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

## Documentation for package ‘hypervolume’ version 3.1.6

- 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_distance_point | Distance from a point to the margin of a hypervolume.
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_set_n_union | Multi-way set union
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