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[PRE REVIEW]: PyForestScan: A Python Library for Calculating Forest Structural Metrics from LiDAR Point Cloud Data #7283

Closed editorialbot closed 2 weeks ago

editorialbot commented 3 weeks ago

Submitting author: !--author-handle-->@iosefa<!--end-author-handle-- (Joseph Emile Honour Percival) Repository: https://github.com/iosefa/PyForestScan Branch with paper.md (empty if default branch): docs/joss-paper Version: v0.1.6 Editor: !--editor-->@mengqi-z<!--end-editor-- Reviewers: @npucino, @giswqs Managing EiC: Kristen Thyng

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Markdown: [![status](https://joss.theoj.org/papers/61114708d8831867a7c7d7e1ef25947d/status.svg)](https://joss.theoj.org/papers/61114708d8831867a7c7d7e1ef25947d)

Author instructions

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

@iosefa 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 3 weeks 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:

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editorialbot commented 3 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1016/j.foreco.2018.11.017 is OK
- 10.1016/j.foreco.2005.08.034 is OK
- 10.1016/S0034-4257(01)00281-4 is OK
- 10.1016/j.rse.2020.112061 is OK
- 10.2307/1934145 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Airborne LiDAR data manipulation and visualization...
- No DOI given, and none found for title: Efficient LiDAR processing software
- No DOI given, and none found for title: Global mapper: GIS and mapping software
- No DOI given, and none found for title: FUSION/LDV: LiDAR processing and visualization sof...

❌ MISSING DOIs

- 10.32614/cran.package.leafr may be a valid DOI for title: leafR: Calculates the leaf area index (LAD) and ot...

❌ INVALID DOIs

- None
editorialbot commented 3 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1084.3 files/s, 107379.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11            409            502           1255
Markdown                         3             77              0            162
TeX                              1             10              0            149
YAML                             4             18              0             92
reStructuredText                 4             61             55             61
XML                              6              0              0             55
DOS Batch                        1              8              1             26
Jupyter Notebook                 1              0            276             25
make                             1              4              7              9
INI                              1              0              0              6
-------------------------------------------------------------------------------
SUM:                            33            587            841           1840
-------------------------------------------------------------------------------

Commit count by author:

    25  iosefa
    22  Iosefa Percival
     3  benleamon
editorialbot commented 3 weeks ago

Paper file info:

📄 Wordcount for paper.md is 851

✅ The paper includes a Statement of need section

editorialbot commented 3 weeks ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 3 weeks ago

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

editorialbot commented 3 weeks ago

Five most similar historical JOSS papers:

lidar: A Python package for delineating nested surface depressions from digital elevation data Submitting author: @giswqs Handling editor: @kbarnhart (Retired) Reviewers: @laijingtao, @cheginit, @amanaster2 Similarity score: 0.7125

DetecTree: Tree detection from aerial imagery in Python Submitting author: @martibosch Handling editor: @kthyng (Active) Reviewers: @JeffWalton-PSC, @rmsare Similarity score: 0.7117

pymccrgb: Color- and curvature-based classification of multispectral point clouds in Python Submitting author: @rmsare Handling editor: @kthyng (Active) Reviewers: @martibosch, @daniellivingston Similarity score: 0.7097

pointcloudset: Efficient Analysis of Large Datasets of Point Clouds Recorded Over Time Submitting author: @tgoelles Handling editor: @hugoledoux (Active) Reviewers: @RonaldEnsing, @hechth Similarity score: 0.7058

bioLEC: A Python package to measure Landscape Elevational Connectivity Submitting author: @tristan-salles Handling editor: @kthyng (Active) Reviewers: @kbarnhart, @hugoledoux Similarity score: 0.7035

⚠️ 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.

kthyng commented 3 weeks ago

Hi @iosefa 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 any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 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.

iosefa commented 3 weeks ago

Hi @iosefa 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 any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 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.

Hi @kthyng, Thank you! I will go through the reviewer list and reply with suggestions. In the meantime, I have two questions:

  1. I need to add an additional statement in the acknowledgements -- is it okay to do this at this point?

  2. the editorial bot came back with this missing DOI:

❌ MISSING DOIs

I dont know that this is a correct and valid DOI for the leafR package. The package itself requests that it be cited as:

citation("leafR")
To cite package ‘leafR’ in publications use:

  Almeida D, Stark S, Silva C, Hamamura C, Valbuena R (2021).
  _leafR: Calculates the Leaf Area Index (LAD) and Other Related
  Functions_. R package version 0.3.5,
  <https://CRAN.R-project.org/package=leafR>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {leafR: Calculates the Leaf Area Index (LAD) and Other Related Functions},
    author = {Danilo Roberti Alves de Almeida and Scott Christopher Stark and Carlos Alberto Silva and Caio Hamamura and Ruben Valbuena},
    year = {2021},
    note = {R package version 0.3.5},
    url = {https://CRAN.R-project.org/package=leafR},
  }

And this is how it is cited in our manuscript. Is it okay to leave it as is without any specific reply to the editor bot?

Many thanks,

kthyng commented 3 weeks ago

I need to add an additional statement in the acknowledgements -- is it okay to do this at this point?

Yes go ahead.

the editorial bot came back with this missing DOI:

Sometimes the DOIs are incorrect. If you checked and know better, that is fine. You'll want to let your topic editor know this later, too.

kthyng commented 3 weeks ago

@iosefa

iosefa commented 3 weeks ago

@kthyng Thank you very much for your feedback.

I will work these in. I assume it is okay to commit directly to the branch with the paper?

iosefa commented 3 weeks ago

@kthyng

Ok. We have fixed the parenthetical and inline references and also checked capitalization on all references in the text. That should be fixed now. We have also added a few figures to the readthedocs for illustrative purposes. There is also a simple example in a jupyter notebook that serves as a tutorial here: https://github.com/iosefa/PyForestScan/blob/main/notebooks/demo.ipynb Thank you!

kthyng commented 2 weeks ago

@iosefa Thank you! The high level checks are complete. We have a backlog of submissions so I will add this to our waitlist. Thanks for your patience.

kthyng commented 2 weeks ago

@mengqi-z Could you edit this submission?

kthyng commented 2 weeks ago

@editorialbot invite @mengqi-z as editor

editorialbot commented 2 weeks ago

Invitation to edit this submission sent!

mengqi-z commented 2 weeks ago

@editorialbot assign me as editor

editorialbot commented 2 weeks ago

Assigned! @mengqi-z is now the editor

mengqi-z commented 2 weeks ago

Hi @iosefa, I will be the handling editor of your submission. While I work on finding reviewers, could you also suggest five potential reviewers? Please list their GitHub names in this thread without tagging them. Thank you!

mengqi-z commented 2 weeks ago

👋 @giswqs @npucino @ebocher - Would any of you be available to review a submission for JOSS? Given your background, I believe you'd be a great fit to review this paper.

JOSS uses a checklist-driven review process, which you can find here: https://joss.readthedocs.io/en/latest/review_criteria.html

If you're unable to review, any recommendations for other potential reviewers with relevant expertise would also be greatly appreciated. Thank you!

npucino commented 2 weeks ago

Absolutely, I will be happy to review it, thanks for the consideration . Nick

Inviato da Outlook per Androidhttps://aka.ms/AAb9ysg

From: Mengqi Zhao @.> Sent: Friday, October 4, 2024 6:55:15 AM To: openjournals/joss-reviews @.> Cc: Nicolas Pucino @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: PyForestScan: A Python Library for Calculating Forest Structural Metrics from LiDAR Point Cloud Data (Issue #7283)

👋 @giswqshttps://github.com/giswqs @npucinohttps://github.com/npucino @ebocherhttps://github.com/ebocher - Would any of you be available to review a submission for JOSS? Given your background, I believe you'd be a great fit to review this paper.

JOSS uses a checklist-driven review process, which you can find here: https://joss.readthedocs.io/en/latest/review_criteria.html

If you're unable to review, any recommendations for other potential reviewers with relevant expertise would also be greatly appreciated. Thank you!

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/7283#issuecomment-2392317780, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKWGSIHBRELCICW7N5MPWI3ZZWVLHAVCNFSM6AAAAABO3HW33CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJSGMYTONZYGA. You are receiving this because you were mentioned.Message ID: @.***>

mengqi-z commented 2 weeks ago

@npucino - Thanks for your quick response and your willingness to review the paper!

mengqi-z commented 2 weeks ago

@editorialbot add @npucino as reviewer

editorialbot commented 2 weeks ago

@npucino added to the reviewers list!

giswqs commented 2 weeks ago

@mengqi-z Yes, I would be happy to review it.

mengqi-z commented 2 weeks ago

@giswqs - Perfect! Thank you for taking on this review!

mengqi-z commented 2 weeks ago

@editorialbot add @giswqs as reviewer

editorialbot commented 2 weeks ago

@giswqs added to the reviewers list!

mengqi-z commented 2 weeks ago

@editorialbot start review

editorialbot commented 2 weeks ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7314.

iosefa commented 2 weeks ago

Hi @iosefa, I will be the handling editor of your submission. While I work on finding reviewers, could you also suggest five potential reviewers? Please list their GitHub names in this thread without tagging them. Thank you!

Hi @mengqi-z Thank you for handling my submission! And sorry for the delay in my response. I have been traveling and am in Samoa at the moment. I am still catching up but it seems like a review thread has already started. Is it still helpful for me to find potential reviewers? Thank you!

mengqi-z commented 2 weeks ago

@iosefa - We've secured two reviewers, so there's no need to provide additional suggestions. Thanks for following up!