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

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editorialbot opened this issue Dec 13, 2023 · 107 comments
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accepted HTML published Papers published in JOSS R recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 6 (ESE) Earth Sciences and Ecology

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editorialbot commented Dec 13, 2023

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

Status

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

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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:

@editorialbot commands

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

@editorialbot generate pdf

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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

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Wordcount for paper.md is 1422

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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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
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👋 @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 #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 added a commit to mikejohnson51/AHGestimation that referenced this issue Dec 22, 2023
@mikejohnson51
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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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crvernon commented Jan 8, 2024

👋 @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
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mabesa commented Jan 8, 2024

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

@mabesa
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mabesa commented Jan 8, 2024

Review checklist for @mabesa

Conflict of interest

  • 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

General checks

  • Repository: Is the source code for this software available at the https://github.com/mikejohnson51/AHGestimation/?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • 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?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • 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.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • 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

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

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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • 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?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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
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mabesa commented Jan 8, 2024

@mikejohnson51
I went through the readme and have summarised my comments in an issue: mikejohnson51/AHGestimation#9

@crvernon
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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@mabesa
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mabesa commented Jan 13, 2024

@mikejohnson51 Many thanks for your edits, great work! I reviewed them in mikejohnson51/AHGestimation#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: mikejohnson51/AHGestimation#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
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👋 @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
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👋 @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
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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
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No problem at all @mengqi-z ! Thank you!

@mabesa
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mabesa commented Jan 30, 2024

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

@crvernon
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Thanks @mabesa !

@mengqi-z
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mengqi-z commented Feb 5, 2024

Review checklist for @mengqi-z

Conflict of interest

  • 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

General checks

  • Repository: Is the source code for this software available at the https://github.com/mikejohnson51/AHGestimation/?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • 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?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • 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.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • 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

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

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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • 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?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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?

@crvernon
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@editorialbot set 10.5281/zenodo.10969037 as archive

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Done! archive is now 10.5281/zenodo.10969037

@crvernon
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crvernon commented Apr 13, 2024

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

  • Double check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

  • Read the text of the paper and offer comments/corrections (as either a list or a pull request)
  • Check that the archive title, author list, version tag, and the license are correct
  • Set archive DOI with @editorialbot set <DOI here> as archive
  • Set version with @editorialbot set <version here> as version
  • Double check rendering of paper with @editorialbot generate pdf
  • Specifically check the references with @editorialbot check references and ask author(s) to update as needed
  • Recommend acceptance with @editorialbot recommend-accept

@crvernon
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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
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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
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👋 @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!

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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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

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

Check final proof 👉📄 Download article

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

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Apr 13, 2024
@kthyng
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kthyng commented Apr 15, 2024

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

  • Check that version was updated
  • Check that software archive exists, has been input to JOSS, and title and author list look good
  • Check paper

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kthyng commented Apr 15, 2024

Paper:

  • pg 2, paragraph 2: ... drainage area assumptions found in Bieger et al (2015), Bieger et al (2016), and Blackburn-Lynch et al (2017).
  • paragraph 3: interoperability is spelled wrong
  • Under 3. Add "They" in front of "Formalize in code". Then the reference "Dingman" should not be parenthetical

@mikejohnson51
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Hello @kthyng, thanks for the review!

  • I have changed the ; in pg 2, paragraph 2 to ,
  • I have fixed the spelling of interoperability
  • I have refined the 3rd item to read:

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

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kthyng commented Apr 17, 2024

@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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kthyng commented Apr 17, 2024

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
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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).

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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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kthyng commented Apr 18, 2024

@editorialbot accept

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Doing it live! Attempting automated processing of paper acceptance...

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Johnson
  given-names: J Michael
  orcid: "https://orcid.org/0000-0002-5288-8350"
- family-names: Afshari
  given-names: Shahab
  orcid: "https://orcid.org/0000-0002-5166-6721"
- family-names: Rad
  given-names: Arash Modaresi
  orcid: "https://orcid.org/0000-0002-6030-7923"
doi: 10.5281/zenodo.10969037
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Johnson
    given-names: J Michael
    orcid: "https://orcid.org/0000-0002-5288-8350"
  - family-names: Afshari
    given-names: Shahab
    orcid: "https://orcid.org/0000-0002-5166-6721"
  - family-names: Rad
    given-names: Arash Modaresi
    orcid: "https://orcid.org/0000-0002-6030-7923"
  date-published: 2024-04-18
  doi: 10.21105/joss.06145
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6145
  title: "AHGestimation: An R package for computing robust, mass
    preserving hydraulic geometries and rating curves"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06145"
  volume: 9
title: "AHGestimation: An R package for computing robust, mass
  preserving hydraulic geometries and rating curves"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06145 joss-papers#5249
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06145
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Apr 18, 2024
@kthyng
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kthyng commented Apr 18, 2024

Congrats on your new publication @mikejohnson51! Many thanks to editor @crvernon and reviewers @mabesa and @mengqi-z for your time, hard work, and expertise!!

@kthyng kthyng closed this as completed Apr 18, 2024
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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06145/status.svg)](https://doi.org/10.21105/joss.06145)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06145">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06145/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06145/status.svg
   :target: https://doi.org/10.21105/joss.06145

This is how it will look in your documentation:

DOI

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