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[PRE REVIEW]: ccviR: an R package and Shiny app to implement the NatureServe Climate Change Vulnerability Index #7097

Closed editorialbot closed 2 months ago

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@see24<!--end-author-handle-- (Sarah Endicott) Repository: https://github.com/LandSciTech/ccviR Branch with paper.md (empty if default branch): Version: v0.1.0 Editor: !--editor-->@mengqi-z<!--end-editor-- Reviewers: @sebdalgarno, @stephpenn1 Managing EiC: Kristen Thyng

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status

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HTML: <a href="https://joss.theoj.org/papers/dc66cbcb331885fad5f2e02ab9fbe198"><img src="https://joss.theoj.org/papers/dc66cbcb331885fad5f2e02ab9fbe198/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/dc66cbcb331885fad5f2e02ab9fbe198/status.svg)](https://joss.theoj.org/papers/dc66cbcb331885fad5f2e02ab9fbe198)

Author instructions

Thanks for submitting your paper to JOSS @see24. Currently, there isn't a JOSS editor assigned to your paper.

@see24 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
editorialbot commented 2 months ago

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 2 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.1002/wsb.478 is OK
- 10.1038/nclimate2448 is OK
- 10.1002/wcc.551 is OK
- 10.1038/s41562-016-0021 is OK

MISSING DOIs

- No DOI given, and none found for title: Gaps in Globular Cluster Streams: Pal 5 and the Ga...
- No DOI given, and none found for title: Galactic Dynamics: Second Edition
- No DOI given, and none found for title: Guidelines for Using the NatureServe Climate Chang...
- No DOI given, and none found for title: Rapid Assessment of Plant and Animal Vulnerability...

INVALID DOIs

- None
editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1844.9 files/s, 310232.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               56           1402           1274           7296
CSV                              6            228              0           1233
Markdown                         4            149              0            614
XML                              1              0              2            441
Rmd                              7            267            486            220
TeX                              2             12              0            133
YAML                             6             27             10            133
Dockerfile                       1              4              8             18
-------------------------------------------------------------------------------
SUM:                            83           2089           1780          10088
-------------------------------------------------------------------------------

Commit count by author:

   457  see24
    26  Sarah Endicott
    15  Adriana Caswell
     3  ilonaECCC
     1  adricaswell
     1  sarahgeargeoura
     1  sarahouimette
editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 1332

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 2 months ago

Five most similar historical JOSS papers:

shinyssdtools: A web application for fitting Species Sensitivity Distributions (SSDs) Submitting author: @sebdalgarno Handling editor: @marcosvital (Active) Reviewers: @elimillera, @meenakshi-kushwaha, @nanhung Similarity score: 0.6913

shinyssd v1.0: Species Sensitivity Distributions for Ecotoxicological Risk Assessment Submitting author: @flor14 Handling editor: @karthik (Retired) Reviewers: @kylehamilton Similarity score: 0.6887

rcites: An R package to access the CITES Speciesplus database Submitting author: @JonasGeschke Handling editor: @karthik (Retired) Reviewers: @arfon Similarity score: 0.6851

Reference Point Calculator (RPC): A Shiny app for exploration of limit reference points for fisheries management Submitting author: @quang-huynh Handling editor: @graciellehigino (Retired) Reviewers: @ivnols, @katherinehebert Similarity score: 0.6840

chirps: API Client for the CHIRPS Precipitation Data in R Submitting author: @kauedesousa Handling editor: @danielskatz (Active) Reviewers: @danielskatz Similarity score: 0.6796

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

kthyng commented 2 months ago

Hi @see24 and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

see24 commented 2 months ago

Hi @kthyng, thanks for your review. I just noticed that one of the figures isn't rendering properly in the PDF so I will look into that.

Potential reviewers:

see24 commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 2 months ago

Five most similar historical JOSS papers:

shinyssdtools: A web application for fitting Species Sensitivity Distributions (SSDs) Submitting author: @sebdalgarno Handling editor: @marcosvital (Active) Reviewers: @elimillera, @meenakshi-kushwaha, @nanhung Similarity score: 0.7084

shinyssd v1.0: Species Sensitivity Distributions for Ecotoxicological Risk Assessment Submitting author: @flor14 Handling editor: @karthik (Retired) Reviewers: @kylehamilton Similarity score: 0.7035

rcites: An R package to access the CITES Speciesplus database Submitting author: @JonasGeschke Handling editor: @karthik (Retired) Reviewers: @arfon Similarity score: 0.7007

gcamreport: An R tool to process and standardize GCAM outputs Submitting author: @klau506 Handling editor: @martinfleis (Active) Reviewers: @bpbond, @ibarraespinosa Similarity score: 0.6977

Reference Point Calculator (RPC): A Shiny app for exploration of limit reference points for fisheries management Submitting author: @quang-huynh Handling editor: @graciellehigino (Retired) Reviewers: @ivnols, @katherinehebert Similarity score: 0.6969

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

kthyng commented 2 months ago

@see24 Please trim down your paper a bit. It shouldn't be more than 1000 words ideally — you could shorten the wording or move some sections to the docs.

kthyng commented 2 months ago

@mengqi-z Could you edit this submission?

kthyng commented 2 months ago

@editorialbot invite @mengqi-z as editor

editorialbot commented 2 months ago

Invitation to edit this submission sent!

mengqi-z commented 2 months ago

@editorialbot assign me as editor

editorialbot commented 2 months ago

Assigned! @mengqi-z is now the editor

mengqi-z commented 2 months ago

👋 @ahasverus, @sebdalgarno, @Pentaonia, @mhesselbarth - Would any of you be interested in and able to take on reviewing this JOSS submission?

see24 commented 2 months ago

@editorialbot commands

editorialbot commented 2 months ago

Hello @see24, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
see24 commented 2 months ago

@editorialbot check repository

editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1847.7 files/s, 319558.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               56           1402           1274           7310
CSV                              6            270              0           1454
Markdown                         4            149              0            614
XML                              1              0              2            441
Rmd                              6            254            448            220
TeX                              2             12              0            133
YAML                             6             27             10            132
Dockerfile                       1              4              8             18
-------------------------------------------------------------------------------
SUM:                            82           2118           1742          10322
-------------------------------------------------------------------------------

Commit count by author:

   457  see24
    37  Sarah Endicott
    15  Adriana Caswell
     3  ilonaECCC
     1  adricaswell
     1  sarahgeargeoura
     1  sarahouimette
editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 1299

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

see24 commented 2 months ago

@see24 Please trim down your paper a bit. It shouldn't be more than 1000 words ideally — you could shorten the wording or move some sections to the docs.

Ok I made an attempt to trim down the wording a little but it didn't achieve much. One option I see would be to remove the whole 2nd paragraph since there is a similar section in the app_details_vignette.Rmd. But would that be too much? I want to make sure people can still understand the context of how the index works. @kthyng or @mengqi-z I would appreciate your guidance!

kthyng commented 2 months ago

@see24 I think it would be good to keep some of the second paragraph for context, like you said, but I think you could cut it off midway, somewhere around the sentence starting with "Factors that cannot be stored...". After do that you can probably call it good, you don't have to be strictly below 1000 words if you aren't at that point, but we appreciate your efforts to do so.

mhesselbarth commented 2 months ago

Hey @mengqi-z, unfortunately I am lacking the time at the moment. But maybe @lmjoconnor or @rcornf are available?

mengqi-z commented 2 months ago

Hey @mengqi-z, unfortunately I am lacking the time at the moment. But maybe @lmjoconnor or @rcornf are available?

@mhesselbarth - Thank you for your reply and recommendations!

@lmjoconnor @rcornf - Would you be interested in reviewing this submission for JOSS? The review process is checklist-driven and conducted directly within JOSS GitHub issues, following these guidelines here: https://joss.readthedocs.io/en/latest/review_criteria.html

sebdalgarno commented 2 months ago

hi @mengqi-z - I can take on reviewing this JOSS submission

mengqi-z commented 2 months ago

@editorialbot add @sebdalgarno as reviewer

editorialbot commented 2 months ago

@sebdalgarno added to the reviewers list!

editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1841.5 files/s, 315791.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               56           1402           1274           7310
CSV                              6            270              0           1454
Markdown                         4            149              0            614
XML                              1              0              2            441
Rmd                              7            267            486            220
TeX                              2             12              0            133
YAML                             6             27             10            132
Dockerfile                       1              4              8             18
-------------------------------------------------------------------------------
SUM:                            83           2131           1780          10322
-------------------------------------------------------------------------------

Commit count by author:

   457  see24
    38  Sarah Endicott
    15  Adriana Caswell
     3  ilonaECCC
     1  adricaswell
     1  sarahgeargeoura
     1  sarahouimette
editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 1299

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

see24 commented 2 months ago

@editorialbot check repository

editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1793.8 files/s, 310246.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               56           1402           1274           7310
CSV                              6            270              0           1454
Markdown                         4            149              0            614
XML                              1              0              2            441
Rmd                              6            254            448            220
TeX                              2             12              0            133
YAML                             6             27             10            132
Dockerfile                       1              4              8             18
-------------------------------------------------------------------------------
SUM:                            82           2118           1742          10322
-------------------------------------------------------------------------------

Commit count by author:

   457  see24
    39  Sarah Endicott
    15  Adriana Caswell
     3  ilonaECCC
     1  adricaswell
     1  sarahgeargeoura
     1  sarahouimette
editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 1198

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

see24 commented 2 months ago

@kthyng I edited paragraph 2 I didn't want to just cut it off half way because then it wouldn't mention how section D is scored so it would be a bit confusing. I tried to simplify the second half though. Let me know if you have any more suggestions!

see24 commented 2 months ago

@editorialbot check repository

editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1843.8 files/s, 316184.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               56           1402           1274           7310
CSV                              6            270              0           1454
Markdown                         4            149              0            614
XML                              1              0              2            441
Rmd                              7            267            486            220
TeX                              2             12              0            133
YAML                             6             27             10            132
Dockerfile                       1              4              8             18
-------------------------------------------------------------------------------
SUM:                            83           2131           1780          10322
-------------------------------------------------------------------------------

Commit count by author:

   457  see24
    39  Sarah Endicott
    15  Adriana Caswell
     4  ilonaECCC
     1  adricaswell
     1  sarahgeargeoura
     1  sarahouimette
editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 1198

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

see24 commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1002/wsb.478 is OK
- 10.1038/nclimate2448 is OK
- 10.1002/wcc.551 is OK
- 10.1038/s41562-016-0021 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Guidelines for Using the NatureServe Climate Chang...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- https://doi.org/10.7208/9780226074641-007 is INVALID because of 'https://doi.org/' prefix
see24 commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1002/wsb.478 is OK
- 10.1038/nclimate2448 is OK
- 10.1002/wcc.551 is OK
- 10.1038/s41562-016-0021 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Guidelines for Using the NatureServe Climate Chang...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- 10.7208/9780226074641-007 is INVALID
see24 commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

Checking the BibTeX entries failed with the following error: 

Failed to parse BibTeX on value "note" (NAME) [#<BibTeX::Bibliography data=[2]>, "@", #<BibTeX::Entry >, {:title=>["Rapid Assessment of Plant and Animal Vulnerability to Climate Change"], :author=>["Young, Bruce E. and Hall, Kimberly R. and Byers, Elizabeth and Gravuer, Kelly and Hammerson, Geoff and Redder, Alan"], :year=>["2012"], :date=>["2012"], :journal=>["Wildlife Conservation in a Changing Climate"], :pages=>["129--152"], :url=>["https://www.degruyter.com/document/doi/10.7208/9780226074641-007/pdf?licenseType=restricted"]}]