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[PRE REVIEW]: rOPTRAM: Implementation of the OPTRAM Algorithm in R #6910

Open editorialbot opened 1 week ago

editorialbot commented 1 week ago

Submitting author: !--author-handle-->@micha-silver<!--end-author-handle-- (Micha Silver) Repository: https://github.com/ropensci/rOPTRAM Branch with paper.md (empty if default branch): Version: v0.2.0 Editor: Pending Reviewers: Pending Managing EiC: Kristen Thyng

Status

status

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HTML: <a href="https://joss.theoj.org/papers/da6075f8a6b47ad603a2ec4849ef3fb3"><img src="https://joss.theoj.org/papers/da6075f8a6b47ad603a2ec4849ef3fb3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/da6075f8a6b47ad603a2ec4849ef3fb3/status.svg)](https://joss.theoj.org/papers/da6075f8a6b47ad603a2ec4849ef3fb3)

Author instructions

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

@micha-silver 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 1 week 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 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (2158.6 files/s, 222103.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               24            225           1166           1459
Markdown                         5            288              0            862
CSV                             17              0              0            828
TeX                              3             42              0            523
JSON                             1              0              0            283
JavaScript                       8             22             15            146
Rmd                              4            216            448             65
SVG                              1              0              0             40
Bourne Shell                     1              4             10             20
YAML                             1              3              6             17
-------------------------------------------------------------------------------
SUM:                            65            800           1645           4243
-------------------------------------------------------------------------------

Commit count by author:

   462  Micha Silver
    49  micha-silver
    30  Ron Beiden
     5  Natalya
editorialbot commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1629

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot commented 1 week ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1126/science.abq4062 is OK
- 10.1016/j.rse.2017.05.041 is OK
- 10.3390/rs12182936 is OK
- 10.1016/j.jag.2020.102113 is OK
- 10.1016/B978-0-12-420022-7.00008-2 is OK
- 10.5194/hess-21-5009-2017 is OK
- 10.3390/s22239143 is OK
- 10.3390/s16081308 is OK
- 10.3390/rs14153801 is OK
- 10.1016/j.rse.2018.04.029 is OK
- 10.1016/j.rse.2015.04.007 is OK
- 10.3390/s7081612 is OK
- 10.1029/2020EA001108 is OK
- 10.3389/fdata.2019.00037 is OK
- 10.1080/01431169608949021 is OK
- 10.1016/j.jag.2022.102817 is OK
- 10.3390/rs12121980 is OK
- 10.1016/j.agwat.2022.107975 is OK
- 10.1029/2021JG006411 is OK
- 10.1016/j.rse.2022.113443 is OK
- 10.3390/rs12203377 is OK
- 10.1016/j.rse.2023.113736 is OK
- 10.5194/esd-2017-4-RC1 is OK
- 10.1016/j.cosust.2020.11.005 is OK
- 10.1029/2007GB002952 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- 10.32614/cran.package.cdse may be a valid DOI for title: CDSE: ’Copernicus Data Space Ecosystem’ API Wrappe...

INVALID DOIs

- None
editorialbot commented 1 week ago

:warning: An error happened when generating the pdf.

kthyng commented 1 week ago

@micha-silver Can you try to fix the error in compiling the paper? On a quick glance it doesn't look like your paper is following the example paper syntax correctly: https://joss.readthedocs.io/en/latest/example_paper.html#example-paper

kthyng commented 1 week ago

Also please remove the backticks around the package name and "R" for it to compile correctly — we can try this first to see if it fixes the issue.

micha-silver commented 1 week ago

@kthyng In the example paper, R package names are surrounded by backticks. i.e.:

# Statement of need
`Gala` is an Astropy-affiliated Python package for galactic dynamics.

??

kthyng commented 1 week ago

Ah, I mean in the title only.

micha-silver commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

micha-silver commented 1 week ago

I made a few changes to the yaml header and then successfully compiled (using the suggested docker image). The only problem I see now is that the two included images do not appear in the final pdf :-(

The images do appear on the github markdown: here

micha-silver commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

micha-silver commented 1 week ago

@kthyng I found the correct format for figures and fixed paper.md accordingly. Now the pdf compiles successfully including images. Thanks for your tips.

micha-silver commented 1 week ago

Suggested reviewers: Carlos Hernandez: Carlitosh David LeBauer: dlebauer

micha-silver commented 1 week ago

@editorialbot commands

editorialbot commented 1 week ago

Hello @micha-silver, 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
kthyng commented 1 week ago

@editorialbot check repository

editorialbot commented 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (2215.5 files/s, 227587.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               24            225           1166           1459
Markdown                         5            283              0            856
CSV                             17              0              0            828
TeX                              3             42              0            523
JSON                             1              0              0            283
JavaScript                       8             22             15            146
Rmd                              4            216            448             65
SVG                              1              0              0             40
Bourne Shell                     1              4             10             20
YAML                             1              3              6             17
-------------------------------------------------------------------------------
SUM:                            65            795           1645           4237
-------------------------------------------------------------------------------

Commit count by author:

   466  Micha Silver
    49  micha-silver
    30  Ron Beiden
     5  Natalya
editorialbot commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1610

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

🟡 License found: Other (Check here for OSI approval)

danielskatz commented 1 week ago

I note that this title include backquotes, which are going to cause problems later, and should be removed

kthyng commented 1 week ago

@danielskatz the author changed them in the paper, do they matter in the issue name?

kthyng commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1126/science.abq4062 is OK
- 10.1016/j.rse.2017.05.041 is OK
- 10.3390/rs12182936 is OK
- 10.1016/j.jag.2020.102113 is OK
- 10.1016/B978-0-12-420022-7.00008-2 is OK
- 10.5194/hess-21-5009-2017 is OK
- 10.3390/s22239143 is OK
- 10.3390/s16081308 is OK
- 10.3390/rs14153801 is OK
- 10.1016/j.rse.2018.04.029 is OK
- 10.1016/j.rse.2015.04.007 is OK
- 10.3390/s7081612 is OK
- 10.1029/2020EA001108 is OK
- 10.3389/fdata.2019.00037 is OK
- 10.1080/01431169608949021 is OK
- 10.1016/j.jag.2022.102817 is OK
- 10.3390/rs12121980 is OK
- 10.1016/j.agwat.2022.107975 is OK
- 10.1029/2021JG006411 is OK
- 10.1016/j.rse.2022.113443 is OK
- 10.3390/rs12203377 is OK
- 10.1016/j.rse.2023.113736 is OK
- 10.5194/esd-2017-4-RC1 is OK
- 10.1016/j.cosust.2020.11.005 is OK
- 10.1029/2007GB002952 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- 10.32614/cran.package.cdse may be a valid DOI for title: CDSE: ’Copernicus Data Space Ecosystem’ API Wrappe...

INVALID DOIs

- None
kthyng commented 1 week ago

Hi @micha-silver 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 that DOI issue. For reviewers, please suggest more reviewers — 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.

kthyng commented 1 week ago

We have a backlog of submissions so I will add this to our waitlist. Thanks for your patience.

danielskatz commented 1 week ago

@danielskatz the author changed them in the paper, do they matter in the issue name?

I don't think so, but you can manually edit the issue name if you want

micha-silver commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

micha-silver commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1126/science.abq4062 is OK
- 10.1016/j.rse.2017.05.041 is OK
- 10.3390/rs12182936 is OK
- 10.1016/j.jag.2020.102113 is OK
- 10.1016/B978-0-12-420022-7.00008-2 is OK
- 10.5194/hess-21-5009-2017 is OK
- 10.3390/s22239143 is OK
- 10.3390/s16081308 is OK
- 10.3390/rs14153801 is OK
- 10.1016/j.rse.2018.04.029 is OK
- 10.1016/j.rse.2015.04.007 is OK
- 10.3390/s7081612 is OK
- 10.1029/2020EA001108 is OK
- 10.3389/fdata.2019.00037 is OK
- 10.1080/01431169608949021 is OK
- 10.1016/j.jag.2022.102817 is OK
- 10.3390/rs12121980 is OK
- 10.1016/j.agwat.2022.107975 is OK
- 10.1029/2021JG006411 is OK
- 10.1016/j.rse.2022.113443 is OK
- 10.3390/rs12203377 is OK
- 10.1016/j.rse.2023.113736 is OK
- 10.5194/esd-2017-4-RC1 is OK
- 10.1016/j.cosust.2020.11.005 is OK
- 10.32614/CRAN.package.CDSE is OK
- 10.1029/2007GB002952 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...

INVALID DOIs

- None
micha-silver commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1126/science.abq4062 is OK
- 10.1016/j.rse.2017.05.041 is OK
- 10.3390/rs12182936 is OK
- 10.1016/j.jag.2020.102113 is OK
- 10.1016/B978-0-12-420022-7.00008-2 is OK
- 10.5194/hess-21-5009-2017 is OK
- 10.3390/s22239143 is OK
- 10.3390/s16081308 is OK
- 10.3390/rs14153801 is OK
- 10.1016/j.rse.2018.04.029 is OK
- 10.1016/j.rse.2015.04.007 is OK
- 10.3390/s7081612 is OK
- 10.1029/2020EA001108 is OK
- 10.3389/fdata.2019.00037 is OK
- 10.1080/01431169608949021 is OK
- 10.1016/j.jag.2022.102817 is OK
- 10.3390/rs12121980 is OK
- 10.1016/j.agwat.2022.107975 is OK
- 10.1029/2021JG006411 is OK
- 10.1016/j.rse.2022.113443 is OK
- 10.3390/rs12203377 is OK
- 10.1016/j.rse.2023.113736 is OK
- 10.5194/esd-2017-4-RC1 is OK
- 10.1016/j.cosust.2020.11.005 is OK
- 10.32614/CRAN.package.CDSE is OK
- 10.1029/2007GB002952 is OK

MISSING DOIs

- None

INVALID DOIs

- None
micha-silver commented 1 week ago

Hi: @kthyng @danielskatz I found the missing doi for the CDSE , and removed the citation to R-cran (No doi available since it's a project, not a single document). I'll choose some additional potential reviewers and post here soon. Thanks, Micha

micha-silver commented 6 days ago

@kthyng @danielskatz

Here's our full list of suggested reviewers:

Maofang Gao, Chinese Academy of Agricultural Sciences, Beijing, gaomaofang@caas.cn Sadeghi, Morteza, Utah State Univ, Dept Plants Soils & Climate, USA, morteza.sadeghi@usu.edu Babaeian, Ebrahim - Univ Arizona, Dept Soil Water & Environm Sci, USA, ebabaeian@email.arizona.edu Carlos Hernandez: Carlitosh David LeBauer: dlebauer

Regards, Micha

micha-silver commented 6 days ago

@editorialbot check repository

editorialbot commented 6 days ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (2238.4 files/s, 229630.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               24            225           1166           1459
Markdown                         5            283              0            856
CSV                             17              0              0            828
TeX                              3             40              0            516
JSON                             1              0              0            283
JavaScript                       8             22             15            146
Rmd                              4            216            448             65
SVG                              1              0              0             40
Bourne Shell                     1              4             10             20
YAML                             1              3              6             17
-------------------------------------------------------------------------------
SUM:                            65            793           1645           4230
-------------------------------------------------------------------------------

Commit count by author:

   470  Micha Silver
    49  micha-silver
    30  Ron Beiden
     5  Natalya
editorialbot commented 6 days ago

Paper file info:

📄 Wordcount for paper.md is 1609

✅ The paper includes a Statement of need section

editorialbot commented 6 days ago

License info:

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

kthyng commented 3 days ago

I updated the title of the issue so it matches the JOSS paper title exactly.

kthyng commented 3 days ago

and yeah, the license tool is imperfect, but helpful.