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[REVIEW]: ShinySSD: Species Sensitivity Distributions for Ecotoxicological Risk Assessment #785

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whedon opened this issue Jun 19, 2018 · 100 comments
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accepted published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review

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@whedon
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whedon commented Jun 19, 2018

Submitting author: @flor14 (María Florencia D'Andrea)
Repository: https://github.com/flor14/paper
Version: v1.0.0
Editor: @karthik
Reviewer: @kylehamilton
Archive: 10.5281/zenodo.3233033

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/55eab2244e9d856826450cb8d9416ec3"><img src="http://joss.theoj.org/papers/55eab2244e9d856826450cb8d9416ec3/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/55eab2244e9d856826450cb8d9416ec3/status.svg)](http://joss.theoj.org/papers/55eab2244e9d856826450cb8d9416ec3)

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 instructions & questions

@kylehamilton, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @karthik know.

Review checklist for @kylehamilton

Conflict of interest

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 (v1.0.0)?
  • Authorship: Has the submitting author (@flor14) 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)?
@whedon
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whedon commented Jun 19, 2018

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @kylehamilton 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 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:

  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

@whedon
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whedon commented Jun 19, 2018

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Jun 19, 2018

PDF failed to compile for issue #785 with the following error:

/app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon/author.rb:36:in block in build_affiliation_string': Problem with affiliations for María Florencia D’Andrea, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon/author.rb:35:in each'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon/author.rb:35:in build_affiliation_string' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon/author.rb:11:in initialize'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon.rb:96:in new' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon.rb:96:in block in parse_authors'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon.rb:94:in each' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon.rb:94:in parse_authors'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon.rb:70:in initialize' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon/processor.rb:32:in new'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/bin/whedon:37:in prepare'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/bin/whedon:99:in <top (required)>' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load'
from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `

'

@flor14
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flor14 commented Jul 12, 2018

If there is something unclear in the submission I can improve it

@arfon
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arfon commented Jul 12, 2018

@flor14 the multiple affiliations need quoting. i.e. change this:

affiliation: 1,2

to this in your paper.md

affiliation: "1,2"

@flor14
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flor14 commented Jul 12, 2018 via email

@arfon
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arfon commented Jul 12, 2018

@whedon generate pdf

@whedon
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whedon commented Jul 12, 2018

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Jul 12, 2018

@flor14
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flor14 commented Jul 13, 2018 via email

@karthik
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karthik commented Jul 30, 2018

@kylehamilton Just wanted to check in on the status of your review. Are you waiting on @flor14 for any pending items? 🙏

@flor14
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flor14 commented Jul 31, 2018 via email

@kylehamilton
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Sorry for the delay I'll have this completed by the end of the day.

@karthik
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karthik commented Aug 7, 2018

Thanks @kylehamilton Let me know if you need any help. 🙏

@flor14
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flor14 commented Aug 7, 2018

I can help if something is confusing.

@flor14
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flor14 commented Aug 23, 2018

Hello! I was thinking about this today. Is there something can I start improving? Thank you so much

@karthik
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karthik commented Aug 28, 2018

@kylehamilton Gentle ping to see if you are able to wrap your review soon?

@karthik
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karthik commented Sep 23, 2018

Hi @kylehamilton, checking in again to see if you've had time to wrap this review up.
🙏

@kylehamilton
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Sorry @karthik I posted the things that needed to be addressed in the issues of the repo https://github.com/flor14/paper/issues

  1. Make the software into an R package so everything would be contained and centralized Make this into an R package  flor14/shinyssd#2
  2. Add tests Tests flor14/shinyssd#3
  3. Just want to make sure that there is a DOI for the source code I didn't see this in the .bib file or in the readme Source Code DOI flor14/shinyssd#4
  4. A minor change would in the name of the repo for production code should be changed from paper to ShinySSD
  5. Needs version numbers, shifting this to an R package would help fix this Version number needed flor14/shinyssd#6
  6. I did not see community guidelines Community guidelines flor14/shinyssd#7

If I did this wrong then I'm really sorry I thought that if I posted them as issues in the repo then it would move on from there.

@flor14
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flor14 commented Sep 24, 2018 via email

@flor14
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flor14 commented Oct 24, 2018

I have completed the review.
I change a little bit the README.md, it is different than the paper.md for publication.

Thank you

@karthik
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karthik commented Oct 26, 2018

Thank you @flor14
@kylehamilton Could you take a look when you get a chance?

🙏

@karthik
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karthik commented Nov 19, 2018

@flor14 I noticed there are couple more issues to fix before we can proceed with this. Can you please address the last two issues (5/6) that Kyle raised. I'd like to wrap this up before the end of the year. Thanks.

@flor14
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flor14 commented Nov 20, 2018 via email

@flor14
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flor14 commented Dec 14, 2018

I completed what was missing from the last review.

@labarba
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labarba commented Jan 19, 2019

👋 @kylehamilton — the author states they have made changes addressing the issues you brought up in review. Could you have a look, and see if you can check off a few more items from the review checklist? If you are satisfied, we'll need a statement from you here saying you recommend publication. Thanks! 🙏

@flor14
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flor14 commented Jan 25, 2019 via email

@flor14
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flor14 commented May 29, 2019 via email

@kyleniemeyer
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@whedon generate pdf

@whedon
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whedon commented May 29, 2019

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented May 29, 2019

@kyleniemeyer
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Hi @flor14, could you add full affiliation information as in a typical article (e.g., department, city, country)?

Also, I made a small PR to fix a few things, if you could accept and merge that: flor14/shinyssd#9

@flor14
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flor14 commented May 29, 2019 via email

@kyleniemeyer
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@flor14 yes, the citation documentation could be improved... I've had to fix this issue in a number of papers.

@kyleniemeyer
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@whedon generate pdf

@whedon
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whedon commented May 29, 2019

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented May 29, 2019

PDF failed to compile for issue #785 with the following error:

Error producing PDF.
! Double subscript.
l.316 ...estimators (HC_1), (HC_5) and (HC_1_

Looks like we failed to compile the PDF

@kyleniemeyer
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@flor14 for the last subscript, I think you need to have HC_{10} (or however you need it styled)

@flor14
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flor14 commented May 29, 2019 via email

@kyleniemeyer
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@whedon generate pdf

@whedon
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whedon commented May 29, 2019

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented May 29, 2019

@kyleniemeyer
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@whedon accept

@whedon
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whedon commented May 29, 2019

Attempting dry run of processing paper acceptance...

@whedon
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whedon commented May 29, 2019


OK DOIs

- 10.1016/j.ecoenv.2016.08.023 is OK
- 10.2903/j.efsa.2013.3290 is OK
- 10.1002/etc.5620190233 is OK
- 10.1201/9781420032314 is OK
- 10.1002/etc.5620190233 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented May 29, 2019

Check final proof 👉 openjournals/joss-papers#721

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#721, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

@kyleniemeyer
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@whedon accept deposit=true

@whedon
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whedon commented May 29, 2019

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

@whedon
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whedon commented May 29, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon
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whedon commented May 29, 2019

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.00785 joss-papers#722
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.00785
  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...

@kyleniemeyer
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Congrats @flor14 on your submission's publication in JOSS! Thanks to @kylehamilton for reviewing and @karthik for editing!

@whedon
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whedon commented May 29, 2019

🎉🎉🎉 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](http://joss.theoj.org/papers/10.21105/joss.00785/status.svg)](https://doi.org/10.21105/joss.00785)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00785">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00785/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00785/status.svg
   :target: https://doi.org/10.21105/joss.00785

This is how it will look in your documentation:

DOI

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