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[REVIEW]: visdat: Visualising Whole Data Frames #355

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whedon opened this Issue Aug 10, 2017 · 10 comments

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whedon commented Aug 10, 2017

Submitting author: @njtierney (Nicholas John Tierney)
Repository: https://github.com/ropensci/visdat
Version: v0.2.0
Editor: @arfon
Reviewer: @arfon
Archive: 10.5281/zenodo.845960

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/c85f57adbc565b064fb4bfc9b59a1b2a"><img src="http://joss.theoj.org/papers/c85f57adbc565b064fb4bfc9b59a1b2a/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/c85f57adbc565b064fb4bfc9b59a1b2a/status.svg)](http://joss.theoj.org/papers/c85f57adbc565b064fb4bfc9b59a1b2a)

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

@arfon, please carry out your review in this issue by updating the checklist below (please make sure you're logged in to GitHub). The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @arfon know.

Conflict of interest

  • 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).

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: Does the release version given match the GitHub release (v0.2.0)?
  • Authorship: Has the submitting author (@njtierney) made major contributions to the software?

Functionality

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

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)?
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whedon Aug 10, 2017

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Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @arfon it looks like you're currently assigned as the reviewer for 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 as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS reviews 😿

To fix this do the following two things:

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

watching

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

notifications

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

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whedon commented Aug 10, 2017

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @arfon it looks like you're currently assigned as the reviewer for 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 as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS reviews 😿

To fix this do the following two things:

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

watching

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

notifications

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

@whedon commands
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arfon Aug 10, 2017

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Hi @njtierney, many thanks for your submission. This should be quick as you've already been through the rOpenSci process.

A couple of issues with your submission paper.md:

It looks like you've got a couple of different paper files, paper.Rmd and paper.md. We need the file to be named paper.md and for the YAML header to be formatted correctly as per this example.

In addition, the markdown citations don't seem to be being picked up correctly (see the pandoc errors below)

pandoc-citeproc: reference dplyr not found
pandoc-citeproc: reference Rcore not found
pandoc-citeproc: reference ggplot2 not found

Finally, the current paper reads a little too much like technical documentation (i.e. naming methods etc) which is not the purpose of the JOSS paper (this material should be in the technical documentation). Please take a look at this guidance as to what your paper should contain 😄

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arfon commented Aug 10, 2017

Hi @njtierney, many thanks for your submission. This should be quick as you've already been through the rOpenSci process.

A couple of issues with your submission paper.md:

It looks like you've got a couple of different paper files, paper.Rmd and paper.md. We need the file to be named paper.md and for the YAML header to be formatted correctly as per this example.

In addition, the markdown citations don't seem to be being picked up correctly (see the pandoc errors below)

pandoc-citeproc: reference dplyr not found
pandoc-citeproc: reference Rcore not found
pandoc-citeproc: reference ggplot2 not found

Finally, the current paper reads a little too much like technical documentation (i.e. naming methods etc) which is not the purpose of the JOSS paper (this material should be in the technical documentation). Please take a look at this guidance as to what your paper should contain 😄

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njtierney Aug 11, 2017

Hi @arfon !

OK sure thing, I'm reviewing these changes at the moment and will have something to you at the end of next week at the latest.

Question - is it OK if I use paper.Rmd (to generate a figure), which will generate paper.md, and then I edit that as per the guidelines?

Cheers! :)

njtierney commented Aug 11, 2017

Hi @arfon !

OK sure thing, I'm reviewing these changes at the moment and will have something to you at the end of next week at the latest.

Question - is it OK if I use paper.Rmd (to generate a figure), which will generate paper.md, and then I edit that as per the guidelines?

Cheers! :)

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Question - is it OK if I use paper.Rmd (to generate a figure), which will generate paper.md, and then I edit that as per the guidelines?

I think that should be OK. Our automated submission tooling will pick up any file named paper.md so just make sure that is the one that has the JOSS paper in.

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arfon commented Aug 11, 2017

Question - is it OK if I use paper.Rmd (to generate a figure), which will generate paper.md, and then I edit that as per the guidelines?

I think that should be OK. Our automated submission tooling will pick up any file named paper.md so just make sure that is the one that has the JOSS paper in.

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njtierney Aug 17, 2017

Hi @arfon !

I've submitted the changes for the paper.md - do you still get the same pandoc citation errors?

njtierney commented Aug 17, 2017

Hi @arfon !

I've submitted the changes for the paper.md - do you still get the same pandoc citation errors?

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arfon Aug 18, 2017

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I've submitted the changes for the paper.md - do you still get the same pandoc citation errors?

It looks good now, thanks!

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.

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arfon commented Aug 18, 2017

I've submitted the changes for the paper.md - do you still get the same pandoc citation errors?

It looks good now, thanks!

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.

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njtierney Aug 21, 2017

Yup!

Here is the DOI link: https://zenodo.org/badge/latestdoi/50553382

And the release: https://github.com/ropensci/visdat/releases/tag/v0.2.1

Is that the info that you need?

njtierney commented Aug 21, 2017

Yup!

Here is the DOI link: https://zenodo.org/badge/latestdoi/50553382

And the release: https://github.com/ropensci/visdat/releases/tag/v0.2.1

Is that the info that you need?

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arfon Aug 22, 2017

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@whedon set 10.5281/zenodo.845960 as archive

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arfon commented Aug 22, 2017

@whedon set 10.5281/zenodo.845960 as archive

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whedon Aug 22, 2017

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OK. 10.5281/zenodo.845960 is the archive.

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whedon commented Aug 22, 2017

OK. 10.5281/zenodo.845960 is the archive.

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arfon Aug 22, 2017

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@njtierney - your paper is now accepted into JOSS. Your DOI is http://dx.doi.org/10.21105/joss.00355 ⚡️ 🚀 💥

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arfon commented Aug 22, 2017

@njtierney - your paper is now accepted into JOSS. Your DOI is http://dx.doi.org/10.21105/joss.00355 ⚡️ 🚀 💥

@arfon arfon closed this Aug 22, 2017

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