could you try reaching out via email to get a status update? The other reviewer has completed his checklist.

[MaciejDanko]

@soodoku thank you very much for the review. I have already checked the package by the replicating the results of Jurges (2007, doi: 10.1002/hec.1134) model. The data and the model slightly differed, however I got almost identical results. I have also double checked the model fitting algorithm.

[alexhanna]

Messaged @mkearney to check if he was able to still serve as a reviewer on the package.

[alexhanna]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[alexhanna]

The paper draft looks good to me. Just a reminder to update the ??? parts of the paper.md file once the review is completed. I'll give @mkearney two weeks to reply to the review.

@openjournals/jose-eics if the reviewer doesn't respond, should we try to find another review for this package before continuing on it?

[arfon]

@openjournals/jose-eics if the reviewer doesn't respond, should we try to find another review for this package before continuing on it?

@alexhanna - there are a couple of options here:

• Find another reviewer.
• If you're comfortable, you could do a quick review yourself.

[mkearney]

My apologies for the delay. The end of summer/beginning of Fall got away from me!

I got the package installed, working, and everything [including the paper] looks great, @MaciejDanko and @alexhanna !!

A few minor notes:

1. I would agree with @soodoku that it'd be nice to see/compare similar estimates from libraries.
2. Overall test coverage is solid, but I would point out there are no tests for functions in R/boot.R. With that said, the main functionality still seems to be supported with automated tests.
3. The installation was a bit picky for me on both Ubuntu linux and Mac OSX. I had to temporarily rename my .Rprofile to get it installed properly. So this was 100% user error, but I don't usually have to rename my .Rprofile to get packages working properly–and this kind of hurdle might prevent some people from using the package.
4. The vignette(s) are only in the form of PDFs. Can source code be supplied? Or a script-only version of the README (which I found to be useful)?

[MaciejDanko]

@mkearney, thank you for your review!

1. @mkearney and @soodoku, here is the mentioned "off-the-shelf-package-example" using a very simple model. I use the vglm function of the VGAM package. The vglm() and the hopit() fit different models, but for this particular (simple) example (and data ?) one can compare (at least) the fit of the health variable coefficients.

library(VGAM)
library(hopit)

# Let us define a very simple model such that both packages can easily run it; i.e.
# no interactions between threshold and health variables,
# no survey design, no fitting of sigma, etc.

latent.formula <- health ~ hypertension + high_cholesterol +
heart_attack_or_stroke + poor_mobility + very_poor_grip +
depression + respiratory_problems +
IADL_problems + obese + diabetes + other_diseases

thresh.formula <- ~ sex + ageclass + country

# Fit the hopit model
model1.hopit <- hopit(latent.formula = latent.formula,
thresh.formula = thresh.formula,
decreasing.levels = TRUE,
data = healthsurvey)

# Fit the vglm model
healthsurvey$health <- ordered(healthsurvey$health)
thresh.right <- deparse(thresh.formula[[2]])
big.formula <- update.formula(latent.formula,paste('. ~ . +',thresh.right))
parallel.formula <- formula(paste('FALSE ~', thresh.right))

model1.vglm<-vglm(big.formula, data = healthsurvey,
family = cumulative(parallel = parallel.formula, link = 'probit'))

# Can compare only health variables; thresholds are modelled in a different way
round(cbind(VGAM= - coef(model1.vglm)[5:15],
hopit=coef(model1.hopit,aslist=TRUE)$latent.params),4)

1. The bootstrapping (boot_hopit) is not present in automated test, because running it takes some time. The boot_hopit is also quite simple function, which is not so prone to errors or changes in the main algorithm. Nonetheless, all examples of the boot_hopit and vignette were tested and work fine.

2. The hopit package (installation, auto-tests, examples, etc.) was tested on Travis (Linux) and AppVeyor (Windows). It was also checked during submission to CRAN. I will try to figure out the issue with .Rprofile, but so far I cannot replicate it. I cannot even guess why it could happen.

3. The script version of README can be seen on GitHub (click raw option or use this link README). I am not sure if it is a common practice to supply a code for vignette on GitHub. Anyway, I am attaching the most recent version of the code here hopit_vignette.zip. I hope it will be helpful :).

[MaciejDanko]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[MaciejDanko]

@alexhanna, the issue with ??? is resolved now.

[MaciejDanko]

@mkearney,
I noticed emoji under my reply, but you haven't ticked "performance" on the functionality checklist off.
Please let me known if you have any questions. I would be happy to help

[alexhanna]

👋 hi @mkearney can you check if you agree that the performance criteria has been met?

[alexhanna]

:wave: @mkearney it's been nearly three weeks. Can you look at this?

[MaciejDanko]

Actually it is almost six weeks since @mkearney replied :-/

[mkearney]

@mkearney,
I noticed emoji under my reply, but you haven't ticked "performance" on the functionality checklist off.
Please let me known if you have any questions. I would be happy to help

I thought I fixed this two different times. That'll teach me to do Github things on my phone... 😅

[MaciejDanko]

Hi @alexhanna, the performance box has been ticked, could we proceed further? :)

[alexhanna]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[alexhanna]

This is looking good to me. Thanks for all your work on this, @mkearney and @soodoku.

[alexhanna]

👋 @MaciejDanko - the last step we need you to do is get a DOI number from Zenodo and post it here. We can then assign the repository a DOI and pass it off to the EIC for acceptance.

[alexhanna]

👋 👋 @MaciejDanko - let's publish this thing! If you can get the DOI number then we can pass it off.

[MaciejDanko]

Hi @alexhanna,
here is the DOI:
10.5281/zenodo.3530634

https://zenodo.org/record/3530634

[MaciejDanko]

:wave: @alexhanna - let's do it asap, next week I am out of office.

[alexhanna]

@whedon set 10.5281/zenodo.3530634 as archive

[whedon]

OK. 10.5281/zenodo.3530634 is the archive.

[alexhanna]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[alexhanna]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.18637/jss.v009.i08 is OK
• 10.1016/j.socscimed.2009.05.013 is OK
• 10.1080/03610928508828893 is OK
• 10.1007/s11205-013-0542-1 is OK
• 10.1111/joes.12002 is OK
• 10.1080/0022250X.1975.9989847 is OK
• 10.1017/S000305540400108X is OK
• 10.1002/hec.1134 is OK
• 10.1007/s10182-006-0228-y is OK
• 10.1007/s10902-004-1753-6 is OK
• 10.1093/ije/dyt088 is OK
• 10.1016/j.socscimed.2019.03.002 is OK
• 10.18637/jss.v052.i05 is OK
• 10.7287/peerj.preprints.3188v1 is OK
• 10.18637/jss.v040.i08 is OK

MISSING DOIs

• https://doi.org/10.1201/b15166 may be missing for title: Dynamic Documents with R and knitr

INVALID DOIs

• None
  ```

[alexhanna]

Hi @MaciejDanko, I made a small PR for a missing DOI (https://github.com/MaciejDanko/hopit/pull/12). Once you accept this, we should be good to go.

[MaciejDanko]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.18637/jss.v009.i08 is OK
• 10.1016/j.socscimed.2009.05.013 is OK
• 10.1080/03610928508828893 is OK
• 10.1007/s11205-013-0542-1 is OK
• 10.1111/joes.12002 is OK
• 10.1080/0022250X.1975.9989847 is OK
• 10.1017/S000305540400108X is OK
• 10.1002/hec.1134 is OK
• 10.1007/s10182-006-0228-y is OK
• 10.1007/s10902-004-1753-6 is OK
• 10.1093/ije/dyt088 is OK
• 10.1016/j.socscimed.2019.03.002 is OK
• 10.18637/jss.v052.i05 is OK
• 10.7287/peerj.preprints.3188v1 is OK
• 10.18637/jss.v040.i08 is OK

MISSING DOIs

• https://doi.org/10.1201/b15166 may be missing for title: Dynamic Documents with R and knitr

INVALID DOIs

• None
  ```

[alexhanna]

@MaciejDanko -- hrm, it looks like it didn't update. if you're not citing the book, you could also choose to remove it.

[MaciejDanko]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[MaciejDanko]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

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

[whedon]

```Reference check summary:

OK DOIs

• 10.18637/jss.v009.i08 is OK
• 10.1016/j.socscimed.2009.05.013 is OK
• 10.1080/03610928508828893 is OK
• 10.1007/s11205-013-0542-1 is OK
• 10.1111/joes.12002 is OK
• 10.1080/0022250X.1975.9989847 is OK
• 10.1017/S000305540400108X is OK
• 10.1002/hec.1134 is OK
• 10.1007/s10182-006-0228-y is OK
• 10.1007/s10902-004-1753-6 is OK
• 10.1093/ije/dyt088 is OK
• 10.1016/j.socscimed.2019.03.002 is OK
• 10.18637/jss.v052.i05 is OK
• 10.7287/peerj.preprints.3188v1 is OK
• 10.18637/jss.v040.i08 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[MaciejDanko]

Hi @alexhanna , it works now, thanks!

[alexhanna]

Excellent. @openjournals/joss-eics, this one is also ready to go.

[labarba]

Hi @MaciejDanko — I found no releases in the repo. Please make a tagged release with the reviewed version of the software and post the version number here to update the metadata.

[MaciejDanko]

Hi @labarba - I made a release tagged v0.10.1.9000

[labarba]

@whedon set v0.10.1.9000 as version

[whedon]

OK. v0.10.1.9000 is the version.

[labarba]

Could you merge my small fix in the .bib?

[MaciejDanko]

Hi @labarba - the small fix was merged, thank you.

[labarba]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• 10.18637/jss.v009.i08 is OK
• 10.1016/j.socscimed.2009.05.013 is OK
• 10.1080/03610928508828893 is OK
• 10.1007/s11205-013-0542-1 is OK
• 10.1111/joes.12002 is OK
• 10.1080/0022250X.1975.9989847 is OK
• 10.1017/S000305540400108X is OK
• 10.1002/hec.1134 is OK
• 10.1007/s10182-006-0228-y is OK
• 10.1007/s10902-004-1753-6 is OK
• 10.1093/ije/dyt088 is OK
• 10.1016/j.socscimed.2019.03.002 is OK
• 10.18637/jss.v052.i05 is OK
• 10.7287/peerj.preprints.3188v1 is OK
• 10.18637/jss.v040.i08 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1103

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1103, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[labarba]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1104
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01508
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[labarba]

Congratulations, @MaciejDanko, your JOSS paper is published! 🚀

Sincere thanks to our editor: @alexhanna, and the reviewers: @soodoku, @mkearney — we couldn't do this without you 🙏

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01508/status.svg)](https://doi.org/10.21105/joss.01508)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01508">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01508/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01508/status.svg
   :target: https://doi.org/10.21105/joss.01508

This is how it will look in your documentation:

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