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hypervolume (version 3.1.3)

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

Description

Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling.

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Version

Install

install.packages('hypervolume')

Monthly Downloads

2,147

Version

3.1.3

License

GPL-3

Maintainer

Benjamin Blonder

Last Published

September 14th, 2023

Functions in hypervolume (3.1.3)

get_occupancy_intersection_bootstrap

Volume of the intersection of a bootstrapped occupancy object
get_occupancy_unshared_bootstrap

Volume of the unshared fraction of a bootstrapped occupancy object
hypervolume_inclusion_test

Inclusion test
hypervolume_box

Hypervolume construction via hyperbox kernel density estimation
hypervolume

Hypervolume construction methods
hypervolume_join

Concatenate hypervolumes
hypervolume_estimate_probability

Estimate probability a given location
hypervolume_distance

Distance between two hypervolumes
hypervolume_funnel

Hypervolumes at different sample sizes
hypervolume_prune

Removes small hypervolumes from a HypervolumeList
hypervolume_project

Geographical projection of hypervolume for species distribution modeling, using the hypervolume as the environmental niche model.
hypervolume_gaussian

Hypervolume construction via Gaussian kernel density estimation
hypervolume_holes

Hole detection
hypervolume_n_occupancy

Operations for groups of hypervolumes
hypervolume_n_occupancy_permute

Hypervolumes through permuting labels of n pairwise groups of hypervolumes
hypervolume_general_model

Generates hypervolume by sampling from arbitrary model object.
hypervolume_n_resample

Bootstrap n hypervolumes
hypervolume_permute

Hypervolumes through permuting data of two hypervolumes
hypervolume_n_occupancy_test

Significance of random points occupancy
hypervolume_overlap_test

Null distribution for overlap statistics
hypervolume_overlap_statistics

Overlap statistics for set operations (Sorensen, Jaccard, etc.)
hypervolume_overlap_confidence

Confidence intervals for overlap statistics
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_save_animated_gif

Saves animated GIF of three-dimensional hypervolume plot.
hypervolume_resample

Hypervolume resampling methods
hypervolume_threshold

Thresholds hypervolume and calculates volume quantile statistics (empirical cumulative distribution function)
hypervolume_redundancy

Redundancy of a point in a hypervolume
hypervolume_to_data_frame

Convert hypervolumes to data.frame
hypervolume_thin

Reduces the number of random points in a hypervolume
hypervolume_svm

Hypervolume construction via one-class support vector machine (SVM) learning model
occupancy_to_unshared

Unshared fraction from an occupancy object
print.Hypervolume

Print summary of hypervolume
padded_range

Generates axis-wise range limits with padding
plot.HypervolumeList

Plot a hypervolume or list of hypervolumes
occupancy_filter

Subset occupancy hypervolumes
occupancy_bootstrap_gof

Goodness of fit metrics for bootstrapped occupancy objects
occupancy_to_intersection

Get the intersection of an occupancy object
occupancy_to_union

Union of hypervolumes from an occupancy object
weight_data

Abundance weighting and prior of data for hypervolume input
to_hv_list

Read hypervolumes from directory
summary.Hypervolume

Summary of hypervolume
morphSnodgrassHeller

Morphological data for Darwin's finches
quercus

Data and demo for Quercus (oak) tree distributions
hypervolume_variable_importance

Hypervolume variable importance
Hypervolume-class

Class "Hypervolume"
copy_param_hypervolume

Generate hypervolumes using pre-existing parameters
HypervolumeList-class

Class "HypervolumeList"
expectation_maximal

Maximal expectation
circles

Circles simulated dataset
estimate_bandwidth

Kernel bandwidth estimators for hypervolumes
acacia_pinus

Data for Acacia and Pinus tree distributions
expectation_ball

Hypersphere expectation
expectation_convex

Convex expectation
expectation_box

Hyperbox expectation
get_volume

Extract volume
hypervolume-package

tools:::Rd_package_title("hypervolume")
find_optimal_occupancy_thin

Find optimal parameters to calculate occupancy
get_relative_volume

Extract the relative volume
get_occupancy_volume_bootstrap

Extract the volume from occupancy bootstrap objects
get_centroid

Get centroid of hypervolume or hypervolume list
get_centroid_weighted

Get weighted centroid of hypervolume or hypervolume list
get_occupancy_stats

Stats from occupancy objects