Package: nicheR 0.1.0

Mariana Castaneda-Guzman

nicheR: Ellipsoid-Based Virtual Niches and Visualization

Provides a robust set of tools for researchers and modelers to construct and define virtual ecological niches using ellipsoid geometries. It enables the identification and extraction of suitable environmental areas, simulation of species occurrence points with various sampling strategies, and visualization of niche boundaries and simulated occurrences in both environmental and geographic space. Inspired by methodologies in 'NicheA' and the 'virtualspecies' R package, 'nicheR' aims to streamline the process of niche conceptualization and data generation for ecological studies. Methodological and theoretical foundations are described in Peterson et al. (2011, ISBN:9780691136882), Etherington et al. (2009) <doi:10.1111/j.1365-2699.2008.02041.x>, Qiao et al. (2015) <doi:10.1111/ecog.01961>, Nunez-Penichet et al. (2021) <doi:10.21425/F5FBG52142>, Cobos and Peterson (2022) <doi:10.17161/bi.v17i.15985>, Alkishe et al. (2022) <doi:10.5194/we-22-33-2022>, and Leroy et al. (2015) <doi:10.1111/ecog.01388>.

Authors:Mariana Castaneda-Guzman [aut, cre], Connor Hughes [aut], Paanwaris Paansri [aut], Marlon E. Cobos [aut]

nicheR_0.1.0.tar.gz
nicheR_0.1.0.zip(r-4.7)nicheR_0.1.0.zip(r-4.6)nicheR_0.1.0.zip(r-4.5)
nicheR_0.1.0.tgz(r-4.6-any)nicheR_0.1.0.tgz(r-4.5-any)
nicheR_0.1.0.tar.gz(r-4.7-any)nicheR_0.1.0.tar.gz(r-4.6-any)
nicheR_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
nicheR/json (API)
NEWS

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

Bug tracker:https://github.com/castanedam/nicher/issues

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

Datasets:
  • back_data - Background environmental data for examples
  • example_sp_1 - Example niche ellipsoid objects for virtual communities
  • example_sp_2 - Example niche ellipsoid objects for virtual communities
  • example_sp_3 - Example niche ellipsoid objects for virtual communities
  • example_sp_4 - Example niche ellipsoid objects for virtual communities
  • ref_ellipse - Reference ellipse for virtual community examples

On CRAN:

Conda:

ecology-modelingniche-modelingsimulationvirtual-speciesvisualization

6.82 score 2 stars 13 scripts 27 exports 2 dependencies

Last updated from:5bc29818a0. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK189
source / vignettesOK230
linux-release-x86_64OK188
macos-release-arm64OK180
macos-oldrel-arm64OK194
windows-develOK182
windows-releaseOK143
windows-oldrelOK152
wasm-releaseOK114

Exports:add_dataadd_data_3dadd_ellipsoidadd_ellipsoid_3dapply_biasbuild_ellipsoidconserved_ellipsescovariance_limitsellipsoid_calculatorellipsoid_volumenested_ellipsesnew_nicheR_communityplot_communityplot_ellipsoidplot_ellipsoid_3dplot_ellipsoid_pairsprepare_biasrandom_ellipsesranges_from_dataranges_from_statsread_nicheRsample_biased_datasample_datasave_nicheRupdate_covarianceupdate_ellipsoid_covariancevirtual_data

Dependencies:Rcppterra

Bias surface

Rendered frombias.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2026-05-29
Started: 2026-04-03

Creating Ellipsoid Based Niches

Rendered fromcreating_ellipsoid_based_niches.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2026-05-29
Started: 2026-04-03

Generate occurrence data

Rendered fromgenerating_occurrence.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2026-05-29
Started: 2026-04-27

Predicting suitability and Mahalanobis distance

Rendered frompredict.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2026-05-22
Started: 2026-04-03

Virtual community simulation

Rendered fromvirtual_communities.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2026-05-22
Started: 2026-03-06

Visualizing ellipsoids in environmental space

Rendered fromplotting_vignette.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2026-04-03
Started: 2026-04-03

Readme and manuals

Help Manual

Help pageTopics
Add occurrence points or other data to an existing E-space plotadd_data
Add data to an existing 3D E-space plotadd_data_3d
Add an ellipsoid boundary to an existing E-space plotadd_ellipsoid
Add an ellipsoid to an existing 3D E-space plotadd_ellipsoid_3d
Apply sampling bias to suitability surfacesapply_bias
Background environmental data for examplesback_data
Build a probabilistic ellipsoidal niche from rangesbuild_ellipsoid
Generate ellipses via multivariate normal biased samplingconserved_ellipses
Calculate safe covariance ranges for positive definitenesscovariance_limits
Calculate n-dimensional ellipsoid metricsellipsoid_calculator
Compute ellipsoid hypervolumeellipsoid_volume
Example niche ellipsoid objects for virtual communitiesexample_ellipsoids example_sp_1 example_sp_2 example_sp_3 example_sp_4
Bioclimatic variables for part of the Americasma_bios
Generate nested ellipses based on a reference ellipsenested_ellipses
Plot a nicheR Community of Ellipsesplot_community
Plot a nicheR ellipsoid in environmental spaceplot_ellipsoid
Plot a nicheR ellipsoid in 3D environmental spaceplot_ellipsoid_3d
Plot all pairwise 2D ellipsoid projectionsplot_ellipsoid_pairs
Predict suitability and Mahalanobis distance from a nicheR ellipsoidpredict predict,nicheR_nicheR_community-method predict,nicheR_nicheR_ellipsoid-method predict.nicheR_community predict.nicheR_ellipsoid
Prepare sampling bias surfacesprepare_bias
Print method for nicheR objectsprint print,nicheR_nicheR_community-method print,nicheR_nicheR_ellipsoid-method print.nicheR_community print.nicheR_ellipsoid
Generate random ellipses constrained by a point cloud and a reference ellipserandom_ellipses
Compute variable ranges from data or statistics with optional expansionranges_from_data ranges_from_stats range_utilities
Read a nicheR object from diskread_nicheR
Reference ellipse for virtual community examplesref_ellipse
Sample occurrence data from a bias-weighted prediction surfacesample_biased_data
Sample occurrence data from a prediction surfacesample_data
Save a nicheR object to disksave_nicheR
Update covariance values and calculate remaining safe limitsupdate_covariance
Update covariances in a nicheR ellipsoid and recompute metricsupdate_ellipsoid_covariance
Generate data based on a ellipsoidal nichevirtual_data