search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
721 stars 38 forks source link

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

Closed whedon closed 5 years ago

whedon commented 6 years ago

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

Functionality

Documentation

Software paper

whedon commented 6 years ago

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 :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:

  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 commented 6 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 6 years ago

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:ineach' 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:ininitialize' 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:inblock 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:inparse_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:innew' 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:inprepare' 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:ininvoke_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:instart' 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:inload' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `

'

flor14 commented 6 years ago

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

arfon commented 6 years ago

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

affiliation: 1,2

to this in your paper.md

affiliation: "1,2"
flor14 commented 6 years ago

done!

El jue., 12 jul. 2018 a las 14:53, Arfon Smith (notifications@github.com) escribió:

@flor14 https://github.com/flor14 the multiple affiliations need quoting. i.e. change this:

affiliation: 1,2

to this in your paper.md

affiliation: "1,2"

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/785#issuecomment-404596017, or mute the thread https://github.com/notifications/unsubscribe-auth/AcPTagYe2_MHb_NCL-8LwalKkwUs1feHks5uF40HgaJpZM4UuY_T .

arfon commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

flor14 commented 6 years ago

Great.

Only one thing: The citation that says "Plan protection Products" is not correct, I have changed the bib file in order to modify that

Sorry about that and thank you

El jue., 12 jul. 2018 a las 16:25, whedon (notifications@github.com) escribió:

--> Check article proof 📄 <-- https://github.com/openjournals/joss-papers/blob/joss.00785/joss.00785/10.21105.joss.00785.pdf

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/785#issuecomment-404623684, or mute the thread https://github.com/notifications/unsubscribe-auth/AcPTav4jcHrs32C9fghSzXsbrG8UXtbZks5uF6K7gaJpZM4UuY_T .

karthik commented 6 years ago

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

flor14 commented 6 years ago

I have not pending items yet

El lun., 30 jul. 2018 a las 17:13, Karthik Ram (notifications@github.com) escribió:

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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/785#issuecomment-408994771, or mute the thread https://github.com/notifications/unsubscribe-auth/AcPTaoeh0IbtuErsohha7yAhoRxle838ks5uL2j1gaJpZM4UuY_T .

kylehamilton commented 6 years ago

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

karthik commented 6 years ago

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

flor14 commented 6 years ago

I can help if something is confusing.

flor14 commented 6 years ago

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

karthik commented 6 years ago

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

karthik commented 6 years ago

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

kylehamilton commented 6 years ago

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 https://github.com/flor14/paper/issues/2
  2. Add tests https://github.com/flor14/paper/issues/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 https://github.com/flor14/paper/issues/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 https://github.com/flor14/paper/issues/6
  6. I did not see community guidelines https://github.com/flor14/paper/issues/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 commented 6 years ago

Thanks! I will do it soon

El lun., 24 sept. 2018 a las 16:44, W. Kyle Hamilton (< notifications@github.com>) escribió:

Sorry @karthik https://github.com/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 flor14/paper#2 https://github.com/flor14/paper/issues/2
  2. Add tests flor14/paper#3 https://github.com/flor14/paper/issues/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 flor14/paper#4 https://github.com/flor14/paper/issues/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 flor14/paper#6 https://github.com/flor14/paper/issues/6
  6. I did not see community guidelines flor14/paper#7 https://github.com/flor14/paper/issues/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.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/785#issuecomment-424100611, or mute the thread https://github.com/notifications/unsubscribe-auth/AcPTaiQ4HmKyRPC06JMs9P7tp-uJHhb8ks5ueTY7gaJpZM4UuY_T .

flor14 commented 6 years ago

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 commented 6 years ago

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

🙏

karthik commented 5 years ago

@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 commented 5 years ago

I will have a look a soon as possible. Thank you.

El lun., 19 nov. 2018 a las 16:56, Karthik Ram (notifications@github.com) escribió:

@flor14 https://github.com/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.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/785#issuecomment-440021895, or mute the thread https://github.com/notifications/unsubscribe-auth/AcPTauZXsGrmncyEGCHeTuNrOEIl7VrMks5uwwztgaJpZM4UuY_T .

flor14 commented 5 years ago

I completed what was missing from the last review.

labarba commented 5 years ago

👋 @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 commented 5 years ago

Hello. The last 4 months I have been finishing my PhD so I had no time to check this (and I will not have until the last week of February). I am not sure how is JOSS policy about timing, but I can test everything again and make improvements on February. Sorry about this, it took a bit longer than expected. Regards

El sáb., 19 ene. 2019 a las 19:23, Lorena A. Barba (< notifications@github.com>) escribió:

👋 @kylehamilton https://github.com/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! 🙏

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/785#issuecomment-455820240, or mute the thread https://github.com/notifications/unsubscribe-auth/AcPTauupddomfiULvTVMQVfaPA-eWWe6ks5vE5rdgaJpZM4UuY_T .

labarba commented 5 years ago

Hi @flor14 — Sure. Take your time, but ping us back here when you are ready for the review to continue.

flor14 commented 5 years ago

Well, I finished improving the app, I hope I have interpreted the comments correctly. Everything seems to work well. Thanks for the valuable suggestions.

El jue., 14 feb. 2019 a las 7:35, Lorena A. Barba (notifications@github.com) escribió:

Hi @flor14 https://github.com/flor14 — Sure. Take your time, but ping us back here when you are ready for the review to continue.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/785#issuecomment-463578219, or mute the thread https://github.com/notifications/unsubscribe-auth/AcPTak3r4M3y_Rqh16kOnwhjK_UH6btHks5vNTwAgaJpZM4UuY_T .

labarba commented 5 years ago

@karthik — take a look at this one to continue the review 🙏

karthik commented 5 years ago

The updates look good to me. @kylehamilton Could you have a look please and check off your remaining items (or raise more issues?) 🙏

labarba commented 5 years ago

Hi @kylehamilton 👋 — It looks like we're waiting for you to check the author's revision and responses to your comments. Can you give us a status update?

flor14 commented 5 years ago

Hello. Maybe he is not receiving the notifications? Is not possible to send him an email?

El sáb., 16 mar. 2019 a las 22:07, Lorena A. Barba (< notifications@github.com>) escribió:

Hi @kylehamilton https://github.com/kylehamilton 👋 — It looks like we're waiting for you to check the author's revision and responses to your comments. Can you give us a status update?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/785#issuecomment-473606116, or mute the thread https://github.com/notifications/unsubscribe-auth/AcPTahvofxrGtwDroE9lYoArz744BbENks5vXZVegaJpZM4UuY_T .

karthik commented 5 years ago

I'll send Kyle an email shortly.

labarba commented 5 years ago

👋 @karthik — did you ever get a reply from @kylehamilton ? This looks stalled and may need more active nudging. Thanks1

karthik commented 5 years ago

Thanks Lorena, I'll follow up again. Otherwise try to assign someone new.

karthik commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
karthik commented 5 years ago

@whedon check references

whedon commented 5 years ago 
Attempting to check references...
whedon commented 5 years ago

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

whedon commented 5 years ago 

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1016/j.ecoenv.2016.08.023 may be missing for title: Aquatic toxicity structure-activity relationships for the zwitterionic surfactant alkyl dimethyl amine oxide to several aquatic species and a resulting species sensitivity distribution
- https://doi.org/10.2903/j.efsa.2013.3290 may be missing for title: Guidance on tiered risk assessment for plant protection products for aquatic organisms in edge-of-field surface waters
- https://doi.org/10.18637/jss.v064.i04 may be missing for title: fitdistrplus: An R Package for Fitting Distributions
- https://doi.org/10.1002/etc.5620190233 may be missing for title: Applying species-sensitivity distributions in ecological risk assessment: assumptions of distribution type and sufficient numbers of species
- https://doi.org/10.1201/9781420032314 may be missing for title: Species sensitivity distributions in ecotoxicology
- https://doi.org/10.1016/s0025-326x(01)00327-7 may be missing for title: Species sensitivity distributions: data and model choice
- https://doi.org/10.1002/9780470057339.vae043.pub2 may be missing for title: EnvStats:  An R Package for Environmental Statistics

INVALID DOIs

- None
karthik commented 5 years ago

@flor14 Can you please fix the missing DOIs for the references noted above? After that I will proceed with the next steps to getting your paper accepted.

flor14 commented 5 years ago

I have just added doi and url to paper.bib. I suppose it solves this

Thank you

Sent from Mail for Windows 10

From: Karthik Ram Sent: lunes, 20 de mayo de 2019 3:58 p. m. To: openjournals/joss-reviews Cc: Florencia; Mention Subject: Re: [openjournals/joss-reviews] [REVIEW]: ShinySSD: SpeciesSensitivity Distributions for Ecotoxicological Risk Assessment (#785)

@flor14 Can you please fix the missing DOIs for the references noted above? After that I will proceed with the next steps to getting your paper accepted. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

karthik commented 5 years ago

@whedon check references

whedon commented 5 years ago 
Attempting to check references...
whedon commented 5 years ago 

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1016/j.ecoenv.2016.08.023 may be missing for title: Aquatic toxicity structure-activity relationships for the zwitterionic surfactant alkyl dimethyl amine oxide to several aquatic species and a resulting species sensitivity distribution
- https://doi.org/10.2903/j.efsa.2013.3290 may be missing for title: Guidance on tiered risk assessment for plant protection products for aquatic organisms in edge-of-field surface waters
- https://doi.org/10.18637/jss.v064.i04 may be missing for title: fitdistrplus: An R Package for Fitting Distributions
- https://doi.org/10.1002/etc.5620190233 may be missing for title: Applying species-sensitivity distributions in ecological risk assessment: assumptions of distribution type and sufficient numbers of species
- https://doi.org/10.1201/9781420032314 may be missing for title: Species sensitivity distributions in ecotoxicology
- https://doi.org/10.1016/s0025-326x(01)00327-7 may be missing for title: Species sensitivity distributions: data and model choice
- https://doi.org/10.1002/9780470057339.vae043.pub2 may be missing for title: EnvStats:  An R Package for Environmental Statistics

INVALID DOIs

- None
flor14 commented 5 years ago

I fixed this again according to the autor’s guidelines https://joss.readthedocs.io/en/latest/submitting.html Now?

Thank you!

Sent from Mail for Windows 10

From: whedon Sent: lunes, 20 de mayo de 2019 4:34 p. m. To: openjournals/joss-reviews Cc: Florencia; Mention Subject: Re: [openjournals/joss-reviews] [REVIEW]: ShinySSD: SpeciesSensitivity Distributions for Ecotoxicological Risk Assessment (#785)

OK DOIs

MISSING DOIs

INVALID DOIs

karthik commented 5 years ago

@whedon check references

whedon commented 5 years ago 
Attempting to check references...