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-any)nicheR_0.1.0.zip(r-4.6-any)nicheR_0.1.0.zip(r-4.5-any)
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✨
DESCRIPTION |NEWS
card.svg |card.png
nicheR/json (API)

# 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

7.04 score 3 stars 17 scripts 292 downloads 27 exports 2 dependencies

Last updated from:1df19f1b26. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK152
source / vignettesOK215
linux-releaseOK171
macos-releaseOK224
macos-oldrelOK237
windows-develOK178
windows-releaseOK155
windows-oldrelOK141
wasm-releaseOK110

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
Summary | Description | Getting ready | Preparing the Bias Layer | Function Arguments | Example: Mixed-Direction Composite Bias | Applying Bias to Predictions | Function Arguments | Example: Comparing Applied Biases | Three-Dimensional Example | Save and export
Rendered frombias.Rmdusingknitr::rmarkdown

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

Creating Ellipsoid Based Niches
Summary | Description | Getting ready | Loading example data | Building and visualizing ellipsoid niches | Background | Creating a basic ellipsoid | Adjusting ellipsoid covariance | Comparing multiple species niches | Save and import | Working in more than 2 dimensions
Rendered fromcreating_ellipsoid_based_niches.Rmdusingknitr::rmarkdown

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

Generate occurrence data
Summary | Description | Getting ready | Part 1: Virtual Data | Basic generation | Visualizing virtual data in 2D | Three-dimensional virtual example | Part 2: Spatially-Explicit Occurrence Data | Basic generation in 2D | Effect of the sampling argument | Effect of the method argument | Effect of the strict argument | Three-Dimensional Example | Part 3: Biased Occurrence Data | Basic biased generation in 2D | Effect of the biased strict argument | Three-Dimensional Biased Example | Save and export
Rendered fromgenerating_occurrence.Rmdusingknitr::rmarkdown

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

Predicting suitability and Mahalanobis distance
Summary | Description | Getting ready | Loading example data | Using predict() | Basic predictions to a data frame | Basic predictions to a SpatRaster | Understanding the output | Mahalanobis distance and the ellipsoid | From distance to suitability: the chi-square and MVN connection | Additional function arguments | All four outputs at once | The role of the confidence level and truncation | Effect of the confidence level on predictions | Visualizing predictions in environmental space | Mahalanobis distance in E-space | Suitability in E-space | Truncated predictions in E-space | Binary suitable vs. unsuitable environments | Visualizing predictions in geographic space | Mahalanobis distance map | Suitability map | Truncated suitability map | Binary potential distribution map | Three-dimensional example | Predicting with virtual data | Two-dimensional virtual data | Three-dimensional virtual data | Save and import
Rendered frompredict.Rmdusingknitr::rmarkdown

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

Virtual community simulation
Summary | Description | Getting ready | Loading example data | Simulating random communities | Effect of background density | Effect of proportion arguments | Simulating nested communities | Effect of proportion argument | Effect of bias argument | Simulating niche conservatism in communities | Predictions for communities | Predict to data frames | Predict to SpatRaster | Truncating predictions | Simple community outcomes | Save and import
Rendered fromvirtual_communities.Rmdusingknitr::rmarkdown

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

Visualizing ellipsoids in environmental space
Summary | Description | Getting ready | Loading example data | plot_ellipsoid() | Ellipsoid boundary only | Background points | Prediction colored by a continuous variable | Truncated predictions and grey outside region | Reversed palette and transparency | Subsampling large datasets | Fixed axis limits for comparing ellipsoids | add_data() and add_ellipsoid() | Layering background, occurrences, and boundary | Coloring occurrence points by a continuous variable | plot_ellipsoid_pairs() | Pairs with background | Pairs with predictions
Rendered fromplotting_vignette.Rmdusingknitr::rmarkdown

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