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'))

Peer review:

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

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

64 exports 21 stars 3.66 score 104 dependencies 6 dependents 9 mentions 159 scripts 1.8k downloads

Last updated 5 months agofrom:593e40613c. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 30 2024
R-4.5-win-x86_64NOTEAug 30 2024
R-4.5-linux-x86_64NOTEAug 30 2024
R-4.4-win-x86_64NOTEAug 30 2024
R-4.4-mac-x86_64NOTEAug 30 2024
R-4.4-mac-aarch64NOTEAug 30 2024
R-4.3-win-x86_64NOTEAug 30 2024
R-4.3-mac-x86_64NOTEAug 30 2024
R-4.3-mac-aarch64NOTEAug 30 2024

Exports:copy_param_hypervolumeestimate_bandwidthexpectation_ballexpectation_boxexpectation_convexexpectation_maximalfind_optimal_occupancy_thinget_centroidget_centroid_weightedget_occupancy_intersection_bootstrapget_occupancy_statsget_occupancy_stats_bootstrapget_occupancy_unshared_bootstrapget_occupancy_volume_bootstrapget_relative_volumeget_volumehypervolumehypervolume_boxhypervolume_distancehypervolume_estimate_probabilityhypervolume_funnelhypervolume_gaussianhypervolume_general_modelhypervolume_holeshypervolume_inclusion_testhypervolume_joinhypervolume_n_occupancyhypervolume_n_occupancy_bootstraphypervolume_n_occupancy_permutehypervolume_n_occupancy_testhypervolume_n_resamplehypervolume_overlap_confidencehypervolume_overlap_statisticshypervolume_overlap_testhypervolume_permutehypervolume_projecthypervolume_prunehypervolume_redundancyhypervolume_resamplehypervolume_save_animated_gifhypervolume_segmenthypervolume_sethypervolume_set_n_intersectionhypervolume_svmhypervolume_thinhypervolume_thresholdhypervolume_to_data_framehypervolume_variable_importanceoccupancy_bootstrap_gofoccupancy_filteroccupancy_to_intersectionoccupancy_to_unionoccupancy_to_unsharedpadded_rangeplot.Hypervolumeplot.HypervolumeListprint.Hypervolumeprint.HypervolumeListshow.Hypervolumeshow.HypervolumeListsummary.Hypervolumesummary.HypervolumeListto_hv_listweight_data

Dependencies:abindcaretclasscliclockcodetoolscolorspacecpp11crayondata.tablediagramdigestdoParalleldplyre1071fansifarverfastclusterFNNforeachfuturefuture.applygenericsgeometryggplot2globalsgluegowergtablehardhathitandrunhmsipredisobanditeratorskernlabKernSmoothkslabelinglatticelavalifecyclelinproglistenvlpSolvelubridatemagicmagrittrmapsMASSMatrixmclustmgcvModelMetricsmulticoolmunsellmvtnormnlmennetnumDerivpalmerpenguinsparallellypbapplypdistpillarpkgconfigplyrpracmaprettyunitspROCprodlimprogressprogressrproxypurrrR6rasterrcddRColorBrewerRcppRcppArmadilloRcppProgressrecipesreshape2rlangrpartscalesshapespSQUAREMstringistringrsurvivalterratibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr

Hypervolume-Resampling

Rendered fromHypervolume-Resampling.Rmdusingknitr::rmarkdownon Aug 30 2024.

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

Introduction to occupancy

Rendered fromoccupancy.Rmdusingknitr::rmarkdownon Aug 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
High Dimensional Geometry, Set Operations, Projection, and Inference Using Kernel Density Estimation, Support Vector Machines, and Convex Hullshypervolume-package
Data for Acacia and Pinus tree distributionsacacia_pinus
Circles simulated datasetcircles
Generate hypervolumes using pre-existing parameterscopy_param_hypervolume
Kernel bandwidth estimators for hypervolumesestimate_bandwidth
Hypersphere expectationexpectation_ball
Hyperbox expectationexpectation_box
Convex expectationexpectation_convex
Maximal expectationexpectation_maximal
Find optimal parameters to calculate occupancyfind_optimal_occupancy_thin
Get centroid of hypervolume or hypervolume listget_centroid
Get weighted centroid of hypervolume or hypervolume listget_centroid_weighted
Volume of the intersection of a bootstrapped occupancy objectget_occupancy_intersection_bootstrap
Stats from occupancy objectsget_occupancy_stats get_occupancy_stats_bootstrap
Volume of the unshared fraction of a bootstrapped occupancy objectget_occupancy_unshared_bootstrap
Extract the volume from occupancy bootstrap objectsget_occupancy_volume_bootstrap
Extract the relative volumeget_relative_volume
Extract volumeget_volume get_volume,Hypervolume-method get_volume,HypervolumeList-method get_volume.Hypervolume get_volume.HypervolumeList
Hypervolume construction methodshypervolume
Hypervolume construction via hyperbox kernel density estimationhypervolume_box
Distance between two hypervolumeshypervolume_distance
Estimate probability a given locationhypervolume_estimate_probability
Hypervolumes at different sample sizeshypervolume_funnel
Hypervolume construction via Gaussian kernel density estimationhypervolume_gaussian
Generates hypervolume by sampling from arbitrary model object.hypervolume_general_model
Hole detectionhypervolume_holes
Inclusion testhypervolume_inclusion_test
Concatenate hypervolumeshypervolume_join
Operations for groups of hypervolumeshypervolume_n_occupancy hypervolume_n_occupancy_bootstrap
Hypervolumes through permuting labels of n pairwise groups of hypervolumeshypervolume_n_occupancy_permute
Significance of random points occupancyhypervolume_n_occupancy_test
Bootstrap n hypervolumeshypervolume_n_resample
Confidence intervals for overlap statisticshypervolume_overlap_confidence
Overlap statistics for set operations (Sorensen, Jaccard, etc.)hypervolume_overlap_statistics
Null distribution for overlap statisticshypervolume_overlap_test
Hypervolumes through permuting data of two hypervolumeshypervolume_permute
Geographical projection of hypervolume for species distribution modeling, using the hypervolume as the environmental niche model.hypervolume_project
Removes small hypervolumes from a HypervolumeListhypervolume_prune
Redundancy of a point in a hypervolumehypervolume_redundancy
Hypervolume resampling methodshypervolume_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 intersectionhypervolume_set_n_intersection
Hypervolume construction via one-class support vector machine (SVM) learning modelhypervolume_svm
Reduces the number of random points in a hypervolumehypervolume_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 importancehypervolume_variable_importance
Class '"Hypervolume"'Hypervolume-class
Class '"HypervolumeList"'HypervolumeList-class
Morphological data for Darwin's finchesmorphSnodgrassHeller
Goodness of fit metrics for bootstrapped occupancy objectsoccupancy_bootstrap_gof
Subset occupancy hypervolumesoccupancy_filter
Get the intersection of an occupancy objectoccupancy_to_intersection
Union of hypervolumes from an occupancy objectoccupancy_to_union
Unshared fraction from an occupancy objectoccupancy_to_unshared
Generates axis-wise range limits with paddingpadded_range
Plot a hypervolume or list of hypervolumesplot.Hypervolume plot.HypervolumeList
Print summary of hypervolumeprint.Hypervolume print.HypervolumeList
Data and demo for Quercus (oak) tree distributionsquercus
Summary of hypervolumeshow.Hypervolume show.HypervolumeList summary.Hypervolume summary.HypervolumeList
Read hypervolumes from directoryto_hv_list
Abundance weighting and prior of data for hypervolume inputweight_data