rsi: Efficiently Retrieve and Process Satellite Imagery

[mikemahoney218]

Date accepted: 2024-10-01 Submitting Author Name: Mike Mahoney Submitting Author Github Handle: !--author1-->@mikemahoney218<!--end-author1-- Repository: https://github.com/Permian-Global-Research/rsi/ Version submitted: Submission type: Standard Editor: !--editor-->@jhollist<!--end-editor-- Reviewers: @mdsumner, @OldLipe

Archive: TBD Version accepted: TBD Language: en

---

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

Package: rsi
Title: Efficiently Retrieve and Process Satellite Imagery
Version: 0.2.0.9000
Authors@R: c(
    person("Michael", "Mahoney", , "mike.mahoney.218@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-2402-304X")),
    person("Permian Global", role = c("cph", "fnd"))
  )
Description: Downloads spatial data from spatiotemporal asset catalogs 
    ('STAC'), computes standard spectral indices from the Awesome Spectral 
    Indices project (Montero et al. (2023) <doi:10.1038/s41597-023-02096-0>) 
    against raster data, and glues the outputs together into predictor bricks. 
    Methods focus on interoperability with the broader spatial ecosystem; 
    function arguments and outputs use classes from 'sf' and 'terra', and data 
    downloading functions support complex 'CQL2' queries using 'rstac'.
License: Apache License (>= 2)
Depends: 
    R (>= 4.0)
Imports: 
    future.apply,
    glue,
    httr,
    jsonlite,
    lifecycle,
    proceduralnames,
    rlang,
    rstac,
    sf,
    terra,
    tibble
Suggests: 
    curl,
    knitr,
    progressr,
    rmarkdown,
    testthat (>= 3.0.0),
    withr
Config/testthat/edition: 3
Config/testthat/parallel: true
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.0
URL: https://github.com/Permian-Global-Research/rsi, https://permian-global-research.github.io/rsi/
BugReports: https://github.com/Permian-Global-Research/rsi/issues
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.):

  • [x] data retrieval
  • [ ] data extraction
  • [x] 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 supports (spatial) data retrieval from APIs implementing the OGC STAC API standard, processing the downloaded data (including automated masking, compositing and rescaling) computing spectral indices from those data, and wrangling the outputs into formats useful for modeling and visualization.

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

Anyone with a need to download and process spatial data, particularly remote sensing data, particularly satellite-based earth observation rasters. We've used rsi to automate the entire data preparation process of forest carbon and structure models (not yet published), but the package is broadly useful to anyone working in Earth surface modeling.

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

Yes:

• rstac is a fantastic package for querying and downloading data from STAC APIs. rstac does not implement the other elements of rsi (compositing, masking, rescaling, computing spectral indices, wrangling the outputs), and rsi provides a "higher level" method for downloading data from STAC APIs (powered by lower-level rstac functions); rsi also uses a faster download method.
• gdalcubes and sits both provide higher-level approaches for accessing data from STAC APIs, organized around data cube models. There is more substantial overlap between these packages and rsi. The biggest difference is that rsi, very intentionally, does not provide a new data model. To quote the vignette:

A core difference between rsi and these packages is that rsi does not have a data model: rsi is focused entirely on finding the bits of data you want from remote endpoints, and getting those bits on your local machine for you to process with your normal spatial data tooling. There are no new classes in rsi (other than the band mapping objects), and the outputs of functions are local rasters. This is an approach that fits better in my head than the more abstract delayed computations in some other packages; at the same time, it’s possible that this approach can be less efficient, downloading more data at finer resolutions than is actually needed for a given task.

There are a few minor things that I think rsi does better than other approaches (we sign items right before each one is downloaded, for instance, whereas some other packages sign items before starting to download the entire set, meaning the signature can expire causing large downloads to fail), but this difference I think is mostly a matter of taste. I'm very familiar with local GDAL, terra, and sf, and so rsi tries to get users back to working with local GDAL, terra, and sf as fast as possible.

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

NA

• 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.

NA

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

~I have never successfully gotten the CI item to be a check, and I have no idea why. I'm using the standard usethis functions to structure my CI, for what it's worth!~ Apparently this is a local-only issue.

I addressed failing covr in https://github.com/ropensci/software-review/issues/636#issuecomment-2028086514

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Confirm each of the following by checking the box.

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

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Code of conduct

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[ropensci-review-bot]

Logged review for mdsumner (hours: 7)

[jhollist]

@ropensci-review-bot submit review https://github.com/ropensci/software-review/issues/636#issuecomment-2218720373 time 5

[ropensci-review-bot]

Logged review for OldLipe (hours: 5)

[jhollist]

@OldLipe thanks for the email. I am recording your response and acceptance of @mikemahoney218 revisions here. No need for you to do it as well.

And I think we are all set to go. Thank you all for your efforts on this! Will work on moving this along later this AM.

[jhollist]

@ropensci-review-bot approve rsi

[ropensci-review-bot]

Approved! Thanks @mikemahoney218 for submitting and @mdsumner, @OldLipe for your reviews! :grin:

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[mikemahoney218]

Thank you so much @jhollist , @mdsumner , and @OldLipe ! This was a fantastic process (as usual with rOpenSci!).

@jhollist -- I mentioned at the start of the review, but I'm not able to transfer this repo to the rOpenSci namespace. I'm not sure which boxes on the checklist still apply -- and I've got the faintest memory that the package needs to get added to a registry somewhere, but I forget where that is. Does this make sense?

[maelle]

:wave: here! https://github.com/ropensci/roregistry/commit/e5d2c0271fd2e66b7d0b42b098b6ac9995992238 should be it but I'll be checking the package and registry building to be sure. :smile_cat:

[mpadge]

Registry now updated as expected. All good!

[maelle]

https://docs.ropensci.org/rsi/ :tada:

[jhollist]

@mpadge and @maelle Is there anything special that @mikemahoney218 needs to do for this since he won't be transferring the package to the rOpenSci org? Looks like things have moved along fine without that.