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[PRE REVIEW]: CNATool - Complex Network Analysis Tool #5103

Closed editorialbot closed 1 year ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@souzamonteiro<!--end-author-handle-- (Roberto L. S. Monteiro) Repository: https://github.com/souzamonteiro/cnatool Branch with paper.md (empty if default branch): Version: 2.0.4 Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @tomalrussell, @ati-ozgur Managing EiC: Arfon Smith

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Markdown: [![status](https://joss.theoj.org/papers/ce81e70bf08a274d0a1b4f8754818744/status.svg)](https://joss.theoj.org/papers/ce81e70bf08a274d0a1b4f8754818744)

Author instructions

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

@souzamonteiro if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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:

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editorialbot commented 1 year 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:

@editorialbot generate pdf
editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

editorialbot commented 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=90.91 s (34.7 files/s, 5834.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                    2706          47233          64958         288004
JSON                           138              0              0          45665
XML                              3              0              0          28999
Markdown                       155           6406              0          14902
SVG                              7              0              1          11076
HTML                            44           5840             82           9104
TypeScript                      85            458           3259           2717
CSS                              7            194            113            876
TeX                              1             39              0            381
YAML                             6              3              4             38
Nix                              1              1              0             19
ERB                              1              1              0             18
Bourne Shell                     2              8              0             17
make                             1              3              0              4
-------------------------------------------------------------------------------
SUM:                          3157          60186          68417         401820
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 3105

editorialbot commented 1 year ago

Failed to discover a Statement of need section in paper

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1016/j.jnca.2007.11.003 may be a valid DOI for title: Visualizing the evolution of a web-based social network
- 10.7155/jgaa.00108 may be a valid DOI for title: Approximating clustering coefficient and transitivity
- 10.1007/978-3-540-77891-2_6 may be a valid DOI for title: A fast algorithm to calculate powers of a Boolean matrix for diameter computation of random graphs
- 10.1016/0378-8733(78)90021-7 may be a valid DOI for title: Centrality in social networks conceptual clarification
- 10.1016/0378-8733(79)90002-9 may be a valid DOI for title: Centrality in social networks: II. Experimental results
- 10.1007/978-3-642-21934-4_44 may be a valid DOI for title: Performance Analysis of an Algorithm for Computation of Betweenness Centrality
- 10.2307/3033543 may be a valid DOI for title: A set of measures of centrality based on betweenness
- 10.1515/9781400841356.301 may be a valid DOI for title: Collective dynamics of small-world networks
- 10.1016/j.neucom.2005.12.070 may be a valid DOI for title: Influence of the neural network topology on the learning dynamics
- 10.1016/s0378-4371(02)00736-7 may be a valid DOI for title: Evolution of the social network of scientific collaborations
- 10.1016/s0378-4371(02)01545-5 may be a valid DOI for title: Efficiency of scale-free networks: error and attack tolerance

INVALID DOIs

- https://doi.org/10.21577/1984-6835.20160088 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1080/17445760.2012.668546 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.physa.2014.02.019 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.physa.2019.121542 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.ress.2019.02.013 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/hbm.25362 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jneuroling.2021.101025 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.2224/sbp.7681 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.physa.2020.125012 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.physa.2021.125848 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.socnet.2021.06.001 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/nrn2575 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1007/s00429-014-0836-3 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1098/rstb.2000.0551 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.2307/29737693 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.physa.2015.08.024 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/S0079-6123(07)68012-1 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1145/321992.321993 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1103/PhysRevLett.87.198701 is INVALID because of 'https://doi.org/' prefix
arfon commented 1 year ago

@souzamonteiro – it looks like this ORCID is invalid, could you please check it? 0000-0001-7576-9267

Also, we're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

souzamonteiro commented 1 year ago

Many thanks for the comments. I already corrected the author's ORCID.

arfon commented 1 year ago

:wave: @csoneson – would you be willing to edit this submission for JOSS?

arfon commented 1 year ago

@editorialbot invite @csoneson as editor

editorialbot commented 1 year ago

Invitation to edit this submission sent!

csoneson commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

csoneson commented 1 year ago

@editorialbot assign @csoneson as editor

editorialbot commented 1 year ago

Assigned! @csoneson is now the editor

csoneson commented 1 year ago

👋🏻 @souzamonteiro - I will handle your submission and start by recruiting at least two suitable reviewers. If you have suggestions, please feel free to mention them here!

In the meanwhile, a couple of comments that you can already address:

csoneson commented 1 year ago

👋🏻 @souzamonteiro - just wanted to check in here - did you have a chance to look into shortening the paper to adhere closer to the JOSS guidelines?

In the meanwhile, a couple of comments that you can already address: Your paper is quite a bit longer than the JOSS guidelines (see here). A typical JOSS paper is 250-1000 words (yours is currently 3105), and it should contain a 'Statement of need' section. Could you please adapt your paper to be more in line with the JOSS guidelines? Also please take a look at the invalid DOIs flagged by @editorialbot above - mostly the issue seems to be that the DOIs include the 'https://doi.org/' prefix.

souzamonteiro commented 1 year ago

👋🏻 @souzamonteiro - just wanted to check in here - did you have a chance to look into shortening the paper to adhere closer to the JOSS guidelines?

In the meanwhile, a couple of comments that you can already address: Your paper is quite a bit longer than the JOSS guidelines (see here). A typical JOSS paper is 250-1000 words (yours is currently 3105), and it should contain a 'Statement of need' section. Could you please adapt your paper to be more in line with the JOSS guidelines? Also please take a look at the invalid DOIs flagged by @editorialbot above - mostly the issue seems to be that the DOIs include the 'https://doi.org/' prefix.

Yes, I did what was asked: removed the 'https://doi.org/' prefixes and reduced the article length.

csoneson commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

csoneson commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21577/1984-6835.20160088 is OK
- 10.1080/17445760.2012.668546 is OK
- 10.1016/j.physa.2014.02.019 is OK
- 10.1016/j.physa.2019.121542 is OK
- 10.1016/j.ress.2019.02.013 is OK
- 10.1002/hbm.25362 is OK
- 10.1016/j.jneuroling.2021.101025 is OK
- 10.2224/sbp.7681 is OK
- 10.1016/j.physa.2020.125012 is OK
- 10.1016/j.physa.2021.125848 is OK
- 10.1016/j.socnet.2021.06.001 is OK
- 10.1038/nrn2575 is OK
- 10.1007/s00429-014-0836-3 is OK
- 10.1098/rstb.2000.0551 is OK
- 10.1016/j.physa.2015.08.024 is OK
- 10.1016/S0079-6123(07)68012-1 is OK
- 10.1145/321992.321993 is OK
- 10.1103/PhysRevLett.87.198701 is OK

MISSING DOIs

- 10.1016/j.jnca.2007.11.003 may be a valid DOI for title: Visualizing the evolution of a web-based social network
- 10.7155/jgaa.00108 may be a valid DOI for title: Approximating clustering coefficient and transitivity
- 10.1007/978-3-540-77891-2_6 may be a valid DOI for title: A fast algorithm to calculate powers of a Boolean matrix for diameter computation of random graphs
- 10.1016/0378-8733(78)90021-7 may be a valid DOI for title: Centrality in social networks conceptual clarification
- 10.1016/0378-8733(79)90002-9 may be a valid DOI for title: Centrality in social networks: II. Experimental results
- 10.1007/978-3-642-21934-4_44 may be a valid DOI for title: Performance Analysis of an Algorithm for Computation of Betweenness Centrality
- 10.2307/3033543 may be a valid DOI for title: A set of measures of centrality based on betweenness
- 10.1515/9781400841356.301 may be a valid DOI for title: Collective dynamics of small-world networks
- 10.1016/j.neucom.2005.12.070 may be a valid DOI for title: Influence of the neural network topology on the learning dynamics
- 10.1016/s0378-4371(02)00736-7 may be a valid DOI for title: Evolution of the social network of scientific collaborations
- 10.1016/s0378-4371(02)01545-5 may be a valid DOI for title: Efficiency of scale-free networks: error and attack tolerance

INVALID DOIs

- 10.2307/29737693 is INVALID
csoneson commented 1 year ago

@souzamonteiro - thanks! Please note that JOSS papers are also required to have a Statement of need section. (also it looks like some DOIs are still missing or invalid).

csoneson commented 1 year ago

👋🏻 @adavidzh, @tomalrussell - would you be interested in reviewing this submission for JOSS?

CNATool - Complex Network Analysis Tool

adavidzh commented 1 year ago

👋🏻 @adavidzh, @tomalrussell - would you be interested in reviewing this submission for JOSS?

CNATool - Complex Network Analysis Tool

Thank you @csoneson. I am afraid that I am not able to commit to review this contribution at this time.

csoneson commented 1 year ago

@adavidzh - no problem, thanks for letting me know!

csoneson commented 1 year ago

@paulgovan - would you be interested in reviewing this submission for JOSS?

CNATool - Complex Network Analysis Tool

souzamonteiro commented 1 year ago

Hi, I made the requested changes.

tomalrussell commented 1 year ago

Hi @csoneson - yes, I'd be happy to review.

paulgovan commented 1 year ago

Hi @csoneson, I’m familiar with network analysis but not Maiascript, so I’m probably not the best reviewer for this.

csoneson commented 1 year ago

Thank you @tomalrussell! Once we have secured a second reviewer I'll assign you and open the review issue.

csoneson commented 1 year ago

@paulgovan - no problem, thanks for the quick response!

csoneson commented 1 year ago

@camillescott - would you be interested in reviewing this submission for JOSS?

CNATool - Complex Network Analysis Tool

souzamonteiro commented 1 year ago

@souzamonteiro - thanks! Please note that JOSS papers are also required to have a Statement of need section. (also it looks like some DOIs are still missing or invalid).

Thanks for the feedback. I already did what was asked.

csoneson commented 1 year ago

👋🏻 @ati-ozgur - would you be interested in reviewing this submission for JOSS?

CNATool - Complex Network Analysis Tool

csoneson commented 1 year ago

@ati-ozgur - sorry, I missed your thumbs-up reaction on the review invite above 🙂 Could you just confirm that I interpret that correctly that you would be happy to review this submission - then I'll assign you and open the review issue. Thanks!

ati-ozgur commented 1 year ago

Yes. I would like to review.

csoneson commented 1 year ago

Brilliant, thanks @ati-ozgur! I'll assign you and open the review issue.

csoneson commented 1 year ago

@editorialbot add @tomalrussell as reviewer

editorialbot commented 1 year ago

@tomalrussell added to the reviewers list!

csoneson commented 1 year ago

@editorialbot add @ati-ozgur as reviewer

editorialbot commented 1 year ago

@ati-ozgur added to the reviewers list!

csoneson commented 1 year ago

@editorialbot start review

editorialbot commented 1 year ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5373.