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[REVIEW]: netrankr: An R package for total, partial, and probabilistic rankings in networks
Submitting author: @schochastics (David Schoch) Repository: https://github.com/schochastics/netrankr Branch with paper.md (empty if default branch): Version: v1.1.1 Editor: @jbytecode Reviewers: @akbaritabar, @briatte Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/783172689e7dbfa52a7d6db4a86de756"><img src="https://joss.theoj.org/papers/783172689e7dbfa52a7d6db4a86de756/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/783172689e7dbfa52a7d6db4a86de756)
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
@akbaritabar & @briatte, 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 @jbytecode 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
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
Software report:
github.com/AlDanial/cloc v 1.88 T=0.06 s (1189.8 files/s, 113843.3 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
R 36 204 1068 1834
C++ 18 121 85 1018
Rmd 10 345 1033 425
Markdown 4 91 0 368
TeX 1 13 0 145
YAML 3 13 6 120
-------------------------------------------------------------------------------
SUM: 72 787 2192 3910
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 684
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.18637/jss.v024.i06 is OK
- 10.1371/journal.pone.0143111 is OK
- 10.1093/bioinformatics/bty819 is OK
- 10.1017/S0956792516000401 is OK
- 10.1016/j.socnet.2017.03.010 is OK
- 10.1016/j.socnet.2017.12.003 is OK
- 10.1177/2059799116630650 is OK
- 10.1023/b:eest.0000027209.93218.d9 is OK
- 10.1038/35075138 is OK
- 10.1371/journal.pone.0017249 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Dear reviewers @akbaritabar and @briatte
This is the review thread. Please type
@editorialbot generate my checklist
to generate your task list. In this list, there are 20 review items. Whenever you complete a task, you can check off the corresponding check box.
You can always interact with the author(s), other reviewers, and the editor during the reviewing process. You can also open issues in the target repo and send pull request. Please mention the review page in those issues, so we can keep tracking outside of our world.
Thank you in advance.
Letter to authors (as comment on review issue of JOSS)
Thanks a lot for the opportunity to review this work and package. The package is nicely documented and many use cases and multiple vignettes and blog posts (http://blog.schochastics.net/post/network-centrality-in-r-introduction/ , http://blog.schochastics.net/post/network-centrality-in-r-neighborhood-inclusion/ , http://blog.schochastics.net/post/network-centrality-in-r-new-ways-of-measuring-centrality/) are provided to users and showcase examples, discuss concepts and why they are implemented and also provide references to literature from author or others.
I must add that my reading of these material and use of the package is mainly "an empirical social scientist's point of view" who uses the proposed techniques but could not contribute to their technical development. Hence, I cannot evaluate the technical aspects of the package and its performance very well and leave that to editor and other reviewers.
The JOSS paper could benefit from including a little bit more detail and examples which are already provided in the package's website and would complement the short paper. It will help the paper be more independent.
Please see below under checklist points only minor suggestions for edits and revisions.
Review checklist for @akbaritabar
Conflict of interest
- [x] 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
- [x] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- [x] Repository: Is the source code for this software available at the https://github.com/schochastics/netrankr?
- [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- On the package website (http://netrankr.schochastics.net/) MIT license is mentioned and a file is provided stating year and copyright holder's name (as suggested by: https://r-pkgs.org/license.html#key-files) but in the repository on GitHub, only that file is shown instead of MIT license that GitHub usually shows and clicking shows permissions (example of what I intended: https://github.com/openjournals/joss-reviews/blob/master/LICENSE)
- [x] Contribution and authorship: Has the submitting author (@schochastics) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Functionality
- [x] Installation: Does installation proceed as outlined in the documentation?
- [x] Functionality: Have the functional claims of the software been confirmed?
- [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
- [x] Guidelines and rules of thumb are provided on the performance and how it drops for larger networks which is very valuable (http://netrankr.schochastics.net/articles/benchmarks.html)
Documentation
- [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- [x] In the package website, there are multiple vignettes and tutorials using different examples.
- [x] It would be great if one of those examples could be included in the paper to make it "stand alone" for those who would read the paper first without trying out the package and vignettes. (a good candidate could be: http://netrankr.schochastics.net/#simple-example)
- [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- [x] 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 [x] There are three issues already created in the repository, and the website (http://netrankr.schochastics.net/index.html) has a button "report a bug" but I couldn't see something on contribution.
Software paper
- [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- [x] Summary presents a very nice definition of "centrality" in networks using examples from different fields.
- [x] But, a simple and accessible definition of "partial" and "probabilistic ranking" could be added (vignettes already have materials that could be used in the paper to to make it "stand alone" for those who would read the paper first without trying out the package and vignettes). I would suggest using materials already present in package's website (i.e., http://netrankr.schochastics.net/#overview ) or for instance, some of the one-liner questions used in the statement of need would be helpful, e.g., "how likely is a node more central than another one?"
- [x] 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?
- [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- Minor point: I would suggest removing citations in the abstract, if possible.
- Minor point: "small packages" --> "small package"
- [x] 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?
A suggestion for JOSS
- Perhaps it would be nice to use the editorial bot currently used by JOSS and set a reminder for when the review is due, after a reviewer accepts the invitation.
@editorialbot remind @briatte in 3 days
Reminder set for @briatte in 3 days
:wave: @briatte, please update us on how your review is going (this is an automated reminder).
Dear editors @akbaritabar and @briatte
Could you please update your status?
@briatte - your checklist is still waiting to be generated.
Sorry for bothering by alerts and emails.
Thank you in advance.
Review checklist for @briatte
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
- [ ] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- [ ] Repository: Is the source code for this software available at the https://github.com/schochastics/netrankr?
- [ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- [ ] Contribution and authorship: Has the submitting author (@schochastics) 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
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?
Letter to authors (as comment on review issue of JOSS)
Thanks a lot for the opportunity to review this work and package. The package is nicely documented and many use cases and multiple vignettes and blog posts (http://blog.schochastics.net/post/network-centrality-in-r-introduction/ , http://blog.schochastics.net/post/network-centrality-in-r-neighborhood-inclusion/ , http://blog.schochastics.net/post/network-centrality-in-r-new-ways-of-measuring-centrality/) are provided to users and showcase examples, discuss concepts and why they are implemented and also provide references to literature from author or others.
I must add that my reading of these material and use of the package is mainly "an empirical social scientist's point of view" who uses the proposed techniques but could not contribute to their technical development. Hence, I cannot evaluate the technical aspects of the package and its performance very well and leave that to editor and other reviewers.
The JOSS paper could benefit from including a little bit more detail and examples which are already provided in the package's website and would complement the short paper. It will help the paper be more independent.
Please see below under checklist points only minor suggestions for edits and revisions.
Review checklist for @akbaritabar
Conflict of interest
- [x] 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
- [x] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
[x] Repository: Is the source code for this software available at the https://github.com/schochastics/netrankr?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- On the package website (http://netrankr.schochastics.net/) MIT license is mentioned and a file is provided stating year and copyright holder's name (as suggested by: https://r-pkgs.org/license.html#key-files) but in the repository on GitHub, only that file is shown instead of MIT license that GitHub usually shows and clicking shows permissions (example of what I intended: https://github.com/openjournals/joss-reviews/blob/master/LICENSE)
[x] Contribution and authorship: Has the submitting author (@schochastics) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Functionality
[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
- [x] Guidelines and rules of thumb are provided on the performance and how it drops for larger networks which is very valuable (http://netrankr.schochastics.net/articles/benchmarks.html)
Documentation
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- [x] In the package website, there are multiple vignettes and tutorials using different examples.
- [x] It would be great if one of those examples could be included in the paper to make it "stand alone" for those who would read the paper first without trying out the package and vignettes. (a good candidate could be: http://netrankr.schochastics.net/#simple-example)
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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 [x] There are three issues already created in the repository, and the website (http://netrankr.schochastics.net/index.html) has a button "report a bug" but I couldn't see something on contribution.
Software paper
[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- [x] Summary presents a very nice definition of "centrality" in networks using examples from different fields.
- [x] But, a simple and accessible definition of "partial" and "probabilistic ranking" could be added (vignettes already have materials that could be used in the paper to to make it "stand alone" for those who would read the paper first without trying out the package and vignettes). I would suggest using materials already present in package's website (i.e., http://netrankr.schochastics.net/#overview ) or for instance, some of the one-liner questions used in the statement of need would be helpful, e.g., "how likely is a node more central than another one?"
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- Minor point: I would suggest removing citations in the abstract, if possible.
- Minor point: "small packages" --> "small package"
[x] 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?
A suggestion for JOSS
- Perhaps it would be nice to use the editorial bot currently used by JOSS and set a reminder for when the review is due, after a reviewer accepts the invitation.
@schochastics - Here are some review notes from one of our reviewers.
@akbaritabar - Since you are editing the old message, we are not be aware of what is new in the thread, could you please provide your next comments as new posts?
thank you in advance.
@akbaritabar Thanks for your comments. Below I address all the open points.
General checks
License I added an MIT license file to github. This is now also displayed in the right panel.
Documentation
example usage I added and revised the example from the README
Community guidelines I added code of conduct for contributors which outlines the guidelines of contribution
Software Paper
Summary I tried to add some more explanations in the example for the terms "partial" and "probabilistic ranking". Happy to include even more but I am wary of the word limit
Quality of writing
Minor point: I would suggest removing citations in the abstract, if possible.
I left the citations because I think the summary is different to an abstract. I also checked some published papers which also had citation. If there is something in the guidelines I missed regarding this, then I will remove the references
Minor point: "small packages" -> "small package"
[fixed]
@editorialbot generate pdf
@editorialbot generate pdf
@schochastics - our bot recognizes commands if the command is located in the first line of the post.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Letter to authors (as comment on review issue of JOSS)
Dear @schochastics, thanks a lot for the updates and revisions in the paper and repository.
I marked all points as finished below.
As a minor suggestion, if I may, please include in the readme of repository, a "Cite As" with APA style and Bibtex style of your JOSSS paper, so that those using the repository can cite the paper and package properly (similar to output of "citation()" function in R copied below but for your JOSS paper). The reason behind this suggestion is that unfortunately, it is usual practice that those using a software do not acknowledge its use in scientific publications by citing them (hence initiatives such as: https://f1000research.com/articles/9-1257 to inspire a change) so I hope JOSS paper will be cited for uses.
r$> citation(package = 'netrankr')
To cite netrankr in publications use:
David Schoch (2017). netrankr: An R package to analyze partial rankings in networks
A BibTeX entry for LaTeX users is
@Manual{,
title = {netrankr: An R package to analyze partial rankings in networks},
author = {David Schoch},
year = {2017},
}
Dear Editor @jbytecode, I recommend acceptance (sorry, was not sure if I should use the @editorialbot recommend-accept
command as a reviewer or not)
Letter to authors (as comment on review issue of JOSS)
Thanks a lot for the opportunity to review this work and package. The package is nicely documented and many use cases and multiple vignettes and blog posts (http://blog.schochastics.net/post/network-centrality-in-r-introduction/ , http://blog.schochastics.net/post/network-centrality-in-r-neighborhood-inclusion/ , http://blog.schochastics.net/post/network-centrality-in-r-new-ways-of-measuring-centrality/) are provided to users and showcase examples, discuss concepts and why they are implemented and also provide references to literature from author or others.
I must add that my reading of these material and use of the package is mainly "an empirical social scientist's point of view" who uses the proposed techniques but could not contribute to their technical development. Hence, I cannot evaluate the technical aspects of the package and its performance very well and leave that to editor and other reviewers.
The JOSS paper could benefit from including a little bit more detail and examples which are already provided in the package's website and would complement the short paper. It will help the paper be more independent.
Please see below under checklist points only minor suggestions for edits and revisions.
Review checklist for @akbaritabar
Conflict of interest
- [x] 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
- [x] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
[x] Repository: Is the source code for this software available at the https://github.com/schochastics/netrankr?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- On the package website (http://netrankr.schochastics.net/) MIT license is mentioned and a file is provided stating year and copyright holder's name (as suggested by: https://r-pkgs.org/license.html#key-files) but in the repository on GitHub, only that file is shown instead of MIT license that GitHub usually shows and clicking shows permissions (example of what I intended: https://github.com/openjournals/joss-reviews/blob/master/LICENSE)
[x] Contribution and authorship: Has the submitting author (@schochastics) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Functionality
[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
- [x] Guidelines and rules of thumb are provided on the performance and how it drops for larger networks which is very valuable (http://netrankr.schochastics.net/articles/benchmarks.html)
Documentation
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- [x] In the package website, there are multiple vignettes and tutorials using different examples.
- [x] It would be great if one of those examples could be included in the paper to make it "stand alone" for those who would read the paper first without trying out the package and vignettes. (a good candidate could be: http://netrankr.schochastics.net/#simple-example)
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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 [x] There are three issues already created in the repository, and the website (http://netrankr.schochastics.net/index.html) has a button "report a bug" but I couldn't see something on contribution.
Software paper
[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- [x] Summary presents a very nice definition of "centrality" in networks using examples from different fields.
- [x] But, a simple and accessible definition of "partial" and "probabilistic ranking" could be added (vignettes already have materials that could be used in the paper to to make it "stand alone" for those who would read the paper first without trying out the package and vignettes). I would suggest using materials already present in package's website (i.e., http://netrankr.schochastics.net/#overview ) or for instance, some of the one-liner questions used in the statement of need would be helpful, e.g., "how likely is a node more central than another one?"
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- Minor point: I would suggest removing citations in the abstract, if possible.
- Minor point: "small packages" --> "small package"
[x] 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?
A suggestion for JOSS
- Perhaps it would be nice to use the editorial bot currently used by JOSS and set a reminder for when the review is due, after a reviewer accepts the invitation.
@akbaritabar - thank you for reviewing and making a decision. After our reviewer @briatte completes their review I will start my editorial stuff and make a final decision.
@briatte - since we are mostly in vacation, i always hesitate to ping our reviewers. If I am not bothering you, could you please update your status or at least set a deadline for your task?
thank you in advance,
Dear @briatte
Our first reviewer has just finished their task and made a decision. We are not able to get even a life signal from you for a while. Please tell us if you are not available so we can find another reviewer. If you plan to get back later, please set a deadline for us.
Thank you in advance.
@editorialbot remind @briatte in two weeks
Reminder set for @briatte in two weeks
@editorialbot remove @briatte from reviewers
@briatte removed from the reviewers list!
@ccamara - Do you still want to be a reviewer for this submission? We have failed to get a response from one of the reviewers, so we need 2nd reviewer for this submission.
https://github.com/openjournals/joss-reviews/issues/4546
Dear @schochastics,
Because of our 2nd reviewer has been unresponsive since the very earlier states of the review, now I am starting to find a new proper reviewer.
Thank you for your patience.
:wave: @briatte, please update us on how your review is going (this is an automated reminder).
@jbytecode no worries. Let me know if I can help finding someone
I have already sent a new invitation to @ccamara and I will wait a couple of days for a response, thank you.
Dear @alexanderfurnas,
Our first reviewer has completed their tasks. Because we failed to reach our 2nd reviewer, I need a second reviewer for this submission.
Would you be willing to review for this submission for JOSS (Journal of Open Source Software)?
Thank you in advance.
Dear @corybrunson,
Our first reviewer has completed their tasks. Because we failed to reach our 2nd reviewer, I need a second reviewer for this submission.
Would you be willing to review for this submission for JOSS (Journal of Open Source Software)?
Thank you in advance.