[REVIEW]: fellingdater: a toolkit to estimate, report and combine felling dates derived from historical tree-ring series.

editorialbot commented 5 months ago

Submitting author: !--author-handle-->@hanecakr@arfon<!--end-editor-- Reviewers: @njtierney, @ajpelu Archive: 10.5281/zenodo.11186275

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3db8c54ec854b575bf5450336ccb000b"><img src="https://joss.theoj.org/papers/3db8c54ec854b575bf5450336ccb000b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3db8c54ec854b575bf5450336ccb000b/status.svg)](https://joss.theoj.org/papers/3db8c54ec854b575bf5450336ccb000b)

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

@njtierney & @ajpelu, 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 @arfon 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

@njtierney, please create your checklist typing: @editorialbot generate my checklist

@ajpelu, please create your checklist typing: @editorialbot generate my checklist

editorialbot commented 5 months ago

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

editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1901.7 files/s, 272564.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               35            347           1229           3315
CSV                              8              0              0           1581
Markdown                         5            146              0            481
TeX                              1             43              0            472
YAML                             8             40             17            235
Rmd                              3            231            227            206
JSON                             1              0              0            173
-------------------------------------------------------------------------------
SUM:                            61            807           1473           6463
-------------------------------------------------------------------------------

Commit count by author:

   128  hanecakr
    11  Koen Van Daele
     2  KriHa
     1  Maëlle Salmon

editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 2317

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 5 months ago

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

OK DOIs

- 10.1016/j.dendro.2011.06.002 is OK
- 10.1016/j.jas.2008.07.005 is OK
- 10.3389/fevo.2022.823622 is OK
- 10.1016/j.dendro.2022.125963 is OK
- 10.1016/j.dendro.2020.125776 is OK
- 10.1179/030554797786050563 is OK
- 10.1016/j.dendro.2011.08.001 is OK
- 10.1016/j.dendro.2019.02.006 is OK
- 10.1016/j.dendro.2013.03.001 is OK
- 10.1179/174962906X158291 is OK
- 10.1016/j.dendro.2008.01.002 is OK
- 10.1016/j.dendro.2009.12.001 is OK
- 10.2458/rc.v51i1.3494 is OK
- 10.1016/j.dendro.2020.125773 is OK
- 10.5281/ZENODO.6110786 is OK
- 10.1016/j.dendro.2015.03.003 is OK
- 10.1111/arcm.12600 is OK
- 10.1017/RDC.2017.108 is OK
- 10.1017/S0033822200030903 is OK
- 10.3959/2010-12.1 is OK
- 10.1017/RDC.2020.95 is OK
- 10.1016/j.dendro.2020.125731 is OK
- 10.1016/j.dendro.2023.126150 is OK

MISSING DOIs

- No DOI given, and none found for title: A slice through time. Dendrochronology and precisi...
- 10.17221/4496-jfs may be a valid DOI for title: Determination of the number of sapwood annual ring...
- No DOI given, and none found for title: A 700 year dating chronology for northern France. ...
- No DOI given, and none found for title: Jahrringchronologische Datierung von Eichenhölzern...
- No DOI given, and none found for title: Mitteleuropäische Eichenchronologie: Trierer dendr...
- No DOI given, and none found for title: Aufbau und Anwendung der Dendrochronologie für Eic...
- No DOI given, and none found for title: A tree-ring chronology from the western part of Sw...
- 10.1016/0305-4403(81)90037-6 may be a valid DOI for title: Sapwood estimates in the interpretation of tree-ri...
- No DOI given, and none found for title: Sapwood estimates and the dating of short ring seq...
- No DOI given, and none found for title: R: A language and environment for statistical comp...
- No DOI given, and none found for title: dplR: Dendrochronology   Program Library in R. R p...
- No DOI given, and none found for title: ggplot2: elegant graphics for data analysis
- No DOI given, and none found for title: De Romeinse houtvoorziening in de Germaanse provin...
- 10.1007/bf02603303 may be a valid DOI for title: Über die Sicherheit jahrringchronologische Datieru...
- No DOI given, and none found for title: RemembeRINGs. The development and application of l...
- No DOI given, and none found for title: A simple crossdating program for tree-ring researc...

INVALID DOIs

- https://doi.org/10.1111/1475-4754.00048 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1179/174962908X365082 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/1475-4754.00048 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1007/BF02741777 is INVALID because of 'https://doi.org/' prefix

arfon commented 5 months ago

@njtierney, @ajpelu – just to re-affirm here, there's no additional work for you to do here!

editorialbot commented 5 months ago

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

arfon commented 5 months ago

@hanecakr – please could you fix up the DOIs that @editorialbot is reporting as having an issue here?

hanecakr commented 5 months ago

@arfon the doi's that were missing or needed some tweeking were addressed in this commit: https://github.com/ropensci/fellingdater/commit/759b253ac35164da35e4219ef4107f90da0ef856

hanecakr commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

arfon commented 5 months ago

Thanks @hanecakr. Please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from the rOpenSci review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

The title of the archive is the same as the JOSS paper title
That the authors of the archive are the same as the JOSS paper authors
I can then move forward with accepting the submission.

hanecakr commented 5 months ago

@arfon: I fixed some typo's (especially related to the bibliographic references) in paper.md -> commit https://github.com/ropensci/fellingdater/commit/4c3d8bc7afc45c804ef9b059dc21331b577b9aa8

hanecakr commented 5 months ago

fellingdater v1.0.1 has been released and archived to Zenodo: https://doi.org/10.5281/zenodo.11186275

hanecakr commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

arfon commented 5 months ago

@editorialbot set 10.5281/zenodo.11186275 as archive

editorialbot commented 5 months ago

Done! archive is now 10.5281/zenodo.11186275

arfon commented 5 months ago

@editorialbot set v1.0.1 as version

editorialbot commented 5 months ago

Done! version is now v1.0.1

arfon commented 5 months ago

@editorialbot recommend-accept

editorialbot commented 5 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 5 months ago

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

OK DOIs

- 10.1016/j.dendro.2011.06.002 is OK
- 10.1016/j.jas.2008.07.005 is OK
- 10.3389/fevo.2022.823622 is OK
- 10.1016/j.dendro.2022.125963 is OK
- 10.1016/j.dendro.2020.125776 is OK
- 10.17221/4496-JFS is OK
- 10.1179/030554797786050563 is OK
- 10.1016/j.dendro.2011.08.001 is OK
- 10.1016/0305-4403(81)90037-6 is OK
- 10.1016/j.dendro.2019.02.006 is OK
- 10.1016/j.dendro.2013.03.001 is OK
- 10.1111/1475-4754.00048 is OK
- 10.1179/174962906X158291 is OK
- 10.1179/174962908X365082 is OK
- 10.1016/j.dendro.2008.01.002 is OK
- 10.1016/j.dendro.2009.12.001 is OK
- 10.2458/rc.v51i1.3494 is OK
- 10.1111/1475-4754.00048 is OK
- 10.1016/j.dendro.2020.125773 is OK
- 10.5281/ZENODO.6110786 is OK
- 10.1016/j.dendro.2015.03.003 is OK
- 10.1007/BF02741777 is OK
- 10.1007/BF02603303 is OK
- 10.1111/arcm.12600 is OK
- 10.1017/RDC.2017.108 is OK
- 10.1017/S0033822200030903 is OK
- 10.3959/2010-12.1 is OK
- 10.1017/RDC.2020.95 is OK
- 10.1016/j.dendro.2020.125731 is OK
- 10.1016/j.dendro.2023.126150 is OK

MISSING DOIs

- No DOI given, and none found for title: A slice through time. Dendrochronology and precisi...
- No DOI given, and none found for title: A 700 year dating chronology for northern France. ...
- No DOI given, and none found for title: Jahrringchronologische Datierung von Eichenhölzern...
- No DOI given, and none found for title: Mitteleuropäische Eichenchronologie: Trierer dendr...
- No DOI given, and none found for title: Aufbau und Anwendung der Dendrochronologie für Eic...
- No DOI given, and none found for title: A tree-ring chronology from the western part of Sw...
- No DOI given, and none found for title: Sapwood estimates and the dating of short ring seq...
- No DOI given, and none found for title: R: A language and environment for statistical comp...
- No DOI given, and none found for title: dplR: Dendrochronology   Program Library in R. R p...
- No DOI given, and none found for title: ggplot2: elegant graphics for data analysis
- No DOI given, and none found for title: De Romeinse houtvoorziening in de Germaanse provin...
- No DOI given, and none found for title: RemembeRINGs. The development and application of l...
- No DOI given, and none found for title: A simple crossdating program for tree-ring researc...

INVALID DOIs

- None

editorialbot commented 5 months ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

IDREFS attribute rid references an unknown ID "fig-sw_interval"
IDREFS attribute rid references an unknown ID "fig-sw_sum"

arfon commented 5 months ago

@hanecakr – looks like some of the internal references to figures aren't working. Can you take a look at these docs and update accordingly? https://joss.readthedocs.io/en/latest/paper.html#tables-and-figures

hanecakr commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

hanecakr commented 5 months ago

@arfon, I used _ instead of - in those two figure references. Sorry for that! Fixed now in the updated version of paper.md.

arfon commented 5 months ago

@editorialbot recommend-accept

editorialbot commented 5 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 5 months ago

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

OK DOIs

- 10.1016/j.dendro.2011.06.002 is OK
- 10.1016/j.jas.2008.07.005 is OK
- 10.3389/fevo.2022.823622 is OK
- 10.1016/j.dendro.2022.125963 is OK
- 10.1016/j.dendro.2020.125776 is OK
- 10.17221/4496-JFS is OK
- 10.1179/030554797786050563 is OK
- 10.1016/j.dendro.2011.08.001 is OK
- 10.1016/0305-4403(81)90037-6 is OK
- 10.1016/j.dendro.2019.02.006 is OK
- 10.1016/j.dendro.2013.03.001 is OK
- 10.1111/1475-4754.00048 is OK
- 10.1179/174962906X158291 is OK
- 10.1179/174962908X365082 is OK
- 10.1016/j.dendro.2008.01.002 is OK
- 10.1016/j.dendro.2009.12.001 is OK
- 10.2458/rc.v51i1.3494 is OK
- 10.1111/1475-4754.00048 is OK
- 10.1016/j.dendro.2020.125773 is OK
- 10.5281/ZENODO.6110786 is OK
- 10.1016/j.dendro.2015.03.003 is OK
- 10.1007/BF02741777 is OK
- 10.1007/BF02603303 is OK
- 10.1111/arcm.12600 is OK
- 10.1017/RDC.2017.108 is OK
- 10.1017/S0033822200030903 is OK
- 10.3959/2010-12.1 is OK
- 10.1017/RDC.2020.95 is OK
- 10.1016/j.dendro.2020.125731 is OK
- 10.1016/j.dendro.2023.126150 is OK

MISSING DOIs

- No DOI given, and none found for title: A slice through time. Dendrochronology and precisi...
- No DOI given, and none found for title: A 700 year dating chronology for northern France. ...
- No DOI given, and none found for title: Jahrringchronologische Datierung von Eichenhölzern...
- No DOI given, and none found for title: Mitteleuropäische Eichenchronologie: Trierer dendr...
- No DOI given, and none found for title: Aufbau und Anwendung der Dendrochronologie für Eic...
- No DOI given, and none found for title: A tree-ring chronology from the western part of Sw...
- No DOI given, and none found for title: Sapwood estimates and the dating of short ring seq...
- No DOI given, and none found for title: R: A language and environment for statistical comp...
- No DOI given, and none found for title: dplR: Dendrochronology   Program Library in R. R p...
- No DOI given, and none found for title: ggplot2: elegant graphics for data analysis
- No DOI given, and none found for title: De Romeinse houtvoorziening in de Germaanse provin...
- No DOI given, and none found for title: RemembeRINGs. The development and application of l...
- No DOI given, and none found for title: A simple crossdating program for tree-ring researc...

INVALID DOIs

- None

editorialbot commented 5 months ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5348, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 5 months ago

@hanecakr – I made a few small edits to the paper in https://github.com/ropensci/fellingdater/pull/16 – could you please review and merge?

arfon commented 5 months ago

@editorialbot recommend-accept

editorialbot commented 5 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 5 months ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5369, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 5 months ago

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

OK DOIs

- 10.1016/j.dendro.2011.06.002 is OK
- 10.1016/j.jas.2008.07.005 is OK
- 10.3389/fevo.2022.823622 is OK
- 10.1016/j.dendro.2022.125963 is OK
- 10.1016/j.dendro.2020.125776 is OK
- 10.17221/4496-JFS is OK
- 10.1179/030554797786050563 is OK
- 10.1016/j.dendro.2011.08.001 is OK
- 10.1016/0305-4403(81)90037-6 is OK
- 10.1016/j.dendro.2019.02.006 is OK
- 10.1016/j.dendro.2013.03.001 is OK
- 10.1111/1475-4754.00048 is OK
- 10.1179/174962906X158291 is OK
- 10.1179/174962908X365082 is OK
- 10.1016/j.dendro.2008.01.002 is OK
- 10.1016/j.dendro.2009.12.001 is OK
- 10.2458/rc.v51i1.3494 is OK
- 10.1111/1475-4754.00048 is OK
- 10.1016/j.dendro.2020.125773 is OK
- 10.5281/ZENODO.6110786 is OK
- 10.1016/j.dendro.2015.03.003 is OK
- 10.1007/BF02741777 is OK
- 10.1007/BF02603303 is OK
- 10.1111/arcm.12600 is OK
- 10.1017/RDC.2017.108 is OK
- 10.1017/S0033822200030903 is OK
- 10.3959/2010-12.1 is OK
- 10.1017/RDC.2020.95 is OK
- 10.1016/j.dendro.2020.125731 is OK
- 10.1016/j.dendro.2023.126150 is OK

MISSING DOIs

- No DOI given, and none found for title: A slice through time. Dendrochronology and precisi...
- No DOI given, and none found for title: A 700 year dating chronology for northern France. ...
- No DOI given, and none found for title: Jahrringchronologische Datierung von Eichenhölzern...
- No DOI given, and none found for title: Mitteleuropäische Eichenchronologie: Trierer dendr...
- No DOI given, and none found for title: Aufbau und Anwendung der Dendrochronologie für Eic...
- No DOI given, and none found for title: A tree-ring chronology from the western part of Sw...
- No DOI given, and none found for title: Sapwood estimates and the dating of short ring seq...
- No DOI given, and none found for title: R: A language and environment for statistical comp...
- No DOI given, and none found for title: dplR: Dendrochronology   Program Library in R. R p...
- No DOI given, and none found for title: ggplot2: elegant graphics for data analysis
- No DOI given, and none found for title: De Romeinse houtvoorziening in de Germaanse provin...
- No DOI given, and none found for title: RemembeRINGs. The development and application of l...
- No DOI given, and none found for title: A simple crossdating program for tree-ring researc...

INVALID DOIs

- None

arfon commented 5 months ago

@editorialbot accept

editorialbot commented 5 months ago

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

editorialbot commented 5 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Haneca given-names: Kristof orcid: "https://orcid.org/0000-0002-7719-8305" doi: 10.5281/zenodo.11186275 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Haneca given-names: Kristof orcid: "https://orcid.org/0000-0002-7719-8305" date-published: 2024-05-22 doi: 10.21105/joss.06716 issn: 2475-9066 issue: 97 journal: Journal of Open Source Software publisher: name: Open Journals start: 6716 title: "fellingdater: a toolkit to estimate, report and combine felling dates derived from historical tree-ring series." type: article url: "https://joss.theoj.org/papers/10.21105/joss.06716" volume: 9 title: "*fellingdater*: a toolkit to estimate, report and combine felling dates derived from historical tree-ring series." ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 5 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 5 months ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5370
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06716
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

hanecakr commented 5 months ago

@crvernon Many thanks for your congratulations 🎉 (but you might wanted to drop this message in https://github.com/openjournals/joss-reviews/issues/6226 😅)

crvernon commented 5 months ago

Hahaha! Thanks @hanecakr! Too many windows open!

hanecakr commented 5 months ago

Thank you very much @arfon, @njtierney & @ajpelu for this very smooth review!

Now moving over to step 3., as recommended by the editorial bot 🎉🌈🦄💃👻🤘

arfon commented 5 months ago

@njtierney, @ajpelu – many thanks for your reviews here! JOSS (and rOpenSci) relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@hanecakr – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 5 months ago

: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.06716/status.svg)](https://doi.org/10.21105/joss.06716)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06716">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06716/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06716/status.svg
   :target: https://doi.org/10.21105/joss.06716

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

openjournals / joss-reviews