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[PRE REVIEW]: RSWAT: An R package for the Soil and Water Assessment Tool models #6320

Closed editorialbot closed 3 months ago

editorialbot commented 7 months ago

Submitting author: !--author-handle-->@tamnva<!--end-author-handle-- (Van Tam Nguyen) Repository: https://github.com/tamnva/R-SWAT Branch with paper.md (empty if default branch): joss_manuscript Version: v4.0.0 Editor: !--editor-->@diazrenata<!--end-editor-- Reviewers: @mps9506, @jonsampedro Managing EiC: Daniel S. Katz

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/89a04bc6f9a2a2b08cbac33fcd91c0c6"><img src="https://joss.theoj.org/papers/89a04bc6f9a2a2b08cbac33fcd91c0c6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/89a04bc6f9a2a2b08cbac33fcd91c0c6/status.svg)](https://joss.theoj.org/papers/89a04bc6f9a2a2b08cbac33fcd91c0c6)

Author instructions

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

@tamnva 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 7 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 7 months ago

Checking the BibTeX entries failed with the following error: 

No paper file path
editorialbot commented 7 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (191.6 files/s, 40689.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             1             62              5            265
TeX                              1             22              0            234
Markdown                         1             12              0             37
-------------------------------------------------------------------------------
SUM:                             3             96              5            536
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 7 months ago

Failed to discover a valid open source license

editorialbot commented 7 months ago

Failed to discover a Statement of need section in paper

editorialbot commented 7 months ago

:warning: An error happened when generating the pdf. Paper file not found.

danielskatz commented 7 months ago

Note from author when submitting:

The original version of this software (v1.0.0) was published in Environmental Modelling & Software (Nguyen et al., 2022). In the submitted version to JOSS (v4.0.0) I have made sustainability changes (please see the manuscipt)

danielskatz commented 7 months ago

👋 @tamnva - I assume the paper is in the joss_manuscript branch? If so, please add the software there too. JOSS wants the paper and the software to be in a branch, which could be main but can also be another branch.

danielskatz commented 7 months ago

@editorialbot set joss_manuscript as branch

editorialbot commented 7 months ago

Done! branch is now joss_manuscript

danielskatz commented 7 months ago

@editorialbot check references

editorialbot commented 7 months ago

Checking the BibTeX entries failed with the following error: 

No paper file path
danielskatz commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

:warning: An error happened when generating the pdf. Paper file not found.

danielskatz commented 7 months ago

@tamnva - Also, JOSS is unhappy if the name of the branch with the paper is the same as the root name of the paper itself, so can you change the name of the files that contain the paper and bib, perhaps paper.md and paper.bib? (and you will, of course, have to change the reference to the bib file in the md file as well)

tamnva commented 7 months ago

@tamnva - Also, JOSS is unhappy if the name of the branch with the paper is the same as the root name of the paper itself, so can you change the name of the files that contain the paper and bib, perhaps paper.md and paper.bib? (and you will, of course, have to change the reference to the bib file in the md file as well)

Thanks for pointing this out. I have changed the name of the paper and bib file to paper.md and paper.bib

danielskatz commented 7 months ago

@editorialbot check references

editorialbot commented 7 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.5281/zenodo.3373859 is OK
- 10.2166/hydro.2023.182 is OK
- 10.3390/rs16020264 is OK
- 10.5194/egusphere-2023-1171 is OK
- 10.5194/hess-27-3293-2023 is OK
- 10.3390/w11081681 is OK

MISSING DOIs

- 10.13031/2013.23637 may be a valid DOI for title: The Soil and Water Assessment Tool: historical development, applications, and future research directions

INVALID DOIs

- https://doi.org/10.1111/1752-1688.12482 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/j.1752-1688.1998.tb05961.x is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jenvman.2022.116799 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1029/2018WR023815 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.envsoft.2022.105497 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jclepro.2023.138575 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.chemosphere.2023.140934 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jhydrol.2024.130629 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.envsoft.2023.105705 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jhydrol.2015.02.013 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.scitotenv.2021.149713 is INVALID because of 'https://doi.org/' prefix
danielskatz commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 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 7 months ago

Five most similar historical JOSS papers:

riversCentralAsia: An R package to support data pre- and postprocessing for hydrological modelling with RS MINERVE Submitting author: @mabesa Handling editor: @crvernon (Active) Reviewers: @mengqi-z, @tonyewong Similarity score: 0.8428

Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle Submitting author: @barneydobson Handling editor: @crvernon (Active) Reviewers: @cheginit, @jlarsen-usgs Similarity score: 0.8399

hddtools: Hydrological Data Discovery Tools Submitting author: @cvitolo Handling editor: @arfon (Active) Reviewers: @karthik Similarity score: 0.8373

rfasst: An R tool to estimate air pollution impacts on health and agriculture Submitting author: @jonsampedro Handling editor: @dhhagan (Active) Reviewers: @nanhung, @ibarraespinosa Similarity score: 0.8286

HydroMT: Automated and reproducible model building and analysis Submitting author: @dirkeilander Handling editor: @elbeejay (Active) Reviewers: @JannisHoch, @mcflugen, <s>@LejoFlores</s> Similarity score: 0.8278

⚠️ 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.

danielskatz commented 7 months ago

👋 @tamnva - now, in addition to my previous request, to merge the code into the joss_manuscript branch, you could also work on the possibly missing DOI that editorialbot suggests, but note that some may be incorrect, and the DOIs that have the prefix 'https://doi.org/'. Please make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

tamnva commented 7 months ago

👋 @tamnva - I assume the paper is in the joss_manuscript branch? If so, please add the software there too. JOSS wants the paper and the software to be in a branch, which could be main but can also be another branch.

Paper and software are now in joss_manuscript branch. Paper is the folder "joss_manuscript/joss"

danielskatz commented 7 months ago

@editorialbot check repository

editorialbot commented 7 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (1332.1 files/s, 215682.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               49           1375           2167           4944
HTML                            11            109              9            846
Markdown                         4            161              0            645
TeX                              1             21              0            221
Rmd                              1             71            122             93
SVG                              1              1              1             62
-------------------------------------------------------------------------------
SUM:                            67           1738           2299           6811
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 7 months ago

Wordcount for paper.md is 657

danielskatz commented 7 months ago

@tamnva - Given that there was a previous publication, I am going to ask other JOSS editors to check this to make sure the updates are of sufficient scope for JOSS to review this. This should take a week or two.

I believe the diffs can be seen via https://github.com/tamnva/R-SWAT/compare/v1.0.0...v4.0.0

danielskatz commented 7 months ago

@editorialbot query scope

editorialbot commented 7 months ago

Submission flagged for editorial review.

tamnva commented 7 months ago

'MISSING' DOIs are suggestions invalid DOIs were fixed

tamnva commented 7 months ago

👋 @tamnva - now, in addition to my previous request, to merge the code into the joss_manuscript branch, you could also work on the possibly missing DOI that editorialbot suggests, but note that some may be incorrect, and the DOIs that have the prefix 'https://doi.org/'. Please make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

@editorialbot check references

danielskatz commented 7 months ago

editorialbot commands need to be the first entry in a new comment.

danielskatz commented 7 months ago

@editorialbot check references

editorialbot commented 7 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1111/1752-1688.12482 is OK
- 10.1111/j.1752-1688.1998.tb05961.x is OK
- 10.13031/2013.23637 is OK
- 10.1016/j.jenvman.2022.116799 is OK
- 10.1029/2018WR023815 is OK
- 10.1016/j.envsoft.2022.105497 is OK
- 10.5281/zenodo.3373859 is OK
- 10.2166/hydro.2023.182 is OK
- 10.1016/j.jclepro.2023.138575 is OK
- 10.1016/j.chemosphere.2023.140934 is OK
- 10.1016/j.jhydrol.2024.130629 is OK
- 10.1016/j.envsoft.2023.105705 is OK
- 10.3390/rs16020264 is OK
- 10.5194/egusphere-2023-1171 is OK
- 10.1016/j.jhydrol.2015.02.013 is OK
- 10.1016/j.scitotenv.2021.149713 is OK
- 10.5194/hess-27-3293-2023 is OK
- 10.3390/w11081681 is OK

MISSING DOIs

- None

INVALID DOIs

- None
danielskatz commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 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 7 months ago

Five most similar historical JOSS papers:

riversCentralAsia: An R package to support data pre- and postprocessing for hydrological modelling with RS MINERVE Submitting author: @mabesa Handling editor: @crvernon (Active) Reviewers: @mengqi-z, @tonyewong Similarity score: 0.8410

Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle Submitting author: @barneydobson Handling editor: @crvernon (Active) Reviewers: @cheginit, @jlarsen-usgs Similarity score: 0.8386

hddtools: Hydrological Data Discovery Tools Submitting author: @cvitolo Handling editor: @arfon (Active) Reviewers: @karthik Similarity score: 0.8362

rfasst: An R tool to estimate air pollution impacts on health and agriculture Submitting author: @jonsampedro Handling editor: @dhhagan (Active) Reviewers: @nanhung, @ibarraespinosa Similarity score: 0.8286

HydroMT: Automated and reproducible model building and analysis Submitting author: @dirkeilander Handling editor: @elbeejay (Active) Reviewers: @JannisHoch, @mcflugen, <s>@LejoFlores</s> Similarity score: 0.8255

⚠️ 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.

tamnva commented 7 months ago

@tamnva - Given that there was a previous publication, I am going to ask other JOSS editors to check this to make sure the updates are of sufficient scope for JOSS to review this. This should take a week or two.

I believe the diffs can be seen via tamnva/R-SWAT@v1.0.0...v4.0.0

Please let me know once the JOSS editor's decision is made, so I can continue and suggest potential reviewers. Thanks

danielskatz commented 7 months ago

@tamnva - We'll go ahead and review this. However, note that one of the editors commented

This isn't really packaged to normal R standards (it seems like users are intended to clone the repo and edit scripts before installing the package, which isn't typical) and there's a lot of odd code choices (long chain of "x == y | x == z |", rather than using %in%; bulky wrappers around built-in functions).

tamnva commented 7 months ago

@tamnva - We'll go ahead and review this. However, note that one of the editors commented

This isn't really packaged to normal R standards (it seems like users are intended to clone the repo and edit scripts before installing the package, which isn't typical) and there's a lot of odd code choices (long chain of "x == y | x == z |", rather than using %in%; bulky wrappers around built-in functions).

Thank you for the Editor's comments. I will check/revise the package regarding those points and provide a detailed response here.

tamnva commented 7 months ago

Please find below the list of potential reviewers which had R packages that are relevant to this work:

cvitolo Sibada ldecicco-USGS odelaigue jmp75

There is also a list of people that starred this GitHub repository (please see the link below), I am not sure whether I am allowed to suggest some of them or not

https://github.com/tamnva/R-SWAT/stargazers

danielskatz commented 7 months ago

There is also a list of people that starred this GitHub repository (please see the link below), I am not sure whether I am allowed to suggest some of them or not

Yes, that's fine to do as long as they are not contributors or otherwise conflicted. Being a user is not a conflict and can be a plus.

tamnva commented 7 months ago

There is also a list of people that starred this GitHub repository (please see the link below), I am not sure whether I am allowed to suggest some of them or not

Yes, that's fine to do as long as they are not contributors or otherwise conflicted. Being a user is not a conflict and can be a plus.

Please find the additional list of potential reviewers below:

mps9506 haleykujawa EdbertoLima

danielskatz commented 7 months ago

@tamnva - It seems this submission came into the wrong track, so I've now moved it. The track editor for the new track should take the next steps.

kthyng commented 6 months ago

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

diazrenata commented 6 months ago

@editorialbot assign me as editor

editorialbot commented 6 months ago

Assigned! @diazrenata is now the editor

diazrenata commented 6 months ago

@tamnva :wave: I'll be editing this submission! To start, have you had the chance to look at this comment and respond?

@tamnva - We'll go ahead and review this. However, note that one of the editors commented

This isn't really packaged to normal R standards (it seems like users are intended to clone the repo and edit scripts before installing the package, which isn't typical) and there's a lot of odd code choices (long chain of "x == y | x == z |", rather than using %in%; bulky wrappers around built-in functions).

Thank you for the Editor's comments. I will check/revise the package regarding those points and provide a detailed response here.

tamnva commented 6 months ago

@tamnva 👋 I'll be editing this submission! To start, have you had the chance to look at this comment and respond?

@tamnva - We'll go ahead and review this. However, note that one of the editors commented

This isn't really packaged to normal R standards (it seems like users are intended to clone the repo and edit scripts before installing the package, which isn't typical) and there's a lot of odd code choices (long chain of "x == y | x == z |", rather than using %in%; bulky wrappers around built-in functions).

Thank you for the Editor's comments. I will check/revise the package regarding those points and provide a detailed response here.

Yes, I am working on these comments. These are short but major comments. There are still some works needed:

Comment: users are intended to clone the repo and edit scripts before installing the package Response: There is no need to edit scripts before installing the package now.

Comment: there's a lot of odd code choices (long chain of "x == y | x == z |", rather than using %in% Response: The updated version uses %in%

Comment: bulky wrappers around built-in functions Response: In this commit I have spitted complex file/functions to smaller files/functions

The server.R file is quite long (around 3000 lines). I have no idea how to break this file into smaller files. Any suggestions would be highly appreciated.

diazrenata commented 6 months ago

Hi @tamnva, thank you for your response! Please let me know when you are through revising the code and the package is ready for review.

On Mon, Feb 19, 2024 at 12:00 PM Tam Nguyen @.***> wrote:

External Email

@tamnva https://github.com/tamnva 👋 I'll be editing this submission! To start, have you had the chance to look at this comment and respond?

@tamnva https://github.com/tamnva - We'll go ahead and review this. However, note that one of the editors commented

This isn't really packaged to normal R standards (it seems like users are intended to clone the repo and edit scripts before installing the package, which isn't typical) and there's a lot of odd code choices (long chain of "x == y | x == z |", rather than using %in%; bulky wrappers around built-in functions).

Thank you for the Editor's comments. I will check/revise the package regarding those points and provide a detailed response here.

Yes, I am working on these comments. These are short but major comments. There are still some works needed:

Comment: users are intended to clone the repo and edit scripts before installing the package Response: There is no need to edit scripts before installing the package now.

Comment: there's a lot of odd code choices (long chain of "x == y | x == z |", rather than using %in% Response: The updated version uses %in%

Comment: bulky wrappers around built-in functions Response: I am working to split complex functions into smaller functions (TO DO)

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6320#issuecomment-1953028662, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEH6DNYFSMFRCO4AT3VD7XTYUOOL3AVCNFSM6AAAAABCZEAX22VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJTGAZDQNRWGI . You are receiving this because you were mentioned.Message ID: @.***>