[REVIEW]: ARDL: An R package for the analysis of level relationships

[whedon]

Submitting author: @Natsiopoulos (Kleanthis Natsiopoulos) Repository: https://github.com/Natsiopoulos/ARDL Branch with paper.md (empty if default branch): Version: v0.2.1 Editor: @sbenthall Reviewers: @ha0ye, @jacobsoj, jessie-dotson Archive: 10.5281/zenodo.7200425

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Status

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Reviewers and authors:

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Reviewer instructions & questions

@ha0ye & @jacobsoj, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @ha0ye

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 (@Natsiopoulos) 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

• [ ] 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)?
• [ ] 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 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)?
• [ ] 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 @jessie-dotson

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 (@Natsiopoulos) 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)?
• [ ] 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

• [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?
• [ ] 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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ha0ye, @jacobsoj it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.02 s (1003.0 files/s, 197493.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               14            177           1313           1561
Markdown                         4            145              0            504
TeX                              1              4              0             50
Rmd                              1             53             83             48
-------------------------------------------------------------------------------
SUM:                            20            379           1396           2163
-------------------------------------------------------------------------------


Statistical information for the repository 'ab97de661f381275f4fd498a' was
gathered on 2021/07/15.
No commited files with the specified extensions were found.

[whedon]

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

OK DOIs

- 10.1371/journal.pone.0228812 is OK
- 10.1002/jae.616 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.annals.2021.103155 is INVALID because of 'https://doi.org/' prefix

[whedon]

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

[whedon]

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

[whedon]

:wave: @ha0ye, please update us on how your review is going (this is an automated reminder).

[ha0ye]

Sorry, I've been caught up with arranging things at my uni. Will try to squeeze this in over the next 2 weeks.

[ha0ye]

My review notes are now in https://github.com/Natsiopoulos/ARDL/issues/6

[sbenthall]

@jacobsoj will you be able to review this submission?

[jacobsoj]

My father died, so I have been out of the country. If you can wait another week(Oct. 11), I can finish this review. If not, then I withdraw. I apologize, but it has been a difficult time. It was under hospice care for 2,months. Jill

Sent from my iPhone

On Sep 20, 2021, at 7:47 AM, Sebastian Benthall @.***> wrote:



@jacobsojhttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjacobsoj&data=04%7C01%7Cjill.jacobson%40queensu.ca%7C94410fcba8a942594d6008d97c34bf93%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637677388259471698%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=uQDHXaXPb%2B5j0wGnQMNW1bKEg3Ck2bciMviDvhM1kn0%3D&reserved=0 will you be able to review this submission?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fopenjournals%2Fjoss-reviews%2Fissues%2F3496%23issuecomment-922895362&data=04%7C01%7Cjill.jacobson%40queensu.ca%7C94410fcba8a942594d6008d97c34bf93%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637677388259481691%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=xa1ZtnlpXvUooKTWwj5OwCk3F3qZa1WESLlGB%2BAOXLo%3D&reserved=0, or unsubscribehttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAFIU35AAK2HHWTYRYCAG353UC4UMPANCNFSM5ANXA3NA&data=04%7C01%7Cjill.jacobson%40queensu.ca%7C94410fcba8a942594d6008d97c34bf93%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637677388259481691%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=qrP8TEiyum7fOjZ9syoaEv1p3ST%2B7S33nP3afJ0p6%2Fk%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cjill.jacobson%40queensu.ca%7C94410fcba8a942594d6008d97c34bf93%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637677388259491684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=1DazF8kEnZYsnU6BXZm%2FE7ZcWyQzOm8f3mcsGHaQY2s%3D&reserved=0 or Androidhttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cjill.jacobson%40queensu.ca%7C94410fcba8a942594d6008d97c34bf93%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637677388259491684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=UZxnPkmzxPTaFNrxMWAtDGaTcH%2Fz7vuUlYtfw%2BeRI%2Fw%3D&reserved=0.

[sbenthall]

@jacobsoj Please accept my sincere condolences for your hardship and loss. I believe this review can wait another week.

[sbenthall]

@jacobsoj I wonder if you can report back on whether you can finish this review, or if we need to find a replacement.

[sbenthall]

@soodoku Hello. Earlier (six months ago) when we reached out to you about this submission, you were unable to review because of other commitments. I wonder if you would be able to step in and review this submission now.

[jacobsoj]

Sorry, Sebastian, I kept hoping I could rally to get this done. I hope the other person can do it.

Could you withdraw my name/contact from future consideration for reviews? I use R a lot, but I rarely use GitHub and have to relearn it each time, which adds to the burden of doing these reviews. Jill

Jill A. Jacobson, Ph.D. Office Phone 613-533-2847 Associate Professor, Social-Personality Program Lab Phone 613-533-6000 x75417 Queen's University FAX 613-533-2499 Department of Psychology Email @.*** Kingston, ON K7L 3N6 CANADA

http://www.queensu.ca/psychology/People/Faculty/Jill-Jacobson

---

From: Sebastian Benthall @.> Sent: Monday, November 29, 2021 12:42 PM To: openjournals/joss-reviews @.> Cc: Jill Jacobson @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: ARDL: An R package for the analysis of level relationships (#3496)

@jacobsojhttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjacobsoj&data=04%7C01%7Cjill.jacobson%40queensu.ca%7C00007bd84b544b2009bf08d9b35f9a8a%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637738045458791986%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=RRdftNEkUXDV2EyO1f3OtTvhuzpYeb9llCT%2FnhYoOs4%3D&reserved=0 I wonder if you can report back on whether you can finish this review, or if we need to find a replacement.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fopenjournals%2Fjoss-reviews%2Fissues%2F3496%23issuecomment-981864361&data=04%7C01%7Cjill.jacobson%40queensu.ca%7C00007bd84b544b2009bf08d9b35f9a8a%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637738045458801966%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=1HY02KYuxQfqbhgJg1duWjRed7cn3ZSTGHUrPG%2BB9Wk%3D&reserved=0, or unsubscribehttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAFIU35HR7RCKQET6CFR5NY3UOO3P7ANCNFSM5ANXA3NA&data=04%7C01%7Cjill.jacobson%40queensu.ca%7C00007bd84b544b2009bf08d9b35f9a8a%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637738045458806957%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=uZI6jElFLRohRNHub9u2AAnWEKLU3fCec9f3aWGHVSY%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cjill.jacobson%40queensu.ca%7C00007bd84b544b2009bf08d9b35f9a8a%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637738045458811948%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=086cE%2FRwprXeiaLrJk8qW0qYkiVYAin8C1vdmDdBDUk%3D&reserved=0 or Androidhttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cjill.jacobson%40queensu.ca%7C00007bd84b544b2009bf08d9b35f9a8a%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637738045458811948%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=4Zv5%2BlDuSVmd420MUVRLFrdp%2F%2B623h4rqIZup9rpDyo%3D&reserved=0.

[sbenthall]

@cdcrabtree Would you be able to step in as a reviewer for this package?

[sbenthall]

@edonnachie Would you be able to step in as reviewer for this package?

[sbenthall]

@czxa Would you be able to step in as a reviewer for this package?

[sbenthall]

@RomainAzais Would you be able to step in as a reviewer for this package?

[sbenthall]

@taqtiqa-mark Would you be able to step in as a reviewer for this package?

[sbenthall]

@jessie-dotson Would you be able to step in as a reviewer for this package?

[edonnachie]

Apologies for the delayed response. I'm unable to take on any new projects for the next few weeks, but would consider doing the review if you don't find anyone else by mid-February.

The package itself looks interesting and useful to me from an applied perspective. But I'm not an expert on these methods, so would not be able to review the implementation.

[jessie-dotson]

This package implements a model that I'm not familiar with, and am unlikely to use -- but it does look interesting and useful for other use cases. If JOSS is ok with having a reviewer who is unlikely to use the package in the future then I'm happy to do a review. (I should be able to complete in the next 2 weeks.)

[taqtiqa-mark]

@sbenthall this is well outside my wheelhouse. Apologies I couldn't be more help this time.

[sbenthall]

@jessie-dotson Yes, it's perfectly fine for reviewers to review packages that they are unlikely to use themselves.

Thank you for volunteering! I'll assign you as the second reviewer.

[sbenthall]

@whedon add jessie-dotson as reviewer

[whedon]

OK, jessie-dotson is now a reviewer

[jessie-dotson]

Suggested edits to JOSS paper in https://github.com/Natsiopoulos/ARDL/issues/7#issue-1117989915

[jessie-dotson]

Recommend fixing use of tibble to avoid compatibility warning. Documented in https://github.com/Natsiopoulos/ARDL/issues/8#issue-1129251801

[jessie-dotson]

Community guidelines missing. Please see https://github.com/Natsiopoulos/ARDL/issues/9

[jessie-dotson]

Tests to verify functionality missing. Please see https://github.com/Natsiopoulos/ARDL/issues/10