[REVIEW]: Using the tidyverse with terra objects: the tidyterra package

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@dieghernan@elbeejay<!--end-editor-- Reviewers: @mikejohnson51, @Yingjie4Science Archive: 10.5281/zenodo.10078157

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2d749c1db022cd5205fdae573f69721e"><img src="https://joss.theoj.org/papers/2d749c1db022cd5205fdae573f69721e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2d749c1db022cd5205fdae573f69721e/status.svg)](https://joss.theoj.org/papers/2d749c1db022cd5205fdae573f69721e)

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

@mikejohnson51 & @Yingjie4Science, 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 @elbeejay 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

📝 Checklist for @Yingjie4Science

📝 Checklist for @mikejohnson51

editorialbot commented 1 year 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 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (258.2 files/s, 59765.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1              0              0            227
Markdown                         1             42              0            194
-------------------------------------------------------------------------------
SUM:                             2             42              0            421
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1166

editorialbot commented 1 year ago

Failed to discover a valid open source license

editorialbot commented 1 year ago

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

OK DOIs

- 10.1101/2023.05.09.540012 is OK
- 10.1111/2041-210X.13168 is OK
- 10.21105/joss.05082 is OK
- 10.1186/s12942-021-00267-z is OK
- 10.21105/joss.01686 is OK
- 10.1201/9781351201315 is OK
- 10.1201/9781351201315 is OK
- 10.32614/RJ-2018-009 is OK
- 10.1201/9780429459016 is OK
- 10.14714/CP69.20 is OK

MISSING DOIs

- None

INVALID DOIs

- None

elbeejay commented 1 year ago

@mikejohnson51 and @Yingjie4Science thank you once again for agreeing to review this submission. This is the "official" review issue, instructions for creating your reviewer checklist and conducting the review should be in the top comment of this issue, but please do not hesitate to reach out to me with any questions or to ask for any clarification.

Ideally we'd like to ask that you complete your reviews within 6 weeks, and I will set up reminder so the bot prods us all in 3 weeks.

Thanks, Jay

editorialbot commented 1 year ago

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

elbeejay commented 1 year ago

@editorialbot remind @mikejohnson51 in three weeks

editorialbot commented 1 year ago

Reminder set for @mikejohnson51 in three weeks

elbeejay commented 1 year ago

@editorialbot remind @Yingjie4Science in three weeks

editorialbot commented 1 year ago

Reminder set for @Yingjie4Science in three weeks

dieghernan commented 1 year ago

@editorialbot set main as branch

editorialbot commented 1 year ago

Done! branch is now main

dieghernan commented 1 year ago

@editorialbot check repository

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.30 s (1120.0 files/s, 196279.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                            173              0              0          32201
R                              125           4773           6032          12261
Markdown                        18            216              0            969
YAML                            12             99             44            466
JSON                             2              0              0            391
Rmd                              5            331            782            387
TeX                              1              0              0            227
XML                              2              0              0             58
-------------------------------------------------------------------------------
SUM:                           338           5419           6858          46960
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Failed to discover a Statement of need section in paper

dieghernan commented 1 year ago

@editorialbot set joss as branch

editorialbot commented 1 year ago

Done! branch is now joss

dieghernan commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

dieghernan commented 1 year ago

@editorialbot check repository

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (336.1 files/s, 67899.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1              0              0            238
Markdown                         1             34              0            132
-------------------------------------------------------------------------------
SUM:                             2             34              0            370
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 907

editorialbot commented 1 year ago

Failed to discover a valid open source license

dieghernan commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1101/2023.05.09.540012 is OK
- 10.1111/2041-210X.13168 is OK
- 10.21105/joss.05082 is OK
- 10.1186/s12942-021-00267-z is OK
- 10.21105/joss.01686 is OK
- 10.1201/9781351201315 is OK
- 10.1201/9781351201315 is OK
- 10.32614/RJ-2018-009 is OK
- 10.1201/9780429459016 is OK
- 10.14714/CP69.20 is OK
- 10.1101/2023.07.24.550358 is OK

MISSING DOIs

- None

INVALID DOIs

- None

dieghernan commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

dieghernan commented 1 year ago

Hi @mikejohnson51, @Yingjie4Science:

Thanks for volunteering on this submission. Please note that after the comment of @elbeejay in https://github.com/openjournals/joss-reviews/issues/5675#issuecomment-1665955080 I modified slightly the Examples section (https://github.com/dieghernan/tidyterra/commit/0820452a2b3ba34307a8c89996c8a44bdfcf48b6) and now the paper wordcount is 907 (therefore between 250-1000 words as per the JOSS Guidelines.

The corresponding pdf have been generated and linked in https://github.com/openjournals/joss-reviews/issues/5751#issuecomment-1673224096.

dieghernan commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1371/journal.pone.0286036 is OK
- 10.1111/2041-210X.13168 is OK
- 10.21105/joss.05082 is OK
- 10.1186/s12942-021-00267-z is OK
- 10.21105/joss.01686 is OK
- 10.1201/9781351201315 is OK
- 10.1201/9781351201315 is OK
- 10.32614/RJ-2018-009 is OK
- 10.1201/9780429459016 is OK
- 10.14714/CP69.20 is OK
- 10.1101/2023.07.24.550358 is OK

MISSING DOIs

- None

INVALID DOIs

- None

dieghernan commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

elbeejay commented 1 year ago

Thank you for the follow-ups @dieghernan - I'll just note that reviewers can also re-generate the paper as they wish and do any additional checks of the references or the repository.

editorialbot commented 1 year ago

:wave: @mikejohnson51, please update us on how your review is going (this is an automated reminder).

editorialbot commented 1 year ago

:wave: @Yingjie4Science, please update us on how your review is going (this is an automated reminder).

elbeejay commented 1 year ago

Checking in @mikejohnson51, and @Yingjie4Science, please let us know how your reviews are going (if they have started) or when you anticipate having time to do a review. Thanks!

mikejohnson51 commented 1 year ago

This is on my agenda for next week. Thanks for checking in!

Yingjie4Science commented 1 year ago

@elbeejay Thanks for the reminder. I am working on it too and will update my review status by this week.

elbeejay commented 1 year ago

Hi @mikejohnson51 and @Yingjie4Science just wanted to reach out for updates on how the reviews are going.

elbeejay commented 1 year ago

Paging @Yingjie4Science and @mikejohnson51 - any updates?

elbeejay commented 1 year ago

@dieghernan - sorry to say that if we don't hear from @Yingjie4Science or @mikejohnson51 this week I may need to search for another reviewer. Apologies for the delay.

Yingjie4Science commented 1 year ago

@editorialbot start review

editorialbot commented 1 year ago

I'm sorry @Yingjie4Science, I'm afraid I can't do that. That's something only editors are allowed to do.

Yingjie4Science commented 1 year ago

Review checklist for @Yingjie4Science

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 https://github.com/dieghernan/tidyterra?
[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 (@dieghernan) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[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?

elbeejay commented 1 year ago

@dieghernan seems like @Yingjie4Science has generated their checklist and started looking at some of the submission. I've heard from @mikejohnson51 via email and it sounds like they will be able to get to this next week as well.

Yingjie4Science commented 1 year ago

@elbeejay Sorry for the delay as I was on a long-distance international trip. I am working on it and will aim to finish the review as soon as possible!

elbeejay commented 1 year ago

Sounds good, thanks for the update @Yingjie4Science

Yingjie4Science commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

openjournals / joss-reviews