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

editorialbot commented 9 months ago

Submitting author: !--author-handle-->@mikejohnson51@crvernon<!--end-editor-- Reviewers: @mabesa, @mengqi-z Archive: 10.5281/zenodo.10969037

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f7a4ff717b4430f053da9c34563e705b"><img src="https://joss.theoj.org/papers/f7a4ff717b4430f053da9c34563e705b/status.svg"></a>
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 9 months ago

Hello humans, 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:

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

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editorialbot commented 9 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (788.2 files/s, 242194.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      11           2613           2665          10087
HTML                            35           1447            114           5287
R                               11            264            185            802
Rmd                              6            295            414            595
CSS                              8            106             82            463
Markdown                         4             96              0            312
TeX                              1              0              0            207
YAML                             6             31              4            165
XML                              1              0              0            105
Sass                             1              4              0             71
SVG                              1              0              1             11
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            86           4856           3465          18106
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 9 months ago

Wordcount for paper.md is 1422

editorialbot commented 9 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 9 months ago

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

OK DOIs

- 10.5281/zenodo.7868764 is OK
- 10.5281/zenodo.2558565 is OK
- 10.5194/hess-26-6121-2022 is OK

MISSING DOIs

- 10.3133/pp252 may be a valid DOI for title: The hydraulic geometry of stream channels and some physiographic implications
- 10.1002/aaai.12035 may be a valid DOI for title: Knowledge graphs to support real-time flood impact evaluation
- 10.1016/j.jhydrol.2018.07.020 may be a valid DOI for title: Field verification of analytical at-a-station hydraulic-geometry relations
- 10.1111/1752-1688.12661 may be a valid DOI for title: River channel geometry and rating curve estimation using height above the nearest drainage
- Errored finding suggestions for "National Flood Interoperability Experiment", please try later
- 10.20944/preprints202212.0390.v1 may be a valid DOI for title: Determining Feature Based Hydraulic Geometry and Rating Curves using a Physically Based, Computationally Efficient Framework
- 10.1016/j.envsoft.2020.104927 may be a valid DOI for title: Mainstems: A logical data model implementing mainstem and drainage basin feature types based on WaterML2 Part 3: HY Features concepts
- 10.22541/essoar.167415214.45806648/v1 may be a valid DOI for title: Comprehensive analysis of the NOAA National Water Model: A call for heterogeneous formulations and diagnostic model selection
- 10.1016/j.jhydrol.2017.01.038 may be a valid DOI for title: Statistical filtering of river survey and streamflow data for improving At-A-Station hydraulic geometry relations
- 10.1111/jawr.12282 may be a valid DOI for title: Development and evaluation of bankfull hydraulic geometry relationships for the physiographic regions of the United States
- 10.1111/1752-1688.12460 may be a valid DOI for title: Development and comparison of multiple regression models to predict bankfull channel dimensions for use in hydrologic models

INVALID DOIs

- None

crvernon commented 9 months ago

:wave: @mikejohnson51 , @mabesa, and @mengqi-z - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6145 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

mikejohnson51 commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 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 8 months ago

👋 @mikejohnson51 , @mabesa, and @mengqi-z

Just checking up on the status of this review to see how things are going. Post a short update here if you wouldn't mind.

Thanks!

mabesa commented 8 months ago

Sorry for the delay and thanks for the kick. I got sick and then pushed the review off...

mabesa commented 8 months ago

Review checklist for @mabesa

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/mikejohnson51/AHGestimation/?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@mikejohnson51) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

mabesa commented 8 months ago

@mikejohnson51 I went through the readme and have summarised my comments in an issue: https://github.com/mikejohnson51/AHGestimation/issues/9

crvernon commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

mabesa commented 7 months ago

@mikejohnson51 Many thanks for your edits, great work! I reviewed them in https://github.com/mikejohnson51/AHGestimation/issues/9 and added a few comments, including from a review of the vignettes.

I ran devtools::test() and got 15 fails. I'm afraid you'll need to update the test scripts. Added this as separate issue here: https://github.com/mikejohnson51/AHGestimation/issues/11

Last thing I'm missing from my checklist above are community guidelines. They can be in a section at the bottom of the readme.

crvernon commented 7 months ago

:wave: @mikejohnson51 , @mabesa, and @mengqi-z

I will be unavailable from Jan. 17-29. Please keep up the great work while I am out and I will be happy to address any questions you have when I come back!

Thanks!

crvernon commented 7 months ago

👋 @mikejohnson51 , @mabesa, and @mengqi-z

I'm back now. Can you all post short updates to how things are going here in this thread?

Thanks!

mengqi-z commented 7 months ago

Hi @crvernon, sorry for the delay. I am currently in the process of reviewing this package. I plan to complete my review by the end of this week. Thank you!

crvernon commented 7 months ago

No problem at all @mengqi-z ! Thank you!

mabesa commented 7 months ago

Hi @crvernon, I encountered an error when running one of the vignettes (https://github.com/mikejohnson51/AHGestimation/issues/9). But I can very quickly wrap the review up as soon as this is resolved.

crvernon commented 7 months ago

Thanks @mabesa !

mengqi-z commented 7 months ago

Review checklist for @mengqi-z

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/mikejohnson51/AHGestimation/?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@mikejohnson51) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

mikejohnson51 commented 7 months ago

Hi @crvernon sorry for not responding here. I have received excellent feedback from both @mabesa and @mengqi-z and have responded to the corresponding issues in the primary repo. Thanks!

crvernon commented 6 months ago

Thanks @mikejohnson51 !

:wave: @mabesa and @mengqi-z - will you give me a short update here on the status of the review? Thanks!

mengqi-z commented 6 months ago

Hi @crvernon, I was a bit busy last week. I will continue my review this week, as @mikejohnson51 has already addressed my first-round comments. Thanks!

mabesa 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:

mabesa commented 6 months ago

Hi @crvernon, I'm going through the paper one last time and encountered an issue. Apart from that all checkboxes are ticked from my side.

mabesa 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:

mabesa commented 6 months ago

@crvernon I'm through. Please let me know if there are any further steps I need to do.

mikejohnson51 commented 6 months ago

Thank you for all your effort @mabesa. I really appreciate it

mengqi-z commented 6 months ago

@crvernon I have completed my review, and I am pleased to confirm that all checks have passed. I recommend accepting the paper.

crvernon commented 6 months ago

Great @mengqi-z and @mabesa thank you! I will make my pass on this over the next few days and provide next steps.

mikejohnson51 commented 6 months ago

Thanks @crvernon! Please let me know what you need from our team.

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
- 10.1002/aaai.12035 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
- 10.20944/preprints202212.0390.v1 is OK
- 10.5194/hess-26-6121-2022 is OK
- 10.1016/j.envsoft.2020.104927 is OK
- 10.22541/essoar.167415214.45806648/v1 is OK
- 10.1016/j.jhydrol.2017.01.038 is OK
- 10.1111/jawr.12282 is OK
- 10.1111/1752-1688.12460 is OK

MISSING DOIs

- 10.1002/env.2711 may be a valid DOI for title: Generalization of the power-law rating curve using hydrodynamic theory and Bayesian hierarchical modeling

INVALID DOIs

- None

crvernon 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
- 10.1002/aaai.12035 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
- 10.20944/preprints202212.0390.v1 is OK
- 10.5194/hess-26-6121-2022 is OK
- 10.1016/j.envsoft.2020.104927 is OK
- 10.22541/essoar.167415214.45806648/v1 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

MISSING DOIs

- None

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:

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
- 10.1002/aaai.12035 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
- 10.20944/preprints202212.0390.v1 is OK
- 10.5194/hess-26-6121-2022 is OK
- 10.1016/j.envsoft.2020.104927 is OK
- 10.22541/essoar.167415214.45806648/v1 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

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: An integrated evaluation of the national water mod...
- No DOI given, and none found for title: Inundation Mapping
- No DOI given, and none found for title: Development of regional curves for hydrologic land...
- 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: Generating a reference flow network with improved ...
- No DOI given, and none found for title: Generating a reference flow network with improved ...

INVALID DOIs

- None

crvernon 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

Hi @crvernon Im not sure if you are waiting on us for anything with this. If so happy to do so! Thanks.

mikejohnson51 commented 5 months ago

Hi @crvernon. Is there anything you need from us here? Thanks!

crvernon commented 5 months ago

@editorialbot generate pdf

openjournals / joss-reviews