# Ellipsoid-Based Virtual Niches and Visualization

## Documentation for package ‘nicheR’ version 0.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

add_data | Add occurrence points or other data to an existing E-space plot
add_data_3d | Add data to an existing 3D E-space plot
add_ellipsoid | Add an ellipsoid boundary to an existing E-space plot
add_ellipsoid_3d | Add an ellipsoid to an existing 3D E-space plot
apply_bias | Apply sampling bias to suitability surfaces
back_data | Background environmental data for examples
build_ellipsoid | Build a probabilistic ellipsoidal niche from ranges
conserved_ellipses | Generate ellipses via multivariate normal biased sampling
covariance_limits | Calculate safe covariance ranges for positive definiteness
ellipsoid_calculator | Calculate n-dimensional ellipsoid metrics
ellipsoid_volume | Compute ellipsoid hypervolume
example_ellipsoids | Example niche ellipsoid objects for virtual communities
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
ma_bios | Bioclimatic variables for part of the Americas
nested_ellipses | Generate nested ellipses based on a reference ellipse
plot_community | Plot a nicheR Community of Ellipses
plot_ellipsoid | Plot a nicheR ellipsoid in environmental space
plot_ellipsoid_3d | Plot a nicheR ellipsoid in 3D environmental space
plot_ellipsoid_pairs | Plot all pairwise 2D ellipsoid projections
predict | Predict suitability and Mahalanobis distance from a nicheR ellipsoid
predict-method | Predict suitability and Mahalanobis distance from a nicheR ellipsoid
predict.nicheR_community | Predict suitability and Mahalanobis distance from a nicheR ellipsoid
predict.nicheR_ellipsoid | Predict suitability and Mahalanobis distance from a nicheR ellipsoid
prepare_bias | Prepare sampling bias surfaces
print | Print method for nicheR objects
print-method | Print method for nicheR objects
print.nicheR_community | Print method for nicheR objects
print.nicheR_ellipsoid | Print method for nicheR objects
random_ellipses | Generate random ellipses constrained by a point cloud and a reference ellipse
ranges_from_data | Compute variable ranges from data or statistics with optional expansion
ranges_from_stats | Compute variable ranges from data or statistics with optional expansion
range_utilities | Compute variable ranges from data or statistics with optional expansion
read_nicheR | Read a nicheR object from disk
ref_ellipse | Reference ellipse for virtual community examples
sample_biased_data | Sample occurrence data from a bias-weighted prediction surface
sample_data | Sample occurrence data from a prediction surface
save_nicheR | Save a nicheR object to disk
update_covariance | Update covariance values and calculate remaining safe limits
update_ellipsoid_covariance | Update covariances in a nicheR ellipsoid and recompute metrics
virtual_data | Generate data based on a ellipsoidal niche