fellingdateR: Estimate, report and combine felling dates of historical tree-ring series

[hanecakr]

Date accepted: 2024-04-08

Submitting Author Name: Kristof Haneca Submitting Author Github Handle: !--author1-->@hanecakr<!--end-author1-- Other Package Authors Github handles: (comma separated, delete if none) Repository: https://github.com/hanecakr/fellingdateR Version submitted: Submission type: Standard Editor: !--editor-->@maelle<!--end-editor-- Reviewers: @njtierney, @ajpelu

Archive: TBD Version accepted: TBD Language: en

---

• Paste the full DESCRIPTION file inside a code block below:

Package: fellingdateR
Title: Estimate, report and combine felling dates of historical tree-ring 
    series
Version: 0.0.0.9003
Authors@R: c(
    person("Kristof", "Haneca", , "Kristof.Haneca@vlaanderen.be",role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-7719-8305")),
    person("Koen", "Van Daele", role = "ctb",
        comment = c(ORCID = "0000-0002-8153-2978")),
    person("Ronald", "Visser", role = "ctb",
        comment = c(ORCID = "0000-0001-6966-1729"))    
    )
Description: `fellingdateR` is an R package that aims to facilitate the 
  analysis and interpretation of tree-ring data from wooden 
  cultural heritage objects and structures. The package standarizes the process
  of computing and combining felling date estimates, both for individual and 
  groups of related tree-ring series.
URL: https://github.com/hanecakr/fellingdateR
BugReports: https://github.com/hanecakr/fellingdateR/issues
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends: 
    R (>= 2.10)
LazyData: true
Imports: 
    dplyr,
    ggplot2,
    ggtext,
    MASS,
    plyr,
    tidyr,
    utils,
    dplR
Suggests: 
    covr,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr

Scope

• Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):

  • [ ] data retrieval
  • [ ] data extraction
  • [ ] data munging
  • [ ] data deposition
  • [ ] data validation and testing
  • [ ] workflow automation
  • [ ] version control
  • [ ] citation management and bibliometrics
  • [ ] scientific software wrappers
  • [x] field and lab reproducibility tools
  • [ ] database software bindings
  • [ ] geospatial data
  • [ ] text analysis

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):

The package aims to facilitate and standardize the computation of felling dates from dated tree-ring series. It covers all steps of processing measured ring-width series from raw data to the reporting of felling date estimates, for single series and for groups of related tree-ring series.

• Who is the target audience and what are scientific applications of this package?

Maily professional tree-ring scientists (dendrochronologists) that work on historical timbers and wooden objects (archaeology, architectural history, sculptures, panel paintings, etc.)

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

No, no other R-packages do the same job.

• (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

yes

• If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

• Explain reasons for any pkgcheck items which your package is unable to pass.

All checks pass

Technical checks

Confirm each of the following by checking the box.

• [x ] I have read the rOpenSci packaging guide.
• [x ] I have read the author guide and I expect to maintain this package for at least 2 years or to find a replacement.

This package:

• [x] does not violate the Terms of Service of any service it interacts with.
• [x] has a CRAN and OSI accepted license.
• [x] contains a README with instructions for installing the development version.
• [x] includes documentation with examples for all functions, created with roxygen2.
• [x] contains a vignette with examples of its essential functions and uses.
• [x] has a test suite.
• [x] has continuous integration, including reporting of test coverage.

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- [ ] The package is novel and will be of interest to the broad readership of the journal. - [ ] The manuscript describing the package is no longer than 3000 words. - [ ] You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see [MEE's Policy on Publishing Code](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html)) - (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/aims-and-scope/read-full-aims-and-scope.html) for your manuscript. We make no guarantee that your manuscript will be within MEE scope.*) - (*Although not required, we strongly recommend having a full manuscript prepared when you submit here.*) - (*Please do not submit your package separately to Methods in Ecology and Evolution*)

Code of conduct

• [x] I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

[maelle]

@hanecakr Regarding renaming, you're in luck, @njtierney wrote a post on this very topic years ago: https://www.njtierney.com/post/2017/10/27/change-pkg-name/ (linked from the dev guide)

[ajpelu]

Hi @hanecakr Thanks for your message. I have seen your changes, and for me it is fine. If you need help to improve the pkg, please let me know. We may want to collaborate on future versions of the package, as this topic (i.e. combining dendrochronology and R) is in line with my research interests. Also if you need any help with the manuscript, let me know.

@maelle Thanks for the opportunity to review this pkg. It was an inspiring experience.

[hanecakr]

@hanecakr thank you! In your answer, it is hard for me to see what is quoted from the reviews, and what is your answer. Could you please consistently use quote formatting > for the parts that come from reviewers please? Thank you!

@maelle: All my comments were in bold-italic, but changed that to >

[hanecakr]

@hanecakr Regarding renaming, you're in luck, @njtierney wrote a post on this very topic years ago: https://www.njtierney.com/post/2017/10/27/change-pkg-name/ (linked from the dev guide)

@maelle: Thanks for the link to @njtierney 's blog. Meanwhile I also got some help from @koenedaele and the package/repository has been renamed to fellingdater.

[maelle]

@hanecakr thank you! I'd have recommended the opposite (quotes using the quote syntax, your comments as is) but whatever works!

@ajpelu thank you! Could you please post your answer with the reviewer's approval template?

@njtierney could you please have a look at the answer to your review?

Thanks all for all your work :pray:

[ajpelu]

Reviewer Response

@hanecakr Thanks for your message. I have seen your changes, and for me it is fine. If you need help to improve the pkg, please let me know. We may want to collaborate on future versions of the package, as this topic (i.e. combining dendrochronology and R) is in line with my research interests. Also if you need any help with the manuscript, let me know.

@maelle Thanks for the opportunity to review this pkg. It was an inspiring experience.

Final approval (post-review)

• [X] The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 13 h

[maelle]

@njtierney could you please have a look at the answer to your review? Please use the reviewer's approval template.

[njtierney]

Reviewer Response

Thanks for the responses, @hanecakr! You have done a great job addressing these comments. Thank you so much for taking the time to implement these. Well done! I've got a couple of minor comments below but I think this is all good to go from my perspective.

Formatting these reviews can be a bit tricky, but I did find it hard to know which parts you were responding to - in particular the documentation parts. This could have been resolved by placing my entire review in block quotes and then you responding either in further nested block quotes (> >) or by responding outside the blockquote.

README

The README looks to be updated substantially, thank you for taking the time to do this! One minor quirk I noticed with the README is:

The presence of partially preserved sapwood (sw) allows to estimate the missing number of sapwood rings ( ? in figure below), and to report an interval in which the actual felling date (fd) likely falls.

I'm not sure what to make of the ? in figure below - is that a typo?

I also really appreciate the new workflow diagram, that is very nice!

package rename

Well done on renaming the package! One small quip - you still have the RStudio project named fellingDateR - I think this should be fellingdater.

Using <-

There is one case in a test: test-sw_model.R where = is used.

Final approval (post-review)

• [x] The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 6.5

[maelle]

@njtierney thanks!!

[maelle]

@ropensci-review-bot approve fellingdater

[ropensci-review-bot]

Approved! Thanks @hanecakr for submitting and @njtierney, @ajpelu for your reviews! :grin:

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[maelle]

@hanecakr thanks so much for your work on your package!

@ajpelu @njtierney thanks a ton again for reviewing!

[hanecakr]

Dear @maelle , @ajpelu and @njtierney thank you so much for all your time and effort you´ve invested in reviewing my package 🙏🙏🙏. It was a first for me and learned a lot. Thanks to you the quality of the package improved significantly! I´m on a short family trip right now (without laptop 😅), but will address the remaining issues and transfer to rOpenSci´s repo next week. My best wishes, Kristof

[hanecakr]

@ropensci-review-bot finalize transfer of fellingdater

[ropensci-review-bot]

Transfer completed. The fellingdater team is now owner of the repository and the author has been invited to the team

[hanecakr]

@maelle, the transfer to rOpenSci's repo succeeded! 🚀 Shall I add you as a reviewer as well in DESCRIPTION? Thanks again for all your time and guidance.

[maelle]

Awesome, great to read! No need to list me, your participation in the process is thanks enough. Thank you for all your work and your kind words!