[REVIEW]: aPhyloGeo: a multi-platform Python package for analyzing phylogenetic trees with climatic parameters

editorialbot commented 8 months ago

Submitting author: !--author-handle-->@TahiriNadia@arfon<!--end-editor-- Reviewers: @annazhukova, @mmore500, @theosanderson Archive: Pending

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📝 Checklist for @mmore500

📝 Checklist for @theosanderson

editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 2258

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

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

TahiriNadia commented 5 months ago

@editorialbot check repository

editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (570.8 files/s, 191733.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Bourne Again Shell                2            308            722           5096
XML                               6              0              0           4149
Python                            9            491            949           1186
CSV                              12            677              0            811
Perl                              2            290            104            670
Ruby                              1             64             66            375
Markdown                          3            108              0            275
TeX                               1              0              0            210
YAML                             10             15             55            205
TOML                              1              8              0             66
DOS Batch                         2              7              6             28
PowerShell                        1              4            161             11
make                              1              3              0             10
--------------------------------------------------------------------------------
SUM:                             51           1975           2063          13092
--------------------------------------------------------------------------------

Commit count by author:

   209  Nadia Tahiri, PhD
   169  my-linh-luu
    69  Nadia Tahiri
    56  Georges Marceau
    37  slepaget
    36  Hazem Ben Said
    30  cetmus
    25  db036
    25  geomarceau
    18  Elie Maalouf
    14  francis.lewis07@gmail.com
    11  Simon Lepage-Trudeau
     9  simlal
     8  Alex
     4  Wanlin Li
     2  Marc-Antoine Bélisle
     2  Mus
     2  Nadia Tahiri, Ph. D
     2  TahiriNadia
     2  jsDesm
     1  KarlP910
     1  Matthew Andres Moreno

editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 1909

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

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

TahiriNadia commented 5 months ago

@editorialbot check repository

editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (561.5 files/s, 188488.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Bourne Again Shell                2            308            722           5096
XML                               6              0              0           4149
Python                            9            491            949           1186
CSV                              12            677              0            811
Perl                              2            290            104            670
Ruby                              1             64             66            375
Markdown                          3            104              0            269
TeX                               1              0              0            210
YAML                             10             15             55            205
TOML                              1              8              0             66
DOS Batch                         2              7              6             28
PowerShell                        1              4            161             11
make                              1              3              0             10
--------------------------------------------------------------------------------
SUM:                             51           1971           2063          13086
--------------------------------------------------------------------------------

Commit count by author:

   209  Nadia Tahiri, PhD
   169  my-linh-luu
    72  Nadia Tahiri
    56  Georges Marceau
    37  slepaget
    36  Hazem Ben Said
    30  cetmus
    25  db036
    25  geomarceau
    18  Elie Maalouf
    14  francis.lewis07@gmail.com
    11  Simon Lepage-Trudeau
     9  simlal
     8  Alex
     4  Wanlin Li
     2  Marc-Antoine Bélisle
     2  Mus
     2  Nadia Tahiri, Ph. D
     2  TahiriNadia
     2  jsDesm
     1  KarlP910
     1  Matthew Andres Moreno

editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 1301

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

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

TahiriNadia commented 5 months ago

@editorialbot check repository

editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (565.3 files/s, 189815.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Bourne Again Shell                2            308            722           5096
XML                               6              0              0           4149
Python                            9            491            949           1186
CSV                              12            677              0            811
Perl                              2            290            104            670
Ruby                              1             64             66            375
Markdown                          3            107              0            270
TeX                               1              0              0            210
YAML                             10             15             55            205
TOML                              1              8              0             66
DOS Batch                         2              7              6             28
PowerShell                        1              4            161             11
make                              1              3              0             10
--------------------------------------------------------------------------------
SUM:                             51           1974           2063          13087
--------------------------------------------------------------------------------

Commit count by author:

   209  Nadia Tahiri, PhD
   169  my-linh-luu
    73  Nadia Tahiri
    56  Georges Marceau
    37  slepaget
    36  Hazem Ben Said
    30  cetmus
    25  db036
    25  geomarceau
    18  Elie Maalouf
    14  francis.lewis07@gmail.com
    11  Simon Lepage-Trudeau
     9  simlal
     8  Alex
     4  Wanlin Li
     2  Marc-Antoine Bélisle
     2  Mus
     2  Nadia Tahiri, Ph. D
     2  TahiriNadia
     2  jsDesm
     1  KarlP910
     1  Matthew Andres Moreno

editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 1095

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

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

TahiriNadia commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

TahiriNadia commented 5 months ago

@editorialbot check repository

editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (570.3 files/s, 191447.7 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Bourne Again Shell                2            308            722           5096
XML                               6              0              0           4149
Python                            9            491            949           1186
CSV                              12            677              0            811
Perl                              2            290            104            670
Ruby                              1             64             66            375
Markdown                          3            105              0            268
TeX                               1              0              0            210
YAML                             10             15             55            205
TOML                              1              8              0             66
DOS Batch                         2              7              6             28
PowerShell                        1              4            161             11
make                              1              3              0             10
--------------------------------------------------------------------------------
SUM:                             51           1972           2063          13085
--------------------------------------------------------------------------------

Commit count by author:

   209  Nadia Tahiri, PhD
   169  my-linh-luu
    75  Nadia Tahiri
    56  Georges Marceau
    37  slepaget
    36  Hazem Ben Said
    30  cetmus
    25  db036
    25  geomarceau
    18  Elie Maalouf
    14  francis.lewis07@gmail.com
    11  Simon Lepage-Trudeau
     9  simlal
     8  Alex
     4  Wanlin Li
     2  Marc-Antoine Bélisle
     2  Mus
     2  Nadia Tahiri, Ph. D
     2  TahiriNadia
     2  jsDesm
     1  KarlP910
     1  Matthew Andres Moreno

editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 1012

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

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

TahiriNadia commented 5 months ago

@editorialbot check repository

editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (567.7 files/s, 190538.9 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Bourne Again Shell                2            308            722           5096
XML                               6              0              0           4149
Python                            9            491            949           1186
CSV                              12            677              0            811
Perl                              2            290            104            670
Ruby                              1             64             66            375
Markdown                          3            105              0            266
TeX                               1              0              0            210
YAML                             10             15             55            205
TOML                              1              8              0             66
DOS Batch                         2              7              6             28
PowerShell                        1              4            161             11
make                              1              3              0             10
--------------------------------------------------------------------------------
SUM:                             51           1972           2063          13083
--------------------------------------------------------------------------------

Commit count by author:

   209  Nadia Tahiri, PhD
   169  my-linh-luu
    77  Nadia Tahiri
    56  Georges Marceau
    37  slepaget
    36  Hazem Ben Said
    30  cetmus
    25  db036
    25  geomarceau
    18  Elie Maalouf
    14  francis.lewis07@gmail.com
    11  Simon Lepage-Trudeau
     9  simlal
     8  Alex
     4  Wanlin Li
     2  Marc-Antoine Bélisle
     2  Mus
     2  Nadia Tahiri, Ph. D
     2  TahiriNadia
     2  jsDesm
     1  KarlP910
     1  Matthew Andres Moreno

editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 988

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

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

TahiriNadia commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

annazhukova commented 5 months ago

I would like to thank the authors for the updates. I have ticked several new checkpoints. There are however still things missing in my opinion.

In particular:

[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

There is a tutotrial now (thank you!) which is very easy to reproduce, however what is missing are explanations on what exactly it does and why and how to interpret the results (see this issue, which you closed). The same holds for the article itself: there is nowhere an explanation nor example on how to use real world data with aPhyloGeo and what would be the results of the analysis and how to interpret them.

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?

See above

[ ] 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?

Formally there is a "statement of need" section however its content "Climat change and human activities are rapidly impacting biodiversity and population dynamics. To understand these complexities, biologists use phylogeography, which examines the interplay between genetics, geography, and past/present climate." does not explain at all how aPhyloGeo comes into play here, and what it brings. Nor what are the alternatives (other work).

[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?

I could not see any other phylogeographic/climatic package being mentioned. The only other software descriptions are descriptions of tools being used as part of aPhyloGeo pipeline.

(I am actually worndering if the paper I am looking at is the good one and whether there is something else with more explanations and information?)

hazem-dev commented 5 months ago

Thank you, @annazhukova, for your thorough review of our paper and for providing such detailed and constructive feedback. We greatly appreciate the time and effort you dedicated to this process. Your comments have been invaluable in guiding us to substantially revise and enhance our manuscript.

In response to your feedback, we have implemented several changes to address the issues you raised. Specifically, we have:

Example Usage: Expanded the tutorial with step-by-step explanations and interpretation guidelines to ensure clarity and understanding for all users.
Software Paper Summary: Refined the description to better convey the high-level functionality and purpose of the software to a wider audience, including potential applications in various analysis scenarios.
Statement of Need: Thoroughly detailed how aPhyloGeo directly addresses the challenges posed by climate change and human activities on biodiversity and population dynamics. Additionally, we have clarified the unique contributions of aPhyloGeo compared to existing tools.
State of the Field: Provided a comprehensive comparison of aPhyloGeo with other widely used phylogeographic and climatic packages, highlighting its unique strengths and advantages.

We apologize for any misunderstanding regarding the initial closure of the comment. Our intention was not to dismiss your valuable feedback. We closed the issue prematurely after implementing initial solutions, believing the matter was resolved. However, we have since reopened the issue and diligently worked to address all of your concerns in this revised version of the manuscript.

We sincerely hope that these revisions meet your expectations and would be grateful for your continued feedback. We value your expertise and believe your input is essential for improving the quality and impact of our work.

Thank you, @annazhukova and @fboehm, again for your time and consideration.

hazem-dev commented 5 months ago

We are pleased to inform you that we have thoroughly addressed your valuable feedback and implemented the suggested revisions in our manuscript. The revised version is now available on our GitHub repository.

In addition to addressing your issue, we have made significant efforts to streamline the manuscript, reducing its length by more than half and ensuring it now adheres to the JOSS word count limit. We believe these revisions have significantly strengthened the paper and enhanced its clarity.

Thank you, @mmore500 and @fboehm, again for your time and consideration.

TahiriNadia commented 5 months ago

@editorialbot check repository

editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (571.7 files/s, 192325.1 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Bourne Again Shell                2            308            722           5096
XML                               6              0              0           4149
Python                            9            491            949           1191
CSV                              12            677              0            811
Perl                              2            290            104            670
Ruby                              1             64             66            375
Markdown                          3            106              0            271
TeX                               1              0              0            237
YAML                             10             15             55            205
TOML                              1              8              0             66
DOS Batch                         2              7              6             28
PowerShell                        1              4            161             11
make                              1              3              0             10
--------------------------------------------------------------------------------
SUM:                             51           1973           2063          13120
--------------------------------------------------------------------------------

Commit count by author:

   209  Nadia Tahiri, PhD
   169  my-linh-luu
    78  Nadia Tahiri
    56  Georges Marceau
    45  Hazem Ben Said
    37  slepaget
    30  cetmus
    25  db036
    25  geomarceau
    18  Elie Maalouf
    14  francis.lewis07@gmail.com
    11  Simon Lepage-Trudeau
     9  simlal
     8  Alex
     4  Wanlin Li
     2  Marc-Antoine Bélisle
     2  Mus
     2  Nadia Tahiri, Ph. D
     2  TahiriNadia
     2  jsDesm
     1  KarlP910
     1  Matthew Andres Moreno

editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 1173

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

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

TahiriNadia commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

TahiriNadia commented 5 months ago

We are pleased to confirm that all issues raised during the review process have been fully addressed. Thank you to the editor (@fboehm) and the reviewers (@annazhukova and @mmore500).

fboehm commented 5 months ago

@mmore500 & @annazhukova - how are the reviews going? have you had a chance to review the changes implemented by the authors?

Please feel free to check off boxes on the checklists if the criteria are now met.

Thanks again!

mmore500 commented 5 months ago

Thank you for the update! I look forward to continuing on with the next steps of the review. I have been traveling the last few days but plan to follow up on this shortly.

TahiriNadia commented 5 months ago

Thank you for the update! I look forward to continuing on with the next steps of the review. I have been traveling the last few days but plan to follow up on this shortly.

Thank you, @mmore500.

TahiriNadia commented 5 months ago

@mmore500 & @annazhukova - how are the reviews going? have you had a chance to review the changes implemented by the authors?

Please feel free to check off boxes on the checklists if the criteria are now met.

Thanks again!

Thank you, @fboehm

annazhukova commented 5 months ago

Thank you for the changes. However, I still do not understand from the article what exactly aPhylogeo does and why cannot this be achieved with other methods (e.g. with the generalized liner model in BEAST, which is not mentioned in the article).

@fboehm and the authors, I am sorry, but I will not have any time to review this further in the near future, so it would be the best if you find another reviewer.

TahiriNadia commented 5 months ago

Thank you for the changes. However, I still do not understand from the article what exactly aPhylogeo does and why cannot this be achieved with other methods (e.g. with the generalized liner model in BEAST, which is not mentioned in the article).

@fboehm and the authors, I am sorry, but I will not have any time to review this further in the near future, so it would be the best if you find another reviewer.

Thank you, @annazhukova, for this note. However, the primary objectives of BEAST and aPhyloGeo are fundamentally different. BEAST is a cross-platform software designed for Bayesian analysis of molecular sequences using Markov Chain Monte Carlo (MCMC) methods, focusing exclusively on sequence data. In contrast, aPhyloGeo aims to elucidate the relationship between genetic evolution and environmental factors of species' habitats (e.g., temperature, humidity, soil composition, sunlight, precipitation, and others). The goal is to identify genetic signatures that explain species adaptation and biodiversity. Thanks for this note; we have added it to the article.

TahiriNadia commented 5 months ago

@fboehm - We are pleased to confirm that all issues have been addressed.

TahiriNadia commented 5 months ago

Dear @fboehm,

As it has been nearly three months (i.e. April, 3rd) since we submitted our article, I'm wondering if it is possible to resume work on the package without interfering with the review process. We paused development on the package during the last three months to avoid disrupting the reviewers. Thank you!

Best.

fboehm commented 5 months ago

@TahiriNadia @annazhukova we will need to find another reviewer before we proceed. I'll begin searching for one right away.

mmore500 commented 5 months ago

Hi, I have just returned from my travel to Britain and will update my review within 24 hours.

fboehm commented 5 months ago

Dear @fboehm,

As it has been nearly three months (i.e. April, 3rd) since we submitted our article, I'm wondering if it is possible to resume work on the package without interfering with the review process. We paused development on the package during the last three months to avoid disrupting the reviewers. Thank you!

Best.

@TahiriNadia - would it be possible for your development to proceed on a new git branch? That way, we could continue to point reviewers to the "main" branch; any issues that reviewers raise could be addressed with git pushes to the main branch. your other development activities could continue on another branch and would not be considered in this joss submission. Is that reasonable?

Following joss publication, you could, of course, merge the new development branch into main, so that users could get the latest updates.

fboehm commented 5 months ago

Hi, I have just returned from my travel to Britain and will update my review within 24 hours.

Thank you, @mmore500 !

fboehm commented 5 months ago

Thank you for the changes. However, I still do not understand from the article what exactly aPhylogeo does and why cannot this be achieved with other methods (e.g. with the generalized liner model in BEAST, which is not mentioned in the article).

@fboehm and the authors, I am sorry, but I will not have any time to review this further in the near future, so it would be the best if you find another reviewer.

Thank you for the work in reviewing this submission, @annazhukova - i hope that we can work together on a future submission.

fboehm commented 5 months ago

@jdalapicolla @AgustinPardo @fredericlemoine - we need another reviewer. Would you be willing to review this submission for JOSS? If you can help, we would try to complete reviews before August 3, 2024.

openjournals / joss-reviews