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hypervolume (version 2.0.12)

High Dimensional Geometry and Set Operations 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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Install

install.packages('hypervolume')

Monthly Downloads

1,801

Version

2.0.12

License

GPL-3

Last Published

December 6th, 2019

Functions in hypervolume (2.0.12)

estimate_bandwidth

Kernel bandwidth estimators for hypervolumes
HypervolumeList-class

Class "HypervolumeList"
hypervolume_distance

Distance between two hypervolumes
expectation_convex

Convex expectation
hypervolume_segment

Segments a hypervolume into multiple separate hypervolumes.
hypervolume_estimate_probability

Estimate probability a given location
hypervolume

Hypervolume construction methods
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_box

Hypervolume construction via hyperbox kernel density estimation
hypervolume_holes

Hole detection
plot.HypervolumeList

Plot a hypervolume or list of hypervolumes
hypervolume_threshold

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

Hypersphere expectation
hypervolume_svm

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

Concatenate hypervolumes
hypervolume_overlap_statistics

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

Inclusion test
hypervolume_redundancy

Redundancy of a point in a hypervolume
hypervolume_save_animated_gif

Saves animated GIF of three-dimensional hypervolume plot.
print.Hypervolume

Print summary of hypervolume
weight_data

Abundance weighting and prior of data for hypervolume input
hypervolume_set

Set operations (intersection / union / unique components)
hypervolume_thin

Reduces the number of random points in a hypervolume
quercus

Data and demo for Quercus (oak) tree distributions
summary.Hypervolume

Summary of hypervolume
hypervolume_variable_importance

Hypervolume variable importance
padded_range

Generates axis-wise range limits with padding
morphSnodgrassHeller

Morphological data for Darwin's finches
hypervolume-package

hypervolume
expectation_maximal

Maximal expectation
get_volume

Extract volume
hypervolume_gaussian

Hypervolume construction via Gaussian kernel density estimation
Hypervolume-class

Class "Hypervolume"
expectation_box

Hyperbox expectation
hypervolume_general_model

Generates hypervolume by sampling from arbitrary model object.
get_centroid

Get centroid of hypervolume or hypervolume list