[REVIEW]: `hopit`: An R Package for Analysis of Reporting Behavior Using Generalized Ordered Probit Models #1508

whedon · 2019-06-17T15:54:31Z

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:

Make sure you're logged in to your GitHub account
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

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Version: v0.10.1.9000
Authorship: Has the submitting author (@MaciejDanko) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
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?
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

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

Review checklist for @mkearney

Conflict of interest

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Version: v0.10.1.9000
Authorship: Has the submitting author (@MaciejDanko) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
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?
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

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

The text was updated successfully, but these errors were encountered:

whedon · 2019-06-17T15:54:35Z

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 🎉.

⭐ Important ⭐

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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

whedon · 2019-06-17T15:54:36Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-06-17T15:54:56Z

👉 Check article proof 📄 👈

MaciejDanko · 2019-07-06T17:16:04Z

@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 · 2019-07-07T18:30:08Z

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

soodoku · 2019-07-13T03:19:38Z

@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 · 2019-08-04T11:18:35Z

@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 · 2019-08-14T10:45:04Z

@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 · 2019-09-01T19:31:27Z

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

alexhanna · 2019-09-01T19:32:18Z

@whedon generate pdf

whedon · 2019-09-01T19:32:20Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-09-01T19:33:16Z

👉 Check article proof 📄 👈

alexhanna · 2019-09-01T19:48:04Z

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 · 2019-09-02T11:30:01Z

@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 · 2019-09-03T20:19:36Z

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:

I would agree with @soodoku that it'd be nice to see/compare similar estimates from libraries.
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.
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.
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 · 2019-09-04T10:12:36Z

@mkearney, thank you for your review!

@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)

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.
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.
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 · 2019-09-04T11:20:09Z

@whedon generate pdf

whedon · 2019-09-04T11:20:12Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-09-04T11:20:58Z

👉 Check article proof 📄 👈

MaciejDanko · 2019-09-04T11:23:05Z

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

MaciejDanko · 2019-09-24T08:08:27Z

@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 · 2019-09-25T02:54:24Z

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

alexhanna · 2019-10-13T19:46:13Z

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

MaciejDanko · 2019-10-14T09:04:06Z

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

mkearney · 2019-10-15T19:12:57Z

@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... 😅

whedon · 2019-11-14T15:59:55Z

Attempting PDF compilation. Reticulating splines etc...

MaciejDanko · 2019-11-14T16:00:18Z

@whedon check references

whedon · 2019-11-14T16:00:21Z

Attempting to check references...

whedon · 2019-11-14T16:00:21Z

👉 Check article proof 📄 👈

whedon · 2019-11-14T16:00:44Z


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 · 2019-11-14T16:02:03Z

Hi @alexhanna , it works now, thanks!

alexhanna · 2019-11-14T18:30:46Z

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

labarba · 2019-11-15T00:05:43Z

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 · 2019-11-15T10:29:33Z

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

labarba · 2019-11-16T22:05:41Z

@whedon set v0.10.1.9000 as version

whedon · 2019-11-16T22:05:45Z

OK. v0.10.1.9000 is the version.

labarba · 2019-11-16T22:15:59Z

Could you merge my small fix in the .bib?

MaciejDanko · 2019-11-17T10:23:23Z

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

labarba · 2019-11-17T18:16:11Z

@whedon accept

whedon · 2019-11-17T18:16:14Z

Attempting dry run of processing paper acceptance...

whedon · 2019-11-17T18:16:42Z


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 · 2019-11-17T18:16:49Z

Check final proof 👉 openjournals/joss-papers#1103

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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 · 2019-11-17T18:21:28Z

@whedon accept deposit=true

whedon · 2019-11-17T18:21:31Z

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

whedon · 2019-11-17T18:22:14Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2019-11-17T18:22:15Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01508 joss-papers#1104
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01508
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

labarba · 2019-11-17T18:23:27Z

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 · 2019-11-17T18:23:31Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

whedon assigned alexhanna Jun 17, 2019

whedon added the review label Jun 17, 2019

whedon mentioned this issue Jun 17, 2019

[PRE REVIEW]: hopit: An R Package for Analysis of Reporting Behavior Using Generalized Ordered Probit Models #1481

Closed

whedon assigned mkearney Jun 18, 2019

whedon assigned soodoku Jun 25, 2019

labarba mentioned this issue Nov 16, 2019

add caps protection in two entries MaciejDanko/hopit#13

Merged

whedon added the accepted label Nov 17, 2019

labarba closed this as completed Nov 17, 2019

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

editorialbot mentioned this issue Jan 23, 2024

[PRE REVIEW]: validateHOT #6268

Closed

editorialbot mentioned this issue Dec 17, 2024

[PRE REVIEW]: calzone: A Python package for measuring calibration of probabilistic models for classification #7598

Open

[REVIEW]: hopit: An R Package for Analysis of Reporting Behavior Using Generalized Ordered Probit Models #1508

[REVIEW]: hopit: An R Package for Analysis of Reporting Behavior Using Generalized Ordered Probit Models #1508

Comments

whedon commented Jun 17, 2019 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @soodoku

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @mkearney

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Jun 17, 2019

whedon commented Jun 17, 2019

whedon commented Jun 17, 2019

MaciejDanko commented Jul 6, 2019

soodoku commented Jul 7, 2019

soodoku commented Jul 13, 2019 • edited Loading

labarba commented Aug 4, 2019

MaciejDanko commented Aug 14, 2019 • edited Loading

alexhanna commented Sep 1, 2019

alexhanna commented Sep 1, 2019

whedon commented Sep 1, 2019

whedon commented Sep 1, 2019

alexhanna commented Sep 1, 2019

arfon commented Sep 2, 2019

mkearney commented Sep 3, 2019 • edited Loading

MaciejDanko commented Sep 4, 2019 • edited Loading

MaciejDanko commented Sep 4, 2019

whedon commented Sep 4, 2019

whedon commented Sep 4, 2019

MaciejDanko commented Sep 4, 2019

MaciejDanko commented Sep 24, 2019

alexhanna commented Sep 25, 2019 • edited Loading

alexhanna commented Oct 13, 2019 • edited Loading

MaciejDanko commented Oct 14, 2019

mkearney commented Oct 15, 2019

whedon commented Nov 14, 2019

MaciejDanko commented Nov 14, 2019

whedon commented Nov 14, 2019

whedon commented Nov 14, 2019

whedon commented Nov 14, 2019

MaciejDanko commented Nov 14, 2019

alexhanna commented Nov 14, 2019

labarba commented Nov 15, 2019

MaciejDanko commented Nov 15, 2019

labarba commented Nov 16, 2019

whedon commented Nov 16, 2019

labarba commented Nov 16, 2019

MaciejDanko commented Nov 17, 2019 • edited Loading

labarba commented Nov 17, 2019

whedon commented Nov 17, 2019

whedon commented Nov 17, 2019

whedon commented Nov 17, 2019

labarba commented Nov 17, 2019

whedon commented Nov 17, 2019

whedon commented Nov 17, 2019

whedon commented Nov 17, 2019

labarba commented Nov 17, 2019

whedon commented Nov 17, 2019

[REVIEW]: `hopit`: An R Package for Analysis of Reporting Behavior Using Generalized Ordered Probit Models #1508

[REVIEW]: `hopit`: An R Package for Analysis of Reporting Behavior Using Generalized Ordered Probit Models #1508

whedon commented Jun 17, 2019 •

edited

Loading

soodoku commented Jul 13, 2019 •

edited

Loading

MaciejDanko commented Aug 14, 2019 •

edited

Loading

mkearney commented Sep 3, 2019 •

edited

Loading

MaciejDanko commented Sep 4, 2019 •

edited

Loading

alexhanna commented Sep 25, 2019 •

edited

Loading

alexhanna commented Oct 13, 2019 •

edited

Loading

MaciejDanko commented Nov 17, 2019 •

edited

Loading