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

[editorialbot]

Submitting author: @iosefa (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: @mengqi-z
Reviewers: @npucino, @giswqs
Managing EiC: Kristen Thyng

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/61114708d8831867a7c7d7e1ef25947d"><img src="https://joss.theoj.org/papers/61114708d8831867a7c7d7e1ef25947d/status.svg"></a>
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

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[editorialbot]

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[editorialbot]

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]

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]

Paper file info:

📄 Wordcount for paper.md is 851

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

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⚠️ 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]

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:

• OSI-approved license
• Installation instructions
• Documentation exists at all
• Tests of some sort
• Check paper (make sure compiles, read through, check for length 250-1000 words)
• Substantial scholarly effort
• Clear research application

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]

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:

• OSI-approved license
• Installation instructions
• Documentation exists at all
• Tests of some sort
• Check paper (make sure compiles, read through, check for length 250-1000 words)
• Substantial scholarly effort
• Clear research application

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

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

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]

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]

@iosefa

• I'm not in your field, but it seems like some plots to help users understand your docs would be great — any possibility of that? These can also act as a tutorial.
• your parenthetical references shouldn't have extra parentheses between them — check out the sample paper for exact syntax so they end up in a list together.
• your inline references shouldn't have parentheses
• Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file. For example, "r" is not capitalized.

[iosefa]

@kthyng
Thank you very much for your feedback.

• Yes, I can and will add figures to the docs.
• will fix
• will fix
• will check and fix

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

[iosefa]

@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]

@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]

@mengqi-z Could you edit this submission?

[kthyng]

@editorialbot invite @mengqi-z as editor

[editorialbot]

Invitation to edit this submission sent!

[mengqi-z]

@editorialbot assign me as editor

[editorialbot]

Assigned! @mengqi-z is now the editor

[mengqi-z]

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]

👋 @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]

Absolutely, I will be happy to review it, thanks for the consideration . Nick Inviato da Outlook per Android<https://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) 👋 @giswqs<https://github.com/giswqs> @npucino<https://github.com/npucino> @ebocher<https://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 GitHub<#7283 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKWGSIHBRELCICW7N5MPWI3ZZWVLHAVCNFSM6AAAAABO3HW33CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJSGMYTONZYGA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[mengqi-z]

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

[mengqi-z]

@editorialbot add @npucino as reviewer

[editorialbot]

@npucino added to the reviewers list!

[giswqs]

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

[mengqi-z]

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

[mengqi-z]

@editorialbot add @giswqs as reviewer

[editorialbot]

@giswqs added to the reviewers list!

[mengqi-z]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7314.

[iosefa]

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]

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