High Dimensional Geometry, Set Operations, Projection, and Inference Using Kernel Density Estimation, Support Vector Machines, and Convex Hulls

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Documentation for package ‘hypervolume’ version 3.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Code demos. Use demo() to run them.

Help Pages

hypervolume-package	High Dimensional Geometry, Set Operations, Projection, and Inference Using Kernel Density Estimation, Support Vector Machines, and Convex Hulls
acacia_pinus	Data for Acacia and Pinus tree distributions
circles	Circles simulated dataset
copy_param_hypervolume	Generate hypervolumes using pre-existing parameters
estimate_bandwidth	Kernel bandwidth estimators for hypervolumes
expectation_ball	Hypersphere expectation
expectation_box	Hyperbox expectation
expectation_convex	Convex expectation
expectation_maximal	Maximal expectation
find_optimal_occupancy_thin	Find optimal parameters to calculate occupancy
get_centroid	Get centroid of hypervolume or hypervolume list
get_centroid_weighted	Get weighted centroid of hypervolume or hypervolume list
get_occupancy_intersection_bootstrap	Volume of the intersection of a bootstrapped occupancy object
get_occupancy_stats	Stats from occupancy objects
get_occupancy_stats_bootstrap	Stats from occupancy objects
get_occupancy_unshared_bootstrap	Volume of the unshared fraction of a bootstrapped occupancy object
get_occupancy_volume_bootstrap	Extract the volume from occupancy bootstrap objects
get_relative_volume	Extract the relative volume
get_volume	Extract volume
get_volume-method	Extract volume
get_volume.Hypervolume	Extract volume
get_volume.HypervolumeList	Extract volume
hypervolume	Hypervolume construction methods
Hypervolume-class	Class '"Hypervolume"'
HypervolumeList-class	Class '"HypervolumeList"'
hypervolume_box	Hypervolume construction via hyperbox kernel density estimation
hypervolume_distance	Distance between two hypervolumes
hypervolume_estimate_probability	Estimate probability a given location
hypervolume_funnel	Hypervolumes at different sample sizes
hypervolume_gaussian	Hypervolume construction via Gaussian kernel density estimation
hypervolume_general_model	Generates hypervolume by sampling from arbitrary model object.
hypervolume_holes	Hole detection
hypervolume_inclusion_test	Inclusion test
hypervolume_join	Concatenate hypervolumes
hypervolume_n_occupancy	Operations for groups of hypervolumes
hypervolume_n_occupancy_bootstrap	Operations for groups of hypervolumes
hypervolume_n_occupancy_permute	Hypervolumes through permuting labels of n pairwise groups of hypervolumes
hypervolume_n_occupancy_test	Significance of random points occupancy
hypervolume_n_resample	Bootstrap n hypervolumes
hypervolume_overlap_confidence	Confidence intervals for overlap statistics
hypervolume_overlap_statistics	Overlap statistics for set operations (Sorensen, Jaccard, etc.)
hypervolume_overlap_test	Null distribution for overlap statistics
hypervolume_permute	Hypervolumes through permuting data of two hypervolumes
hypervolume_project	Geographical projection of hypervolume for species distribution modeling, using the hypervolume as the environmental niche model.
hypervolume_prune	Removes small hypervolumes from a HypervolumeList
hypervolume_redundancy	Redundancy of a point in a hypervolume
hypervolume_resample	Hypervolume resampling methods
hypervolume_save_animated_gif	Saves animated GIF of three-dimensional hypervolume plot.
hypervolume_segment	Segments a hypervolume into multiple separate hypervolumes.
hypervolume_set	Set operations (intersection / union / unique components)
hypervolume_set_n_intersection	Multi-way set intersection
hypervolume_svm	Hypervolume construction via one-class support vector machine (SVM) learning model
hypervolume_thin	Reduces the number of random points in a hypervolume
hypervolume_threshold	Thresholds hypervolume and calculates volume quantile statistics (empirical cumulative distribution function)
hypervolume_to_data_frame	Convert hypervolumes to 'data.frame'
hypervolume_variable_importance	Hypervolume variable importance
morphSnodgrassHeller	Morphological data for Darwin's finches
occupancy_bootstrap_gof	Goodness of fit metrics for bootstrapped occupancy objects
occupancy_filter	Subset occupancy hypervolumes
occupancy_to_intersection	Get the intersection of an occupancy object
occupancy_to_union	Union of hypervolumes from an occupancy object
occupancy_to_unshared	Unshared fraction from an occupancy object
padded_range	Generates axis-wise range limits with padding
plot.Hypervolume	Plot a hypervolume or list of hypervolumes
plot.HypervolumeList	Plot a hypervolume or list of hypervolumes
print.Hypervolume	Print summary of hypervolume
print.HypervolumeList	Print summary of hypervolume
quercus	Data and demo for Quercus (oak) tree distributions
show.Hypervolume	Summary of hypervolume
show.HypervolumeList	Summary of hypervolume
summary.Hypervolume	Summary of hypervolume
summary.HypervolumeList	Summary of hypervolume
to_hv_list	Read hypervolumes from directory
weight_data	Abundance weighting and prior of data for hypervolume input