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[REVIEW]: AHGestimation: An R package for Computing robust, mass preserving Hydraulic Geometries and Rating Curves #6145

Closed editorialbot closed 6 months ago

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@mikejohnson51<!--end-author-handle-- (J. Micahel Johnson) Repository: https://github.com/mikejohnson51/AHGestimation/ Branch with paper.md (empty if default branch): Version: 0.2.0 Editor: !--editor-->@crvernon<!--end-editor-- Reviewers: @mabesa, @mengqi-z Archive: 10.5281/zenodo.10969037

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Markdown: [![status](https://joss.theoj.org/papers/f7a4ff717b4430f053da9c34563e705b/status.svg)](https://joss.theoj.org/papers/f7a4ff717b4430f053da9c34563e705b)

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

@mabesa & @mengqi-z, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @crvernon know.

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

Checklists

📝 Checklist for @mabesa

📝 Checklist for @mengqi-z

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:

mikejohnson51 commented 7 months ago

I updated a citation to point to the published (recent) version opposed to a preprint!

@editorialbot generate pdf

danielskatz commented 7 months ago

FYI, editorialbot commands need to be the first thing in a comment

crvernon 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:

crvernon commented 7 months ago

:wave: Great work on this @mikejohnson51 !

Here are some things that need to be addressed in the paper:

Once these are knocked out, we can move to the next step towards getting this published. Thanks!

crvernon commented 7 months ago

Just following up on the status of the above @mikejohnson51. Thanks!

crvernon commented 6 months ago

Just a reminder on the status of the above @mikejohnson51. Thanks!

mikejohnson51 commented 6 months ago

Hi @crvernon thanks for all the feedback (and patience!), we have incorporated this, and the internal review we were required to go through. I think is in in good shape now!

This now reads: These equations collectively define the "at a station hydraulic geometry" (AHG), with coefficients (a, c, k) and exponents (b, f, m) for the Q-TW, Q-Y, and Q-V relationships. Further we modified the text to say mean velocity (V)

Fixed throughout. Thank you!

Fixed and changed to NOAA.

Changed throughout text.

changed to read ... accuracy within 0.4% NRMSE of the source data

Thank you this has been fixed!

Now reads This reduction to a consistent AHG formulation not only enhances interoperability with efforts such as those by Enzminger (2023) or Afshari (2019), but....

Now reads The development of this package began following the 2017 NOAA/NWS Office of Water Prediction Summer Institute (Johnson et al. 2017) where discussions highlighted the potential influence of channel shap representation on the performance of the National Water Model.

Resolved. Thank you!

This has been added!

This has been added!

Fixed.

Fixed.

mikejohnson51 commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

crvernon commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3133/pp252 is OK
- 10.1002/aaai.12035 is OK
- 10.1016/j.jhydrol.2018.07.020 is OK
- 10.5281/zenodo.7868764 is OK
- 10.5281/zenodo.2558565 is OK
- 10.1111/1752-1688.12661 is OK
- 10.1111/1752-1688.12474 is OK
- 10.5194/nhess-19-2405-2019 is OK
- 10.1111/1752-1688.12540 is OK
- 10.20944/preprints202212.0390.v1 is OK
- 10.5194/hess-26-6121-2022 is OK
- 10.1016/j.envsoft.2020.104927 is OK
- 10.1016/j.envsoft.2023.105726 is OK
- 10.1029/2023JD038534 is OK
- 10.1016/j.jhydrol.2017.01.038 is OK
- 10.1111/jawr.12282 is OK
- 10.1111/1752-1688.12460 is OK
- 10.1002/env.2711 is OK
- 10.4211/technical.20171009 is OK
- 10.1111/1752-1688.13184 is OK
- 10.1002/2015WR017498 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: National Hydrologic Geospatial Fabric Reference an...
- No DOI given, and none found for title: mco: Multiple Criteria Optimization Algorithms and...
- No DOI given, and none found for title: Inundation Mapping
- No DOI given, and none found for title: The WRF-Hydro® modeling system technical descripti...
- No DOI given, and none found for title: Height Above Nearest Drainage (HAND) and Hydraulic...

INVALID DOIs

- None
crvernon commented 6 months ago

Thanks @mikejohnson51 this is looking good! I just see a few more things that need to be corrected before we move on to the next steps...

Thanks so much and great work!

mikejohnson51 commented 6 months ago

Thank you for the very careful review @crvernon! I have made the following changes to the paper and bib files.

Removed in Line 44

Fixed. Thank you!

Added this comma and tweaked the third element to be more grammatically correct.

Added the complete script URL opposed to the relative repo path. Thank you!. I will test this when the new version is rendered.

I added a call out to the figure in the sentence that now reads: The script to generate the plot found in Figure 1 can be found here...

I wrapped all titles in {...} to ensure capitalization is retained throughout. Thank you for this tip!

mikejohnson51 commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

mikejohnson51 commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3133/pp252 is OK
- 10.1002/aaai.12035 is OK
- 10.1016/j.jhydrol.2018.07.020 is OK
- 10.5281/zenodo.7868764 is OK
- 10.5281/zenodo.2558565 is OK
- 10.1111/1752-1688.12661 is OK
- 10.1111/1752-1688.12474 is OK
- 10.5194/nhess-19-2405-2019 is OK
- 10.1111/1752-1688.12540 is OK
- 10.20944/preprints202212.0390.v1 is OK
- 10.5194/hess-26-6121-2022 is OK
- 10.1016/j.envsoft.2020.104927 is OK
- 10.1016/j.envsoft.2023.105726 is OK
- 10.1029/2023JD038534 is OK
- 10.1016/j.jhydrol.2017.01.038 is OK
- 10.1111/jawr.12282 is OK
- 10.1111/1752-1688.12460 is OK
- 10.1002/env.2711 is OK
- 10.4211/technical.20171009 is OK
- 10.1111/1752-1688.13184 is OK
- 10.1002/2015WR017498 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: National Hydrologic Geospatial Fabric Reference an...
- No DOI given, and none found for title: mco: Multiple Criteria Optimization Algorithms and...
- No DOI given, and none found for title: Inundation Mapping
- No DOI given, and none found for title: The WRF-Hydro® modeling system technical descripti...
- No DOI given, and none found for title: Height Above Nearest Drainage (HAND) and Hydraulic...
- No DOI given, and none found for title: Improved National-Scale Above-Normal Flow Predicti...

INVALID DOIs

- 129787b468aa4d55ace7b124ed27dbde is INVALID
mikejohnson51 commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

mikejohnson51 commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3133/pp252 is OK
- 10.1002/aaai.12035 is OK
- 10.1016/j.jhydrol.2018.07.020 is OK
- 10.5281/zenodo.7868764 is OK
- 10.5281/zenodo.2558565 is OK
- 10.1111/1752-1688.12661 is OK
- 10.1111/1752-1688.12474 is OK
- 10.5194/nhess-19-2405-2019 is OK
- 10.1111/1752-1688.12540 is OK
- 10.20944/preprints202212.0390.v1 is OK
- 10.5194/hess-26-6121-2022 is OK
- 10.1016/j.envsoft.2020.104927 is OK
- 10.1016/j.envsoft.2023.105726 is OK
- 10.1029/2023JD038534 is OK
- 10.1016/j.jhydrol.2017.01.038 is OK
- 10.1111/jawr.12282 is OK
- 10.1111/1752-1688.12460 is OK
- 10.1002/env.2711 is OK
- 10.4211/technical.20171009 is OK
- 10.1111/1752-1688.13184 is OK
- 10.1002/2015WR017498 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: National Hydrologic Geospatial Fabric Reference an...
- No DOI given, and none found for title: National Hydrologic Geospatial Fabric (Hydrofabric...
- No DOI given, and none found for title: mco: Multiple Criteria Optimization Algorithms and...
- No DOI given, and none found for title: Inundation Mapping
- No DOI given, and none found for title: The WRF-Hydro® modeling system technical descripti...
- No DOI given, and none found for title: Height Above Nearest Drainage (HAND) and Hydraulic...
- No DOI given, and none found for title: Improved National-Scale Above-Normal Flow Predicti...

INVALID DOIs

- None
mikejohnson51 commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

mikejohnson51 commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3133/pp252 is OK
- 10.1002/aaai.12035 is OK
- 10.1016/j.jhydrol.2018.07.020 is OK
- 10.5281/zenodo.7868764 is OK
- 10.5281/zenodo.2558565 is OK
- 10.1111/1752-1688.12661 is OK
- 10.1111/1752-1688.12474 is OK
- 10.5194/nhess-19-2405-2019 is OK
- 10.1111/1752-1688.12540 is OK
- 10.20944/preprints202212.0390.v1 is OK
- 10.5194/hess-26-6121-2022 is OK
- 10.1016/j.envsoft.2020.104927 is OK
- 10.1016/j.envsoft.2023.105726 is OK
- 10.1029/2023JD038534 is OK
- 10.1016/j.jhydrol.2017.01.038 is OK
- 10.1111/jawr.12282 is OK
- 10.1111/1752-1688.12460 is OK
- 10.1002/env.2711 is OK
- 10.4211/technical.20171009 is OK
- 10.1111/1752-1688.13184 is OK
- 10.1002/2015WR017498 is OK
- 10.1029/2023WR034557 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: National Hydrologic Geospatial Fabric Reference an...
- No DOI given, and none found for title: National Hydrologic Geospatial Fabric (Hydrofabric...
- No DOI given, and none found for title: mco: Multiple Criteria Optimization Algorithms and...
- No DOI given, and none found for title: Inundation Mapping
- No DOI given, and none found for title: The WRF-Hydro® modeling system technical descripti...
- No DOI given, and none found for title: Height Above Nearest Drainage (HAND) and Hydraulic...

INVALID DOIs

- None
crvernon commented 6 months ago

👋 @mikejohnson51 - Thanks for making the changes to the paper, it looks great! We are almost there! Next is just setting up the archive for your new release.

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

I can then move forward with accepting the submission.

mikejohnson51 commented 6 months ago

Hi @crvernon thanks for the very clear directions. I have uploaded a release artifact on Zenodo, using a MIT license and modified metadata. The DOI is: 10.5281/zenodo.10969037.

Please let me know what else is needed!

crvernon commented 6 months ago

@editorialbot set 0.2.0 as version

editorialbot commented 6 months ago

Done! version is now 0.2.0

crvernon commented 6 months ago

@editorialbot set 10.5281/zenodo.10969037 as archive

editorialbot commented 6 months ago

Done! archive is now 10.5281/zenodo.10969037

crvernon commented 6 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

crvernon commented 6 months ago

Thanks @mikejohnson51! You missed one of your co-author's names in the Zenodo archive. No need to do an additional release, but could you please edit the metadata in your Zenodo record to show the same authors and author order as you have in your paper? Thanks!

mikejohnson51 commented 6 months ago

Thanks @crvernon. Sorry about that. I was confused by inclusion comment about code contributions. While Shahab was not able to contribute to the code directly, the work, ideas, and progression of the project could not have been done without him. I have added him to the Zenodo archive along with both authors ORCID.

crvernon commented 6 months ago

👋 @mikejohnson51 - I am recommending that this submission be accepted for publication. An EiC will review shortly and if all goes well this will go live soon! Thanks to @mabesa and @mengqi-z for a timely and constructive review! Congrats!

crvernon commented 6 months ago

@editorialbot recommend-accept

editorialbot commented 6 months ago
Attempting dry run of processing paper acceptance...
editorialbot commented 6 months ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3133/pp252 is OK
- 10.1002/aaai.12035 is OK
- 10.1016/j.jhydrol.2018.07.020 is OK
- 10.5281/zenodo.7868764 is OK
- 10.5281/zenodo.2558565 is OK
- 10.1111/1752-1688.12661 is OK
- 10.1111/1752-1688.12474 is OK
- 10.5194/nhess-19-2405-2019 is OK
- 10.1111/1752-1688.12540 is OK
- 10.20944/preprints202212.0390.v1 is OK
- 10.5194/hess-26-6121-2022 is OK
- 10.1016/j.envsoft.2020.104927 is OK
- 10.1016/j.envsoft.2023.105726 is OK
- 10.1029/2023JD038534 is OK
- 10.1016/j.jhydrol.2017.01.038 is OK
- 10.1111/jawr.12282 is OK
- 10.1111/1752-1688.12460 is OK
- 10.1002/env.2711 is OK
- 10.4211/technical.20171009 is OK
- 10.1111/1752-1688.13184 is OK
- 10.1002/2015WR017498 is OK
- 10.1029/2023WR034557 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: National Hydrologic Geospatial Fabric Reference an...
- No DOI given, and none found for title: National Hydrologic Geospatial Fabric (Hydrofabric...
- No DOI given, and none found for title: mco: Multiple Criteria Optimization Algorithms and...
- No DOI given, and none found for title: Inundation Mapping
- No DOI given, and none found for title: The WRF-Hydro® modeling system technical descripti...
- No DOI given, and none found for title: Height Above Nearest Drainage (HAND) and Hydraulic...

INVALID DOIs

- None
editorialbot commented 6 months ago

:wave: @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5242, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kthyng commented 6 months ago

Hi @mikejohnson51, I'll be taking over. Here is my to do list:

kthyng commented 6 months ago

Paper:

mikejohnson51 commented 6 months ago

Hello @kthyng, thanks for the review!

These functions formalize many of the concepts derived in Dingman and Afshari (2018) that relate AHG coefficients and exponents to cross-section hydraulics and geometry

kthyng commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

kthyng commented 6 months ago

For the first bullet point I meant to change it to a proper sentence when changing the ";" to "," and add an "and" too as in (I can't copy paste so it's hard to write out...)

... Bieger, Bieger, and Blackburn-Lynch.

Otherwise keep it as ";" but have them be parenthetical and don't incorporate them into the sentence. Does that make sense?

mikejohnson51 commented 6 months ago

Good morning @kthyng! Yes this makes sense. The sentence now reads

For instance, the National Oceanic and Atmospheric Administration National Water Model (Cosgrove et al. 2024)
uses trapezoidal geometries (Gochis et al. 2020) that are in part derived from hydraulic geometry relationships
and drainage area assumptions found in Bieger et al. (2015), Bieger et al. (2016), and Blackburn-Lynch,
Agouridis, and Barton (2017).
mikejohnson51 commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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