Ellipsoid-Based Virtual Niches and Visualization

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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