[REVIEW]: R-Opitools – An Opinion Analytical Tool for Big Digital Text Document (DTD)

whedon commented 3 years ago

Submitting author: @MAnalytics (Monsuru Adepeju) Repository: https://github.com/MAnalytics/opitools Version: v2.0.0 Editor: @ajstewartlang Reviewers: @cjbarrie, @justinchuntingho, @jaeyk Archive: 10.5281/zenodo.5346595

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Reviewer instructions & questions

@cjbarrie & @justinchuntingho, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @cjbarrie

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@MAnalytics) 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.)

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] 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

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] 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 and who the target audience is?
[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)?
[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?

Review checklist for @justinchuntingho

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@MAnalytics) 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.)

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] 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

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] 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 and who the target audience is?
[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)?
[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?

Review checklist for @jaeyk

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@MAnalytics) 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.)

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] 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

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] 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 and who the target audience is?
[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)?
[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?

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @cjbarrie, @justinchuntingho it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 3 years ago

Wordcount for paper.md is 586

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.05 s (487.8 files/s, 82157.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             1             43              2           1189
R                               17            344            811            974
TeX                              2             25              0            167
Rmd                              1            129            196            138
Markdown                         4             69              0            124
-------------------------------------------------------------------------------
SUM:                            25            610           1009           2592
-------------------------------------------------------------------------------

Statistical information for the repository '6ed8a2a44ac7209874d9083c' was
gathered on 2021/08/11.
No commited files with the specified extensions were found.

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/frobt.2018.00138 is OK
- 10.21105/joss.00764 is OK
- 10.4236/jgis.2021.132008 is OK

MISSING DOIs

- 10.1186/s40163-020-00129-2 may be a valid DOI for title: “Show this thread”: policing, disruption and mobilisation through Twitter. An analysis of UK law enforcement tweeting practices during the Covid-19 pandemic
- 10.1016/j.procs.2020.03.201 may be a valid DOI for title: Analysis of Political Sentiment Orientations on Twitter

INVALID DOIs

- None

whedon commented 3 years ago

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

ajstewartlang commented 3 years ago

Thanks very much for agreeing to review this submission @cjbarrie @justinchuntingho

ajstewartlang commented 3 years ago

@whedon add @jaeyk as reviewer

whedon commented 3 years ago

OK, @jaeyk is now a reviewer

ajstewartlang commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

whedon commented 3 years ago

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

jaeyk commented 3 years ago

1. Quality of writing @MAnalytics Excellent R pkg. I recommend tidying up some wordings in the paper.md. I provided examples in this issue: https://github.com/MAnalytics/opitools/issues/4

2. Example usage When providing usages, consider specifying the expected data type of input as it's the area where users make common mistakes. For instance, below, policing_dtd is a dataframe or a character vector?

opi_impact(textdoc = policing_dtd, theme_keys=covid_theme, metric = 1, fun = NULL, nsim = 99, alternative="two.sided", pplot = TRUE, quiet=FALSE)

3. Functionality documentation I recommend creating a package homepage using pkgdown (https://pkgdown.r-lib.org/articles/pkgdown.html) and helping users to look at the list of the functions provided by the package: https://pkgdown.r-lib.org/articles/pkgdown.html Also, you can log how you've updated the pkg in the same space.

4. Community guideline It would be great if you can provide an issue template for how people can contribute to your package.

jaeyk commented 3 years ago

@MAnalytics As for the installation guideline, it might be useful to explain that the {remotes} is an extra package that users need to install.

MAnalytics commented 3 years ago

Dear @jaeyk @justinchuntingho @cjbarrie @ajstewartlang

All of the above have now been addressed accordingly. Btw, the package website can be accessed here: https://manalytics.github.io/opitools/index.html

Thanks, MA.

whedon commented 3 years ago

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

whedon commented 3 years ago

:wave: @cjbarrie, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @justinchuntingho, please update us on how your review is going (this is an automated reminder).

cjbarrie commented 3 years ago

I have created a PR, which just tweaks a few things. Otherwise, my editing suggestions are limited to those edits to paper.md described in https://github.com/MAnalytics/opitools/issues/4.

Once these have been resolved, I'd be happy to accept!

Great work @MAnalytics !

jaeyk commented 3 years ago

I'm good with the submission. I think that @cjbarrie's suggestions are great. Thanks for your contribution @MAnalytics.

MAnalytics commented 3 years ago

@cjbarrie @jaeyk @justinchuntingho Thank you all very much for the excellent reviews. All the issues have now been addressed accordingly.

MA.

cjbarrie commented 3 years ago

All boxes ticked on my side: I'm happy recommend acceptance

ajstewartlang commented 3 years ago

Many thanks for your thorough reviews @cjbarrie @jaeyk and @justinchuntingho. @justinchuntingho can I check whether you're happy that all issues that you raised have been addressed?

cjbarrie commented 3 years ago

Many thanks for your thorough reviews @cjbarrie @jaeyk and @justinchuntingho. @justinchuntingho can I check whether you're happy that all issues that you raised have been addressed?

I'm happy!

justinchuntingho commented 3 years ago

Yes! I am happy to recommend acceptance.

ajstewartlang commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

ajstewartlang commented 3 years ago

@whedon check references

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/frobt.2018.00138 is OK
- 10.21105/joss.00764 is OK
- 10.4236/jgis.2021.132008 is OK

MISSING DOIs

- 10.1186/s40163-020-00129-2 may be a valid DOI for title: “Show this thread”: policing, disruption and mobilisation through Twitter. An analysis of UK law enforcement tweeting practices during the Covid-19 pandemic
- 10.1016/j.procs.2020.03.201 may be a valid DOI for title: Analysis of Political Sentiment Orientations on Twitter

INVALID DOIs

- None

ajstewartlang commented 3 years ago

Hi @MAnalytics the two suggested DOIs above look correct to me - can you double check and add them to the paper please? Thanks :-)

MAnalytics commented 3 years ago

@ajstewartlang DOIs added!

Thank you very much.

MAnalytics commented 3 years ago

@whedon check references

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/frobt.2018.00138 is OK
- 10.21105/joss.00764 is OK
- 10.4236/jgis.2021.132008 is OK
- 10.1186/s40163-020-00129-2 is OK
- 10.1016/j.procs.2020.03.201 is OK

MISSING DOIs

- None

INVALID DOIs

- None

ajstewartlang commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

ajstewartlang commented 3 years ago

@whedon check references

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/frobt.2018.00138 is OK
- 10.21105/joss.00764 is OK
- 10.4236/jgis.2021.132008 is OK
- 10.1186/s40163-020-00129-2 is OK
- 10.1016/j.procs.2020.03.201 is OK

MISSING DOIs

- None

INVALID DOIs

- None

ajstewartlang commented 3 years ago

@whedon generate pdf

MAnalytics commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

whedon commented 3 years ago

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

ajstewartlang commented 3 years ago

Many thanks @cjbarrie @jaeyk @justinchuntingho for your helpful and detailed reviews. I've had a read through myself @MAnalytics and agree that this is a very nice and useful piece of software. Congrats!

@MAnalytics can I now ask you to do the following please?

Make a tagged release of the software.
Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add your ORCID.
Please list the DOI of the archived version here.

MAnalytics commented 3 years ago

@ajstewartlang Tasks completed! Thank you very much for the instruction.

Did the followings:

A tagged release of the software has now been made. Final release version: v2.0.0
Software archived in Zenodo with the correct metadata, including the title, author name, and ORCID number.
Software DOI: 10.5281/zenodo.5346595

Thanks as I look forward to the next step. M.

ajstewartlang commented 3 years ago

@whedon set 10.5281/zenodo.5346595 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5346595 is the archive.

ajstewartlang commented 3 years ago

@whedon set v2.0.0 as version

whedon commented 3 years ago

OK. v2.0.0 is the version.

ajstewartlang commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/frobt.2018.00138 is OK
- 10.21105/joss.00764 is OK
- 10.4236/jgis.2021.132008 is OK
- 10.1186/s40163-020-00129-2 is OK
- 10.1016/j.procs.2020.03.201 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2554

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2554, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

openjournals / joss-reviews