Joss-reviews: [REVIEW]: tabula: An R Package for Analysis, Seriation and Visualization of Archaeological Count Data

[whedon]

Submitting author: @nfrerebeau (Nicolas Frerebeau)
Repository: https://github.com/nfrerebeau/tabula
Version: v1.4.0
Editor: @oliviaguest
Reviewer: @izaromanowska, @soodoku
Archive: 10.5281/zenodo.3552904

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d4f9ee7bc85e4e6cb66bb12406570b73"><img src="https://joss.theoj.org/papers/d4f9ee7bc85e4e6cb66bb12406570b73/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d4f9ee7bc85e4e6cb66bb12406570b73/status.svg)](https://joss.theoj.org/papers/d4f9ee7bc85e4e6cb66bb12406570b73)

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

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

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @oliviaguest know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @izaromanowska

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 (@nfrerebeau) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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 @soodoku

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 (@nfrerebeau) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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]

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

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[oliviaguest]

Hey @izaromanowska and @soodoku!

This is where the reviewing proper happens. You need to go through the checklist and feel free to post questions here and open review issues in the submission repository: https://github.com/nfrerebeau/tabula (If you do please link to them here to help keep track.)

[izaromanowska]

Hi @oliviaguest, I've done the review following the checklist. All works well as far as I can tell and is impressively well described. Do you need a written review as well?
One tiny suggestion is to mention in the readme that khroma needs to be installed and loaded. Probably unnecessary for most users but it's the only dependency that kicked off when checking examples on a freshly installed RStudio.

[oliviaguest]

@izaromanowska thank you!

All works well as far as I can tell and is impressively well described. Do you need a written review as well?

It's up to you how much further feedback or ideas you want to share with the authors.

[oliviaguest]

@soodoku any chance you can get this done within the next week?

[soodoku]

@oliviaguest --- plausibly. will work on the weekend on this, getting started sooner.

[oliviaguest]

@soodoku thanks!
@nfrerebeau have you made any edits with respect to what @izaromanowska has given you feedback on?

[nfrerebeau]

As suggested by @izaromanowska, I have modified the README so that khroma is installed and loaded.

[oliviaguest]

@soodoku any luck finding time? I can set up an automated reminder for you if you want/think it can be helpful? :smile:

[soodoku]

not yet, @oliviaguest but soon. on my agenda.

[soodoku]

I have created a few issues. None are blockers but would love to get @nfrerebeau's eyes on them.

https://github.com/nfrerebeau/tabula/issues

once that's done, we can move fast.

[oliviaguest]

@soodoku thank you!

[nfrerebeau]

@soodoku thank you for all these constructive remarks. I will look in detail before the weekend and make the necessary changes.

[soodoku]

good to go from my end. thanks @nfrerebeau for bearing with me.

[oliviaguest]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[oliviaguest]

@nfrerebeau please check the article and let me know if everything looks good to you. :smile:

[nfrerebeau]

@oliviaguest I fixed a small typo, everything else is OK!

[oliviaguest]

@whedon accept

[whedon]

No archive DOI set. Exiting...

[oliviaguest]

@nfrerebeau oh, forgot to ask you to archive this using a DOI service you want, e.g., Zenodo, figshare, etc. Post the DOI back so I or you can run:

@whedon set 10.0000/zenodo.00000 as archive

[nfrerebeau]

@oliviaguest I don't know which DOI you need:

• DOI of version 1.4.0 (including changes made during the review): 10.5281/zenodo.3552904
• DOI for all versions: 10.5281/zenodo.1489944

[oliviaguest]

@nfrerebeau ah, I need the one of the software that is the most updated and with the edits you made during the review.

[nfrerebeau]

@oliviaguest this one: 10.5281/zenodo.3552904

[oliviaguest]

@whedon set 10.5281/zenodo.3552904 as archive

[whedon]

OK. 10.5281/zenodo.3552904 is the archive.

[oliviaguest]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• 10.1016/j.jas.2011.06.031 is OK
• 10.18637/jss.v022.i04 is OK
• 10.2307/278341 is OK
• 10.1016/j.jas.2016.05.006 is OK
• 10.1007/3-540-28084-7_34 is OK
• 10.1371/journal.pone.0124942 is OK

MISSING DOIs

• https://doi.org/10.2307/501681 may be missing for title: A Quantitative Method for Deriving Cultural Chronology
• https://doi.org/10.2307/2843012 may be missing for title: Sequences in Prehistoric Remains

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1132

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1132, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[oliviaguest]

@nfrerebeau can you check the final proof and add any missing DOIs that apply, please? 😊

[nfrerebeau]

@oliviaguest only one of the two references had a DOI missing. I just added it!

The final proof is OK for me!

[oliviaguest]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• 10.1016/j.jas.2011.06.031 is OK
• 10.18637/jss.v022.i04 is OK
• 10.2307/278341 is OK
• 10.1016/j.jas.2016.05.006 is OK
• 10.1007/3-540-28084-7_34 is OK
• 10.1371/journal.pone.0124942 is OK
• 10.2307/2843012 is OK

MISSING DOIs

• https://doi.org/10.2307/501681 may be missing for title: A Quantitative Method for Deriving Cultural Chronology

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1133

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1133, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[oliviaguest]

@openjournals/joss-eics can somebody please accept this? Thank you. :smile_cat:

[oliviaguest]

@nfrerebeau is that other missing one a false alarm?

[nfrerebeau]

@oliviaguest yes, the suggested DOI points to a review of the article and not the original publication. As far as I know, this reference does not have a DOI.

[oliviaguest]

@labarba :wave: I assumed tagging @openjournals/joss-eics above is enough to get this accepted... What am I missing?

[Kevin-Mattheus-Moerman]

@oliviaguest No further steps required. It is my turn this week. Apologies for the delay I'll get to it later this evening.

[oliviaguest]

@Kevin-Mattheus-Moerman ah, thanks! I tagged Lorena because she is helping me out. Sorry for the extra pressure (none intended) — was more worried I did something wrong. Thanks again!

[Kevin-Mattheus-Moerman]

@whedon set v1.4.0 as version

[whedon]

OK. v1.4.0 is the version.

[Kevin-Mattheus-Moerman]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Kevin-Mattheus-Moerman]

@nfrerebeau below are some suggested changes for your paper:

• [x] The paper contains 1 instance of ...allowed the... and 3 instances of ...allow the.... Please consider adding for, i.e. so it reads ... allowed for the..., and ... allow for the... (or change to use enabled, enables).
• [x] In this sentence the referencing can be improved It may use a priori information, e.g., absolute dates or stratigraphical constraints: Poblome & Groenen (2003), and allows the analysis of chronological patterns in a socio-economic or cultural perspective, e.g., Bellanger & Husi (2012), Lipo, Madsen, & Dunnell (2015).,
  Consider reformatting to:
  It may use a priori information, e.g., absolute dates or stratigraphical constraints (Poblome & Groenen 2003), and allows for the analysis of chronological patterns in a socio-economic or cultural perspective (e.g., (Bellanger & Husi 2012), (Lipo, Madsen, & Dunnell 2015)).
• [x] In ...count data, e.g., artifacts, faunal remains, etc. consider rephrasing to ...count data, such as artifacts and faunal remains, which reads better and avoids the use of etc. at the end of a sentence.
• [x] In ...of diversity indices and implements seriation/ordination methods, but..., since packages is plural this should have implement not implements.
• [x] Should the [a] be added here? ...Estimated dates can then be displayed as [a] tempo or activity plot...
• [x] If I understand the following correctly: ...abundance plots, heatmaps, Ford (1962), and Bertin (1977) diagrams. , perhaps it should read this instead: ...abundance plots, heatmaps, and Ford (1962) and Bertin (1977) diagrams.
• [x] In All the contributors have made..., I suggest: The following contributors have made...

[Kevin-Mattheus-Moerman]

@nfrerebeau

• [x] Please amend the meta data for the Zenodo archived version such that the title and the author set matches that of the paper.
• [x] The archived version lists version v1.4.0 (which I've updated here already), can you confirm this is correct (and that this is the version of the reviewed and archived software)?

[nfrerebeau]

@Kevin-Mattheus-Moerman I made the changes you suggested. Thank you for taking the time to improve my text.

I modified the title of the Zenodo archive. The author set in the meta data already matches that of the paper, or am I missing something?

I confirm that v1.4.0 is the version of the reviewed and archived software.

[oliviaguest]

@nfrerebeau if you can tick them off, that will help — thanks! :smile:

[Kevin-Mattheus-Moerman]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Kevin-Mattheus-Moerman]

@nfrerebeau nearly there. I left one box unchecked :point_up: . You introduced [a] but I meant for you to introduce a, so please remove the square brackets. You can call @whedon generate pdf here when you are done. Thanks.

[nfrerebeau]

@Kevin-Mattheus-Moerman I was a little too fast on this one :sweat_smile:

[nfrerebeau]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Kevin-Mattheus-Moerman]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• 10.1016/j.jas.2011.06.031 is OK
• 10.18637/jss.v022.i04 is OK
• 10.2307/278341 is OK
• 10.1016/j.jas.2016.05.006 is OK
• 10.1007/3-540-28084-7_34 is OK
• 10.1371/journal.pone.0124942 is OK
• 10.2307/2843012 is OK

MISSING DOIs

• https://doi.org/10.2307/501681 may be missing for title: A Quantitative Method for Deriving Cultural Chronology

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1141

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1141, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[Kevin-Mattheus-Moerman]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1142
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01821
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01821/status.svg)](https://doi.org/10.21105/joss.01821)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01821">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01821/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01821/status.svg
   :target: https://doi.org/10.21105/joss.01821

This is how it will look in your documentation:

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[nfrerebeau]

@izaromanowska, @soodoku, @oliviaguest and @Kevin-Mattheus-Moerman many thanks!!