Package: bean 0.2.0
Paanwaris Paansri
bean: Data Thinning of Species Occurrences in Environmental Space
A suite of tools to mitigate sampling bias in species occurrence records by thinning data in the environmental space (E-space). This process can improve the accuracy and precision of species distribution models (SDM, also known as ecological niche models, ENM). The package offers a data-driven protocol to determine thinning parameters using kernel-density bandwidth selection. Two thinning methods are provided (stochastic and deterministic) to reduce over-sampled environmental conditions and down-weight outlier observations. The name 'bean' reflects the core principle of the method: each 'pod' (a grid cell in E-space) is allowed to contain only a limited number of 'beans' (occurrence points). See Silverman (1986, ISBN:978-0-412-24620-3) and Rousseeuw and Leroy (2003, ISBN:978-0-471-48855-2) for the underlying statistical methods.
Authors:
bean_0.2.0.tar.gz
bean_0.2.0.tar.gz(r-4.7-any)bean_0.2.0.tar.gz(r-4.6-any)
bean_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
bean/json (API)
NEWS
| # Install 'bean' in R: |
| install.packages('bean', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/paanwaris/bean/issues
Pkgdown/docs site:https://paanwaris.github.io
- occ_data_raw - Raw Rusa unicolor occurrence data
- origin_dat_prepared - Cleaned and scaled occurrence data
- origin_ellipse - Fitted niche ellipsoid for Rusa unicolor
- thinned_deterministic - Deterministically thinned environmental data
- thinned_stochastic - Stochastically thinned environmental data
Last updated from:1bf9b7e66b. Checks:4 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 169 | ||
| source / vignettes | OK | 199 | ||
| linux-release-x86_64 | OK | 185 | ||
| wasm-release | OK | 132 |
Exports:find_env_resolutionfit_ellipsoidplot_beanprepare_beanthin_env_centerthin_env_nd
Data preparation
Rendered fromdata-preparation.Rmdusingknitr::rmarkdownon May 30 2026.Last update: 2026-05-30
Started: 2026-05-30
Environmental thinning
Rendered fromenvironmental-thinning.Rmdusingknitr::rmarkdownon May 30 2026.Last update: 2026-05-30
Started: 2026-05-30
Niche modeling
Rendered fromniche-modeling.Rmdusingknitr::rmarkdownon May 30 2026.Last update: 2026-05-30
Started: 2026-05-30
bean: an overview
Rendered frombean-overview.Rmdusingknitr::rmarkdownon May 30 2026.Last update: 2026-05-30
Started: 2026-05-30
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Find an objective environmental grid resolution | find_env_resolution |
| Fit an environmental niche ellipsoid | fit_ellipsoid |
| Raw Rusa unicolor occurrence data | occ_data_raw |
| Cleaned and scaled occurrence data | origin_dat_prepared |
| Fitted niche ellipsoid for Rusa unicolor | origin_ellipse |
| Visualize n-dimensional environmental thinning results | plot_bean |
| Predict suitability and Mahalanobis distance from a bean ellipsoid | predict.bean_ellipsoid |
| Prepare data for environmental thinning | prepare_bean |
| Deterministic centroid | thin_env_center |
| Thin occurrence data in n-dimensional environmental space | thin_env_nd |
| Deterministically thinned environmental data | thinned_deterministic |
| Stochastically thinned environmental data | thinned_stochastic |