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[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

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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 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 Looks like you removed all the dois?

flor14 commented 5 years ago

After the failed attempts, I regenerated the file again. I added again the DOIs now to this new file.

El jue., 23 may. 2019 a las 16:46, Karthik Ram (notifications@github.com) escribió:

@flor14 https://github.com/flor14 Looks like you removed all the dois?

— 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?email_source=notifications&email_token=AHB5G2WHL2CLXRI43XW2JSTPW3YA7A5CNFSM4FFZR7J2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWDJLUA#issuecomment-495359440, or mute the thread https://github.com/notifications/unsubscribe-auth/AHB5G2R3QUOIDGMFSZNU5NDPW3YA7ANCNFSM4FFZR7JQ .

karthik commented 5 years ago

@whedon check references

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

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
karthik commented 5 years ago

@flor14 Great! Now can you archive your software on Zenodo and share a DOI here please?

flor14 commented 5 years ago

Here is the DOI number: 10.5281/zenodo.3233033

El lun., 27 may. 2019 a las 15:06, Karthik Ram (notifications@github.com) escribió:

@flor14 https://github.com/flor14 Great! Now can you archive your software on Zenodo and share a DOI here please?

— 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?email_source=notifications&email_token=AHB5G2XPJQKMDX4P55VAOA3PXQPKDA5CNFSM4FFZR7J2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWKJR7Q#issuecomment-496277758, or mute the thread https://github.com/notifications/unsubscribe-auth/AHB5G2QM2TAP3IODETH6HZDPXQPKDANCNFSM4FFZR7JQ .

karthik commented 5 years ago

@whedon generate pdf

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

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

karthik commented 5 years ago

@whedon set 10.5281/zenodo.3233033 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3233033 is the archive.

karthik commented 5 years ago

@whedon accept

whedon commented 5 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 5 years ago 

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 commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/718

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/718, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
karthik commented 5 years ago

This is ready @openjournals/joss-eics

flor14 commented 5 years ago

A subindex is missing, also the format of the citation is not correct. Can I change it or is late?

El mar., 28 may. 2019 a las 15:23, 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?email_source=notifications&email_token=AHB5G2XDE5KFNLZ6JPGFLTLPXV2DJA5CNFSM4FFZR7J2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWNAIMY#issuecomment-496632883, or mute the thread https://github.com/notifications/unsubscribe-auth/AHB5G2UKAZXWEOF7T77PKFTPXV2DJANCNFSM4FFZR7JQ .

kyleniemeyer commented 5 years ago

@flor14 please go ahead and make any changes to the paper

flor14 commented 5 years ago

Can you build it again, please?

El mar., 28 may. 2019 a las 16:23, Kyle Niemeyer (notifications@github.com) escribió:

@flor14 https://github.com/flor14 please go ahead and make any changes to the paper

— 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?email_source=notifications&email_token=AHB5G2Q5KVQOEB67Z5D2UITPXWBCLA5CNFSM4FFZR7J2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWNFJTY#issuecomment-496653519, or mute the thread https://github.com/notifications/unsubscribe-auth/AHB5G2VCFJSLF5Q2WGWJBTTPXWBCLANCNFSM4FFZR7JQ .

karthik commented 5 years ago

@whedon generate pdf

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

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

kyleniemeyer commented 5 years ago

@flor14 thanks! I will make the final checks on your submission later today.

flor14 commented 5 years ago

I made a new change. I realize subscripts should be included also as a formula with $. Hope it works.

El mié., 29 may. 2019 a las 12:53, Kyle Niemeyer (notifications@github.com) escribió:

@flor14 https://github.com/flor14 thanks! I will make the final checks on your submission later today.

— 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?email_source=notifications&email_token=AHB5G2UEMVG6UJFANYQAT3LPX2RHDA5CNFSM4FFZR7J2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWPZDEY#issuecomment-496996755, or mute the thread https://github.com/notifications/unsubscribe-auth/AHB5G2RCROM6UVH3HA4OZHTPX2RHDANCNFSM4FFZR7JQ .

kyleniemeyer commented 5 years ago

@whedon generate pdf

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

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

kyleniemeyer commented 5 years ago

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: https://github.com/flor14/shinyssd/pull/9

flor14 commented 5 years ago

I improved what you mentioned. If citations are ok, and subscripts are correct in the second paragraph: " HC1, HC5 and HC10" for me it is ready. Maybe citations could be more detailed in the author's guidelines? Mentioning the 3 main cases: 1- @author:2001 -> author et al. (2001) 2- [@author:2001] -> (author et al. 2001) 3- [@author1:2001; @author2:2001] -> (author1 et al. 2001; author2 et al. 2002)? I mention this just to save your time.

Thank you Kyle! You was very kind

El mié., 29 may. 2019 a las 16:40, Kyle Niemeyer (notifications@github.com) escribió:

Hi @flor14 https://github.com/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 https://github.com/flor14/shinyssd/pull/9

— 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?email_source=notifications&email_token=AHB5G2RYJYQWRB46ZUJGMNLPX3L2PA5CNFSM4FFZR7J2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWQNVPI#issuecomment-497081021, or mute the thread https://github.com/notifications/unsubscribe-auth/AHB5G2XV5ECE2RUUBASW3CTPX3L2PANCNFSM4FFZR7JQ .

kyleniemeyer commented 5 years ago

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

kyleniemeyer commented 5 years ago

@whedon generate pdf

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

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

Error producing PDF. ! Double subscript. l.316 ...estimators (HC_1), (HC_5) and (HC1

Looks like we failed to compile the PDF

kyleniemeyer commented 5 years ago

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

flor14 commented 5 years ago

I've changed subscripts to this now: $HC_1$, $HC5$ and $HC{10}$ The problem seems the last one with 2 digits

El mié., 29 may. 2019 a las 18:29, whedon (notifications@github.com) escribió:

PDF failed to compile for issue #785 https://github.com/openjournals/joss-reviews/issues/785 with the following error:

Error producing PDF. ! Double subscript. l.316 ...estimators (HC_1), (HC_5) and (HC1

Looks like we failed to compile the 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?email_source=notifications&email_token=AHB5G2THZKL5WNW32FH5HNTPX3YT5A5CNFSM4FFZR7J2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWQWH6Y#issuecomment-497116155, or mute the thread https://github.com/notifications/unsubscribe-auth/AHB5G2ULZLFHDGRQC433KKTPX3YT5ANCNFSM4FFZR7JQ .

kyleniemeyer commented 5 years ago

@whedon generate pdf

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

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

kyleniemeyer commented 5 years ago

@whedon accept

whedon commented 5 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 5 years ago 

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 commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/721

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 5 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 5 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/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 commented 5 years ago

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

whedon commented 5 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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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