[REVIEW]: shinyssdtools: A web application for fitting Species Sensitivity Distributions (SSDs)

[whedon]

Submitting author: @sebdalgarno (Sebastian Dalgarno)
Repository: https://github.com/bcgov/shinyssdtools
Version: v0.0.3
Editor: @marcosvital
Reviewer: @elimillera, @meenakshi-kushwaha, @nanhung
Archive: 10.5281/zenodo.4448253

⚠️ JOSS reduced service mode ⚠️

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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) by leaving comments 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

@elimillera & @meenakshi-kushwaha & @nanhung, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @elimillera

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@sebdalgarno) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @meenakshi-kushwaha

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@sebdalgarno) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @nanhung

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@sebdalgarno) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @elimillera, @meenakshi-kushwaha, @nanhung it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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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 😿

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[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/etc.4925 is OK
- 10.21105/joss.01082 is OK
- 10.21105/joss.00785 is OK

MISSING DOIs

- 10.1201/9781420032314 may be a valid DOI for title: Species Sensitivity Distributions in Ecotoxicology

INVALID DOIs

- None

[sebdalgarno]

I've updated DOI for Species Sensitivity Distributions in Ecotoxicology

[sebdalgarno]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[marcosvital]

@elimillera, @meenakshi-kushwaha and @nanhung: thank you again for for accepting review this submission for JOSS.

Even if you are not starting the review right now, please accept the invite, as it has an expiration date (there is a link under Reviewer instructions & questions and you should also get an email notification). Furthermore, please check the instructions and checklists above, and let me know if you need any assistance.

You can also tag @sebdalgarno if you need to ask specific questions about the submission or to address any changes that might be necessary in the submitted paper or in the repository.

[whedon]

👋 @meenakshi-kushwaha, please update us on how your review is going.

[whedon]

👋 @nanhung, please update us on how your review is going.

[whedon]

👋 @elimillera, please update us on how your review is going.

[elimillera]

The review is currently in progress. Should finish up today.

[elimillera]

@sebdalgarno My review is complete. Should be good to go once the license issues are resolved.

[nanhung]

@sebdalgarno I appreciate your developed shiny app that makes ssdtools more accessible and easy to use. I like this "minimalist" design, but have some comments to you to improve your app. Here are my comments after testing shinyssdtools.

My main recommendation is about the interface. I suggest you can use different colors, font types (e.g., bold), and size to make the interface more friendly to your users. For example in 1. Data, The title Choose one of the following options: should be emphasized by using a larger font or bold. Also, the font of Note on the bottom can be emphasized as well.

Some specific comments are:

1. Starting from 1. Data. Is it possible to add a widget to define the number of rows (or columns) that the users want to add? So they do not need to right-click the table and add a single row (or column), repeatedly. In addition, I find that the column name is not able to revise. Can you add the function to edit them? Moreover, can you add a function that can let users export the CSV file that they created in the table?

2. When finishing up the data import. The current setting is to move the cursor and click the 2.Fit tab on the top ribbon. I would like it if you can add the [Next] button at the panel bottom. I think it is very intuitive to general users. It takes me a while to know how this app work.

3. When using the Boron data in the model fitting. It shows "llogis, lgumbel, gompertz distribution(s) failed to fit. Run R code to get more information."

However, these models work in the ssdtools.

You might need to check this bug. Also, Suggest using the different font to emphasize the warning message.

4. In 3. Predicted. The same comment to enhance the title Estimate hazard concentration using a larger font.

5. I don't understand the usage of plot.rds?

6. Another feature request: Add CL in the predicted plot.

7. The dashed line (threshold) does not appear when using the concentration as the threshold.

Minor comments:

1. The current Tab name looks like the source code. Suggest to revise it to the title such as shinyssdtools v1.0

2. Can you add a button to return to the default setting? It is like recovery mode if users want to reset theirs definitions.

3. The weird direction of tabs appeared when adjusting the window size to the mobile mode

[marcosvital]

Hi, @meenakshi-kushwaha, any news about this review? Let us know if you have any problems.

@sebdalgarno, let us know if you made any progress on the issues raised by nanhung, ok?

[sebdalgarno]

thanks @marcosvital. I'll be working on this over the next few days and will update you when they are addressed.

[marcosvital]

OK, thanks for the update, @sebdalgarno!

[meenakshi-kushwaha]

Thank you for the reminder. I plan to work on the the review this week.

On 12-Dec-2020, at 6:20 AM, Marcos Vital (LEQ-UFAL) ***@***.***> wrote: Hi, @meenakshi-kushwaha <https://github.com/meenakshi-kushwaha>, any news about this review? Let us know if you have any problems. @sebdalgarno <https://github.com/sebdalgarno>, let us know if you made any progress on the issues raised by nanhung, ok? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2848 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMRQP63PCNWO4IXCHOJQYTLSUKLLVANCNFSM4T3KQDNA>.

Meenakshi Kushwaha, MPH, MS Environmental and Occupational Health Phone: +886 972022173 Skype: meenakshi.kushwaha @envhealthspeak http://www.linkedin.com/in/mee

[meenakshi-kushwaha]

Thank you for inviting me for the review. I think this app is useful in extending the functionalities of the original ssdtools package. I especially like the R code feature that can help the user customize the analysis and plots further. Since authors have already responded to key suggestions from earlier reviewers, I have only a few suggestions left

Minor

• The clean layout app is great. Authors could consider using larger font or bold font for table/plot headings - ex. Goodness of Fit table, Plot fitted distributions, etc. for better clarity
• In goodness of fit table title row, consider changing "dist" to Distribution for better aesthetics
• The selected values in the png file formatting options are not completely visible. In the following image, I have selected 10 and 6
  

Major

• Appropriate license file is missing. The current license file in the repo has details of the Apache license, but not the actual license with Copyright information
• I noticed that the project has multiple contributors who are not included as authors in the paper. This is my first JOSS review so I will defer to @marcosvital on expected authorship norms.
  

~Meenakshi

[sebdalgarno]

hi @marcosvital I will respond to each of the three reviewers comments in separate comments below

[sebdalgarno]

@elimillera I've made the requested license changes in this commit: sebdalgarno/shinyssdtools@435ee79

I have also fixed the app title issue (i.e. as seen in tab title) in this commit:
sebdalgarno/shinyssdtools@f2ff3fa

I will make a pull request to finalize once I'm done with the rest of the changes.

[sebdalgarno]

@nanhung I will respond to each of your comments in bold

@sebdalgarno I appreciate your developed shiny app that makes ssdtools more accessible and easy to use. I like this "minimalist" design, but have some comments to you to improve your app. Here are my comments after testing shinyssdtools.

My main recommendation is about the interface. I suggest you can use different colors, font types (e.g., bold), and size to make the interface more friendly to your users. For example in 1. Data, The title Choose one of the following options: should be emphasized by using a larger font or bold. Also, the font of Note on the bottom can be emphasized as well.

Some specific comments are:

1. Starting from 1. Data. Is it possible to add a widget to define the number of rows (or columns) that the users want to add? So they do not need to right-click the table and add a single row (or column), repeatedly. In addition, I find that the column name is not able to revise. Can you add the function to edit them? Moreover, can you add a function that can let users export the CSV file that they created in the table?

This is not possible as it uses the rhandsontable R package which itself has limited features.

2. When finishing up the data import. The current setting is to move the cursor and click the 2.Fit tab on the top ribbon. I would like it if you can add the [Next] button at the panel bottom. I think it is very intuitive to general users. It takes me a while to know how this app work.

I don't agree that this would help as I think that numbering the tabs makes this obvious

3. When using the Boron data in the model fitting. It shows "llogis, lgumbel, gompertz distribution(s) failed to fit. Run R code to get more information."

However, these models work in the ssdtools.

You might need to check this bug. Also, Suggest using the different font to emphasize the warning message.

I cannot reproduce this issue. Perhaps you need to reinstall the package?

1. In 3. Predicted. The same comment to enhance the title Estimate hazard concentration using a larger font.

fixed this in bcgov/shinyssdtools#62

2. I don't understand the usage of plot.rds?

this is useful for R users to download the ggpot2 object and work with it

3. Another feature request: Add CL in the predicted plot.

fixed in this issue: bcgov/shinyssdtools#63

4. The dashed line (threshold) does not appear when using the concentration as the threshold.

This is not important enough to warrant the required changes that would have to be made to the ssdtools R package (which I don't maintain)

Minor comments:

1. The current Tab name looks like the source code. Suggest to revise it to the title such as shinyssdtools v1.0

fixed in this issue: bcgov/shinyssdtools#60

1. Can you add a button to return to the default setting? It is like recovery mode if users want to reset theirs definitions.

I don't agree that this is necessary

2. The weird direction of tabs appeared when adjusting the window size to the mobile mode

This is due to bootstrap. There is no way to change this within my chosen framework

[marcosvital]

@whedon set v0.0.3 as version

[whedon]

OK. v0.0.3 is the version.

[marcosvital]

@whedon set 10.5281/zenodo.4448253 as archive

[whedon]

OK. 10.5281/zenodo.4448253 is the archive.

[marcosvital]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2047

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2047, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/etc.4925 is OK
- 10.1201/9781420032314 is OK
- 10.21105/joss.01082 is OK
- 10.21105/joss.00785 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@marcosvital - I notice that @meenakshi-kushwaha didn't check 2 boxes. Can you comment on this?

[meenakshi-kushwaha]

I just checked off the boxes. all good. thank you for the reminder.

…

On 25-Jan-2021, at 9:28 PM, Daniel S. Katz ***@***.***> wrote: @marcosvital <https://github.com/marcosvital> - I notice that @meenakshi-kushwaha <https://github.com/meenakshi-kushwaha> didn't check 2 boxes. Can you comment on this? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2848 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMRQP62BLIOTLRYYQ5GJAWLS3VWZNANCNFSM4T3KQDNA>.

[danielskatz]

@sebdalgarno - I've suggested two small changes in bcgov/shinyssdtools#68 - please merge this when you get a chance

[sebdalgarno]

merged. Thanks @danielskatz!

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/etc.4925 is OK
- 10.1201/9781420032314 is OK
- 10.21105/joss.01082 is OK
- 10.21105/joss.00785 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2048

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2048, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02848 joss-papers#2049
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02848
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @sebdalgarno (Sebastian Dalgarno)!!

And thanks to @elimillera & @meenakshi-kushwaha & @nanhung for reviewing, and @marcosvital for editing!

[whedon]

🎉🎉🎉 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](https://joss.theoj.org/papers/10.21105/joss.02848/status.svg)](https://doi.org/10.21105/joss.02848)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.02848/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02848/status.svg
   :target: https://doi.org/10.21105/joss.02848

This is how it will look in your documentation:

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