Implementation of OPTRAM algorithm to derive soil moisture from remote sensing imagery

[micha-silver]

Date accepted: 2024-06-05

Submitting Author Name: Micha Silver Submitting Author Github Handle: !--author1-->@micha-silver<!--end-author1-- Other Package Authors Github handles: (comma separated, delete if none) @github_handle1, @github_handle2 Repository: https://gitlab.com/rsl-bidr/roptram Version submitted: 0.0.1.000 Submission type: Standard Editor: !--editor-->@adamhsparks<!--end-editor-- Reviewers: @harryeslick, @obrl-soil

Archive: TBD Version accepted: TBD Language: en

---

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

Package: rOPTRAM
Title: Derive soil moisture using the OPTRAM algorithm
Version: 0.0.1.000
Authors@R: c(
  person("Micha", "Silver", , "silverm@post.bgu.ac.il", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-1128-1325")),
  person("Arnon", "Karnieli", , "karnieli@bgu.ac.il", role = c("ctb", "fnd"),
          comment = c(ORCID = "0000-0001-8065-9793"))
  )
Description: The OPtical TRapezoid Model (OPTRAM) derives soil moisture
  based on the linear relation between a vegetation index
  and Land Surface Temperature (LST). The Short Wave Infra-red (SWIR) band
  is used as a proxy for LST. See:
  Sadeghi, M., Babaeian, E., Tuller, M., Jones, S.B., 2017.
  The optical trapezoid model:
  A novel approach to remote sensing of soil moisture 
  applied to Sentinel-2 and Landsat-8 observations.
  Remote Sensing of Environment 198, 52–68,
  https://doi.org/10.1016/j.rse.2017.05.041 .
License: GPL (>= 3) + file LICENSE
URL: https://gitlab.com/rsl-bidr/roptram.git
BugReports: https://gitlab.com/rsl-bidr/
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends:
  R (>= 4.1.0)
Imports:
    dplyr,
    ggplot2,
    sf,
    terra,
    tools,
    utils
Suggests:
    geojsonio,
    geojsonlint,
    stats,
    sen2r (> 1.5.0),
    testthat (>= 3.0.0),
    xml2
Config/testthat/edition: 3

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.):

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

• Explain how and why the package falls under these categories (briefly, 1-2 sentences): This package includes acquiring satellite imagery, and preparing spatially explicit soil moisture raster grids.

• Who is the target audience and what are scientific applications of this package? Researchers in ecology, agriculture, sustainability. Agricultural management of grazing lands, reforestration.

• 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

• (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.

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.

Publication options

• [ ] Do you intend for this package to go on CRAN?

• [ ] Do you intend for this package to go on Bioconductor?

• [x] Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

MEE Options

- [ ] 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.

[micha-silver]

I also added an initial NEWS.md

[harryeslick]

Nothing further to add from me 👍🎉

[micha-silver]

@adamhsparks @obrl-soil ping...

[adamhsparks]

@micha-silver, sorry, I'm still waiting on Lauren as well.

[micha-silver]

@adamhsparks No need for apologies. We're all busy. :laughing:

[obrl-soil]

Hey sorry - I've no time to look over this in detail but am happy with the response as documented above.

[adamhsparks]

Thank you, @harryeslick and @obrl-soil!

[adamhsparks]

@ropensci-review-bot approve roptram

[ropensci-review-bot]

Approved! Thanks @micha-silver for submitting and @harryeslick, @obrl-soil for your reviews! :grin:

To-dos:

• [ ] Transfer the repo to rOpenSci's "ropensci" GitHub organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You will need to enable two-factor authentication for your GitHub account. This invitation will expire after one week. If it happens write a comment @ropensci-review-bot invite me to ropensci/<package-name> which will re-send an invitation.
• [ ] After transfer write a comment @ropensci-review-bot finalize transfer of <package-name> where <package-name> is the repo/package name. This will give you admin access back.
• [ ] Fix all links to the GitHub repo to point to the repo under the ropensci organization.
• [ ] Delete your current code of conduct file if you had one since rOpenSci's default one will apply, see https://devguide.ropensci.org/collaboration.html#coc-file
• [ ] If you already had a pkgdown website and are ok relying only on rOpenSci central docs building and branding,
  • deactivate the automatic deployment you might have set up
  • remove styling tweaks from your pkgdown config but keep that config file
  • replace the whole current pkgdown website with a redirecting page
  • replace your package docs URL with https://docs.ropensci.org/package_name
  • In addition, in your DESCRIPTION file, include the docs link in the URL field alongside the link to the GitHub repository, e.g.: URL: https://docs.ropensci.org/foobar, https://github.com/ropensci/foobar
• [ ] Skim the docs of the pkgdown automatic deployment, in particular if your website needs MathJax.
• [ ] Fix any links in badges for CI and coverage to point to the new repository URL.
• [ ] Increment the package version to reflect the changes you made during review. In NEWS.md, add a heading for the new version and one bullet for each user-facing change, and each developer-facing change that you think is relevant.
• [ ] We're starting to roll out software metadata files to all rOpenSci packages via the Codemeta initiative, see https://docs.ropensci.org/codemetar/ for how to include it in your package, after installing the package - should be easy as running codemetar::write_codemeta() in the root of your package.
• [ ] You can add this installation method to your package README install.packages("<package-name>", repos = "https://ropensci.r-universe.dev") thanks to R-universe.

Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them "rev"-type contributors in the Authors@R field (with their consent).

Welcome aboard! We'd love to host a post about your package - either a short introduction to it with an example for a technical audience or a longer post with some narrative about its development or something you learned, and an example of its use for a broader readership. If you are interested, consult the blog guide, and tag @ropensci/blog-editors in your reply. They will get in touch about timing and can answer any questions.

We maintain an online book with our best practice and tips, this chapter starts the 3d section that's about guidance for after onboarding (with advice on releases, package marketing, GitHub grooming); the guide also feature CRAN gotchas. Please tell us what could be improved.

Last but not least, you can volunteer as a reviewer via filling a short form.

[micha-silver]

@ropensci-review-bot finalize transfer of rOPTRAM

[ropensci-review-bot]

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