`chopin`: Computation for Climate and Health research On Parallelized INfrastructure

[sigmafelix]

Submitting Author Name: Insang Song Submitting Author Github Handle: !--author1-->@sigmafelix<!--end-author1-- Other Package Authors Github handles: (comma separated, delete if none) !--author-others-->@kyle-messier<!--end-author-others-- Repository: https://github.com/NIEHS/chopin Version submitted: 0.6.2.20240423 Submission type: Standard Editor: !--editor-->@beatrizmilz<!--end-editor-- Reviewers: @robitalec, @Aariq

Archive: TBD Version accepted: TBD Language: en

---

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

Package: chopin
Title: CHOPIN: Computation for Climate and Health research On Parallelized INfrastructure
Version: 0.6.2.20240423
Authors@R: c(
    person("Insang", "Song", , "geoissong@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-8732-3256")),
    person("Kyle", "Messier", role = c("aut", "ctb"),
           comment = c(ORCID = "0000-0001-9508-9623"))
  )
Description: It enables users with basic understanding on geospatial data
    and sf and terra functions to parallelize geospatial operations for
    geospatial exposure assessment modeling and covariate computation.
    Parallelization is done by dividing large datasets into sub-regions
    with regular grids and data's own hierarchy. A computation over the
    large number of raster files can be parallelized with a chopin
    function as well.
License: MIT + file LICENSE
URL: https://github.com/NIEHS/chopin
BugReports: https://github.com/NIEHS/chopin/issues
Depends: 
    R (>= 4.1)
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports: 
    anticlust,
    dplyr (>= 1.1.0),
    exactextractr (>= 0.8.2),
    future.apply,
    igraph,
    methods,
    rlang (>= 0.4.9),
    sf (>= 1.0-10),
    stars (>= 0.6-0),
    terra (>= 1.7-18)
Suggests: 
    callr,
    covr,
    DiagrammeR,
    doFuture,
    doParallel,
    future,
    future.batchtools,
    future.callr,
    knitr,
    rmarkdown,
    spatstat.random,
    testthat (>= 3.0.0),
    units,
    withr
VignetteBuilder: knitr
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.):

  • [ ] data retrieval
  • [ ] 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): : chopin supports parallel processing for functions in popular spatial data manipulation packages sf and terra on a high-level parallelization framework future. This feature fits to the geospatial data category.

• Who is the target audience and what are scientific applications of this package? : Our first target audience group is spatial epidemiologists and health geographers who want to calculating spatial covariates from spatial and spatiotemporal datasets including climate, transportation, demographics, topography, hydrography, and others. We expect that users are cognizant of basic geographic information system/science. The wider audience could take advantage of the flexibility of this package for expediting spatial operations.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category? : A selection of functions in terra (e.g., *app and predict) supports internal parallelization, where a single dataset is accepted. To the best of our knowledge, no packaged solution exists for parallelization of spatial operations where two datasets are involved. sprawl (GitHub-only; not maintained) partially overlaps this package's functionality in that it includes convenience functions connecting multiple basic spatial operations. Besides the R functions, a handful of teaching or demonstration materials briefly covered parallelization of spatial data applications ([1], [2], [3]).

• (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research? : Not applicable

• 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. : Presubmission inquiry of the previous version of this package -- #630 commented by @ldecicco-USGS

• Explain reasons for any pkgcheck items which your package is unable to pass. : Coverage rate (99%) and installation size (25.7 MB; of which data (2.0 MB) and extdata (23.1 MB) exceeded recommended sizes) resulted in notes.

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

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

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

• [ ] 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.

Thank you very much for your consideration!

[beatrizmilz]

Approximately 8 hours @beatrizmilz

Thank you all!

Wow @robitalec ! Thank you so much for your review! Thank you both! @robitalec @Aariq