mctq: An R Package for the Munich ChronoType Questionnaire

@danielvartan

Date accepted: 2021-10-29
Submitting Author Name: Daniel Vartanian
Submitting Author Github Handle: @danielvartan
Other Package Authors Github handles: (comma separated, delete if none) @AnaAmeliaBeneditoSIlva, @pedrazzo
Repository: https://github.com/gipso/mctq
Version submitted: 0.0.0.9000
Editor: @jooolia
Reviewers: @leocadio-miguel, @jonkeane

Due date for @leocadio-miguel: 2021-05-26

Due date for @jonkeane: 2021-05-27
Archive: TBD
Version accepted: TBD

Paste the full DESCRIPTION file inside a code block below:

Package: mctq
Title: An R Package for the Munich ChronoType Questionnaire
Version: 0.0.0.9000
Authors@R: 
    c(person(given = "Daniel",
             family = "Vartanian",
             role = c("aut", "cre", "cph"),
             email = "danvartan@gmail.com",
             comment = c(ORCID = "0000-0001-7782-759X")),
      person(given = "Ana Amelia",
             family = "Benedito-Silva",
             email = "aamelia@usp.br",
             role = c("aut", "sad"),
             comment = c(ORCID = "0000-0003-4976-2623")),
      person(given = "Mario",
             family = "Pedrazzoli",
             email = "pedrazzo@usp.br",
             role = c("aut", "sad"),
             comment = c(ORCID = "0000-0002-5257-591X")),
      person(given = "Interdisciplinary Sleep Research Group (GIPSO)",
             role = "fnd"),
      person(given = "University of Sao Paulo (USP)",
             role = "fnd"))
Maintainer: Daniel Vartanian <danvartan@gmail.com>
Description: A complete and consistent toolkit to process the Munich ChronoType 
    Questionnaire (MCTQ) for all of its three versions (standard, micro, 
    and shift).
License: MIT + file LICENSE
URL: https://gipso.github.io/mctq/, https://github.com/gipso/mctq/
BugReports: https://github.com/gipso/mctq/issues/
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Depends:
    R (>= 3.6)
Imports: 
    checkmate,
    dplyr,
    hms,
    lifecycle,
    lubridate
Suggests:
    covr,
    crayon,
    datasets,
    ggplot2,
    grDevices,
    knitr,
    magrittr,
    mockr,
    readr,
    rmarkdown,
    spelling,
    stats,
    testthat (>= 2.0.0),
    utils
Config/testthat/edition: 2
VignetteBuilder: knitr
Language: en-US

Scope

Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):
- data retrieval
- data extraction
- data munging
- data deposition
- workflow automation
- version control
- citation management and bibliometrics
- scientific software wrappers
- field and lab reproducibility tools
- database software bindings
- geospatial data
- text analysis
Explain how and why the package falls under these categories (briefly, 1-2 sentences):

The Munich Chronotype Questionnaire (MCTQ) may look like a simple questionnaire, but it requires a lot of date/time manipulation. This can be really challenging, especially if you’re dealing with a large set of data. mctq provides reliable tools, thoroughly tested, to help scientists with that task.

Who is the target audience and what are scientific applications of this package?

mctq was designed for researchers in the field of sleep and chronobiology. The scientific applications of the package are the same as the scale it addresses, i.e. to assess peoples' sleep behavior and characteristics of circadian rhythms.

Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

No other packages do the same thing (to my knowledge).

(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

I don't think this is applicable to our package.

If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

N/A

Technical checks

Confirm each of the following by checking the box.

I have read the guide for authors and rOpenSci packaging guide.

This package:

does not violate the Terms of Service of any service it interacts with.
has a CRAN and OSI accepted license.
contains a README with instructions for installing the development version.
includes documentation with examples for all functions, created with roxygen2.
contains a vignette with examples of its essential functions and uses.
has a test suite.
has continuous integration, including reporting of test coverage using services such as Travis CI, Coveralls and/or CodeCov.

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(Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
(Please do not submit your package separately to Methods in Ecology and Evolution)

Code of conduct

I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

@jooolia

Thanks for submitting! @jooolia will be the Handling editor.

Editor checks:

Documentation: The package has sufficient documentation available online (README, pkgdown docs) to allow for an assessment of functionality and scope without installing the package.
Fit: The package meets criteria for fit and overlapcovr
Automated tests: Package has a testing suite and is tested via a CI service.
License: The package has a CRAN or OSI accepted license
Repository: The repository link resolves correctly

Editor comments

Thanks for the submission. I did some initial automated checks on the spelling, recommended practices, and the code coverage and everything looks shipshape! I will now proceed to looking for reviewers.

Thanks! Julia

@ropensci-review-bot

@ropensci-review-bot seeking reviewers

Please add this badge to the README of your package repository:

[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/434_status.svg)](https://github.com/ropensci/software-review/issues/434)

Furthermore, if your package does not have a NEWS.md file yet, please create one to capture the changes made during the review process. See https://devguide.ropensci.org/releasing.html#news

@danielvartan

Hi @danielvartan,
Just to let you know I am still looking for reviewers. Many are interested but not available. Thank you for your patience.
Cheers, Julia

@jonkeane

Hello @jonkeane,
@danielvartan has responded to your comments. Please have a look and let us know your thoughts on his response and whether you would encourage further changes.
Thanks!

Hello,

Thank you for the very very detailed responses. I've read through all of them and all of the changes or explanations are great.

There were two questions (though let me know if I'm missing others!):

re: goodpractice::gp() reports

I've re-run it again, and that error has gone away (either I've resolved my tex dependencies, or the docs causing them have changed), either way this is resolved!

re: Documentation simplification

I don't see any of the repeated chunks that I remember seeing the first time — so either I imagined those or they were cleaned up already, but we can consider that resolved. In looking through, I see that there has been a lot more added to the docs, and all of that looks really great + helpful for understanding how to use {mctq}. Great job!

One last comment/suggestion (though you absolutely don't need to do this, just a possible work around if you wanted):

gu()

This is also true for all calls to this, checkmate::assert_class("se", "hms") results in the error: Error: Assertion on '"se"' failed: Must inherit from class 'hms', but has class 'character'. I know what that means, but do you think that would be something that the target users of {mctq} would know + be able to fix? You might consider making this more friendly, something like "se" must be an hms object, and not a 'character'. See ?convert for help on converting objects.

Have you considered using trycatch() here to raise a slightly more friendly error? Doing this everywhere would be hard to maintain / a code smell, but doing it in this one case might be justified.

Thanks both for this great package as well as the very detailed responses and explanations.

@jonkeane

Hi @jonkeane ,

About the gu() comment. Unfortunately, that same check is used in several other functions (e.g., mctq::so(), mctq::se). A change only for gu() wouldn't resolve this issue.

The checkmate error messages can be a little unfriendly, but at least it have a regular pattern. Changing one check breaks this pattern, and, I think, this can be more detrimental for the user. That's a trade-off for not having to built a lot of error constructors.

@jooolia

Hi @jooolia,

@jonkeane agreed to the changes. Is there anything else I need to do?

@ropensci-review-bot

@ropensci-review-bot approve mctq

@danielvartan

Approved! Thanks @danielvartan for submitting and @leocadio-miguel, @jonkeane for your reviews! 😁

To-dos:

Transfer the repo to rOpenSci's "ropensci" GitHub organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You'll be made admin once you do.
Fix all links to the GitHub repo to point to the repo under the ropensci organization.
Delete your current code of conduct file if you had one since rOpenSci's default one will apply, see https://devguide.ropensci.org/collaboration.html#coc-file
If you already had a pkgdown website and are ok relying only on rOpenSci central docs building and branding,
- deactivate the automatic deployment you might have set up
- remove styling tweaks from your pkgdown config but keep that config file
- replace the whole current pkgdown website with a redirecting page
- replace your package docs URL with https://docs.ropensci.org/package_name
- In addition, in your DESCRIPTION file, include the docs link in the URL field alongside the link to the GitHub repository, e.g.: URL: https://docs.ropensci.org/foobar (website) https://github.com/ropensci/foobar
Fix any links in badges for CI and coverage to point to the new repository URL.
Increment the package version to reflect the changes you made during review. In NEWS.md, add a heading for the new version and one bullet for each user-facing change, and each developer-facing change that you think is relevant.
We're starting to roll out software metadata files to all rOpenSci packages via the Codemeta initiative, see https://docs.ropensci.org/codemetar/for how to include it in your package, after installing the package - should be easy as running codemetar::write_codemeta() in the root of your package.

Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them "rev"-type contributors in the Authors@R field (with their consent).

Welcome aboard! We'd love to host a post about your package - either a short introduction to it with an example for a technical audience or a longer post with some narrative about its development or something you learned, and an example of its use for a broader readership. If you are interested, consult the blog guide, and tag @stefaniebutland in your reply. She will get in touch about timing and can answer any questions.

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@danielvartan

Thanks @danielvartan all looks good to me. Thanks again for the nice package and also the nicely documented response to the reviewers' comments. It was a pleasure to look through the package and to participate in this process.

I am working on getting the team ready for the transfer of the repo and you will get an invite when it is ready. Thanks! Julia

@danielvartan

Hi @danielvartan the invitation has been sent for the team in Github. Let me know if you don't receive it and/or if you have any issues.
Thanks, Julia

@jooolia

Thank you @jooolia, @jonkeane and @leocadio-miguel for all your attention and dedication in reviewing our package.

I learned a lot during this process and was very happy to be a part of and contribute to the rOpenSci initiative! I already have a few other package projects underway and will soon be submitting them to the same review process.

I've already transferred the package to rOpenSci and I'm now taking care of the final details. I will soon post the checklist here for you to follow this process.

All set. Thanks again!

To-dos:

Transfer the repo to rOpenSci's "ropensci" GitHub organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You'll be made admin once you do.
Fix all links to the GitHub repo to point to the repo under the ropensci organization.
Delete your current code of conduct file if you had one since rOpenSci's default one will apply, see https://devguide.ropensci.org/collaboration.html#coc-file
If you already had a pkgdown website and are ok relying only on rOpenSci central docs building and branding,
- deactivate the automatic deployment you might have set up
- remove styling tweaks from your pkgdown config but keep that config file
- replace the whole current pkgdown website with a redirecting page
- replace your package docs URL with https://docs.ropensci.org/package_name
- In addition, in your DESCRIPTION file, include the docs link in the URL field alongside the link to the GitHub repository, e.g.: URL: https://docs.ropensci.org/foobar (website) https://github.com/ropensci/foobar
Fix any links in badges for CI and coverage to point to the new repository URL.
Increment the package version to reflect the changes you made during review. In NEWS.md, add a heading for the new version and one bullet for each user-facing change, and each developer-facing change that you think is relevant.
We're starting to roll out software metadata files to all rOpenSci packages via the Codemeta initiative, see https://docs.ropensci.org/codemetar/for how to include it in your package, after installing the package - should be easy as running codemetar::write_codemeta() in the root of your package.

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mctq: An R Package for the Munich ChronoType Questionnaire #434

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mctq: An R Package for the Munich ChronoType Questionnaire #434

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melvidoni commented on Mar 14, 2021

jooolia commented on Mar 20, 2021

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jooolia commented on Mar 20, 2021

ropensci-review-bot commented on Mar 20, 2021

jooolia commented on Apr 15, 2021

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jooolia commented on Oct 15, 2021

jonkeane commented on Oct 17, 2021

danielvartan commented on Oct 17, 2021

danielvartan commented on Oct 29, 2021

jooolia commented on Oct 29, 2021

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jooolia commented on Oct 29, 2021

jooolia commented on Oct 29, 2021

danielvartan commented on Oct 30, 2021

danielvartan commented on Oct 30, 2021

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