Package: divvy 1.0.1.9000

divvy: Spatial Subsampling of Biodiversity Occurrence Data

Divide taxonomic occurrence data into geographic regions of fair comparison, with three customisable methods to standardise area and extent. Calculate common biodiversity and range-size metrics on subsampled data. Background theory and practical considerations for the methods are described in Antell and others (2024) <doi:10.1017/pab.2023.36>.

Authors:Gawain Antell [aut, cre, cph]

divvy_1.0.1.9000.tar.gz
divvy_1.0.1.9000.zip(r-4.7)divvy_1.0.1.9000.zip(r-4.6)divvy_1.0.1.9000.zip(r-4.5)
divvy_1.0.1.9000.tgz(r-4.6-any)divvy_1.0.1.9000.tgz(r-4.5-any)
divvy_1.0.1.9000.tar.gz(r-4.7-any)divvy_1.0.1.9000.tar.gz(r-4.6-any)
divvy_1.0.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
divvy/json (API)

# Install 'divvy' in R:
install.packages('divvy', repos = c('https://gawainantell.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gawainantell/divvy/issues

Pkgdown/docs site:https://gawainantell.github.io

Datasets:
  • bivalves - Paleobiology Database occurrences of Pliocene fossil bivalves
  • collSilur - Paleobiology Database collections of Silurian marine fossils
  • occSilur - Paleobiology Database occurrences of Silurian fossil brachiopods

On CRAN:

Conda:

4.43 score 27 scripts 521 downloads 7 exports 45 dependencies

Last updated from:1459231b3c. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK184
source / vignettesOK260
linux-release-x86_64OK189
macos-release-arm64OK201
macos-oldrel-arm64OK182
windows-develOK206
windows-releaseOK190
windows-oldrelOK161
wasm-releaseOK130

Exports:banditclassRastclustrcookiesrangeSizesdSumryuniqify

Dependencies:classclassIntcliclustercpp11DBIe1071farverggplot2gluegtableiNEXTisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvnlmepermuteplyrproxyR6rbibutilsRColorBrewerRcppRdpackreshape2rlangs2S7scalessfstringistringrterraunitsvctrsveganviridisLitewithrwk

Environmental and geographic standardisation case study
Goals and limitations of the vignette | Background on geographic ranges between marine environments | Prepare taxonomic occurrence data | Categorise environment associated with occurrences | Assign per-taxon environmental preferences | Spatially subsample each environment | Summed Common Occurrence Rate between environments | Contrast results from non-subsampled data | Average taxon range size between environments | References
Rendered fromhabitat-rangesize-case-study.Rmdusingknitr::rmarkdown

Last update: 2023-10-24
Started: 2023-07-14

Spatial subsampling tutorial
Contents | Why to subsample spatially | Prepare Paleobiology Database records | Subsampling examples | Circular subsampling | PBDB collections, references, and duplicate entries | Nearest-neighbour subsampling | Latitudinal subsampling | Analysis on subsampled data | References
Rendered fromsubsampling-vignette.Rmdusingknitr::rmarkdown

Last update: 2023-10-23
Started: 2022-04-21