Package: hypervolume 3.1.4

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

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.

Authors:Benjamin Blonder, with contributions from Cecina Babich Morrow, Stuart Brown, Gregoire Butruille, Daniel Chen, Alex Laini, and David J. Harris

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hypervolume.pdf |hypervolume.html✨
hypervolume/json (API)

# Install 'hypervolume' in R:

install.packages('hypervolume', repos = c('https://bblonder.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bblonder/hypervolume/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

acacia_pinus - Data for Acacia and Pinus tree distributions
circles - Circles simulated dataset
morphSnodgrassHeller - Morphological data for Darwin's finches
quercus - Data and demo for Quercus (oak) tree distributions

On CRAN:

8.44 score 21 stars 7 packages 193 scripts 1.6k downloads 64 exports 104 dependencies

Last updated 7 months agofrom:593e40613c. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 29 2024
R-4.5-win-x86_64	NOTE	Oct 29 2024
R-4.5-linux-x86_64	NOTE	Oct 29 2024
R-4.4-win-x86_64	NOTE	Oct 29 2024
R-4.4-mac-x86_64	NOTE	Oct 29 2024
R-4.4-mac-aarch64	NOTE	Oct 29 2024
R-4.3-win-x86_64	NOTE	Oct 29 2024
R-4.3-mac-x86_64	NOTE	Oct 29 2024
R-4.3-mac-aarch64	NOTE	Oct 29 2024

Exports:copy_param_hypervolume estimate_bandwidth expectation_ball expectation_box expectation_convex expectation_maximal find_optimal_occupancy_thin get_centroid get_centroid_weighted get_occupancy_intersection_bootstrap get_occupancy_stats get_occupancy_stats_bootstrap get_occupancy_unshared_bootstrap get_occupancy_volume_bootstrap get_relative_volume get_volume hypervolume hypervolume_box hypervolume_distance hypervolume_estimate_probability hypervolume_funnel hypervolume_gaussian hypervolume_general_model hypervolume_holes hypervolume_inclusion_test hypervolume_join hypervolume_n_occupancy hypervolume_n_occupancy_bootstrap hypervolume_n_occupancy_permute hypervolume_n_occupancy_test hypervolume_n_resample hypervolume_overlap_confidence hypervolume_overlap_statistics hypervolume_overlap_test hypervolume_permute hypervolume_project hypervolume_prune hypervolume_redundancy hypervolume_resample hypervolume_save_animated_gif hypervolume_segment hypervolume_set hypervolume_set_n_intersection hypervolume_svm hypervolume_thin hypervolume_threshold hypervolume_to_data_frame hypervolume_variable_importance occupancy_bootstrap_gof occupancy_filter occupancy_to_intersection occupancy_to_union occupancy_to_unshared padded_range plot.Hypervolume plot.HypervolumeList print.Hypervolume print.HypervolumeList show.Hypervolume show.HypervolumeList summary.Hypervolume summary.HypervolumeList to_hv_list weight_data

Dependencies:abind caret class cli clock codetools colorspace cpp11 crayon data.table diagram digest doParallel dplyr e1071 fansi farver fastcluster FNN foreach future future.apply generics geometry ggplot2 globals glue gower gtable hardhat hitandrun hms ipred isoband iterators kernlab KernSmooth ks labeling lattice lava lifecycle linprog listenv lpSolve lubridate magic magrittr maps MASS Matrix mclust mgcv ModelMetrics multicool munsell mvtnorm nlme nnet numDeriv palmerpenguins parallelly pbapply pdist pillar pkgconfig plyr pracma prettyunits pROC prodlim progress progressr proxy purrr R6 raster rcdd RColorBrewer Rcpp RcppArmadillo RcppProgress recipes reshape2 rlang rpart scales shape sp SQUAREM stringi stringr survival terra tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite withr

Hypervolume-Resampling

Rendered fromHypervolume-Resampling.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2023-09-14
Started: 2020-11-14

Introduction to occupancy

Rendered fromoccupancy.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2023-08-09
Started: 2023-08-09

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

Package: hypervolume 3.1.4

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

Hypervolume-Resampling

Introduction to occupancy

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)