Package: philentropy 0.9.0

Hajk-Georg Drost

philentropy: Similarity and Distance Quantification Between Probability Functions

Computes 46 optimized distance and similarity measures for comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>). These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of this package is to provide a core framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.

Authors:Hajk-Georg Drost [aut, cre], Jakub Nowosad [ctb]

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philentropy.pdf |philentropy.html✨
philentropy/json (API)
NEWS

# Install 'philentropy' in R:
install.packages('philentropy', repos = c('https://drostlab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/drostlab/philentropy/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

distance-measuresdistance-quantificationinformation-theoryjensen-shannon-divergenceparametric-distributionssimilarity-measuresstatistics

12.42 score 132 stars 22 packages 420 scripts 4.0k downloads 6 mentions 60 exports 3 dependencies

Last updated 8 days agofrom:8859a12c0b. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-win-x86_64OKNov 12 2024
R-4.5-linux-x86_64OKNov 12 2024
R-4.4-win-x86_64OKNov 12 2024
R-4.4-mac-x86_64OKNov 12 2024
R-4.4-mac-aarch64OKNov 12 2024
R-4.3-win-x86_64OKNov 12 2024
R-4.3-mac-x86_64OKNov 12 2024
R-4.3-mac-aarch64OKNov 12 2024

Exports:additive_symm_chi_sqavgbhattacharyyabinned.kernel.estcanberraCEchebyshevclark_sqcosine_distczekanowskidice_distdist_many_manydist_one_manydist_one_onedist.diversitydistancedivergence_sqestimate.probabilityeuclideanfidelitygetDistMethodsgJSDgowerHharmonic_mean_disthellingerinner_productintersection_distjaccardJEjeffreysjensen_differencejensen_shannonJSDk_divergenceKLkulczynski_dkullback_leibler_distancekumar_hassebrookkumar_johnsonlin.corlorentzianmanhattanmatusitaMIminkowskimotykaneyman_chi_sqpearson_chi_sqprob_symm_chi_sqruzickasoergelsorensensquared_chi_sqsquared_chordsquared_euclideantanejatanimototopsoewave_hedges

Dependencies:KernSmoothpoormanRcpp

Comparing many probability density functions

Jakub Nowosad

Rendered fromMany_Distances.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2021-08-20
Started: 2021-08-20

Distances

Rendered fromDistances.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2022-11-06
Started: 2015-03-26

Information Theory

Rendered fromInformation_Theory.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2022-11-06
Started: 2015-04-28

Introduction

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2022-11-06
Started: 2015-03-26

Readme and manuals

Help Manual

Help pageTopics
Additive symmetric chi-squared distance (lowlevel function)additive_symm_chi_sq
AVG distance (lowlevel function)avg
Bhattacharyya distance (lowlevel function)bhattacharyya
Kernel Density Estimationbinned.kernel.est
Canberra distance (lowlevel function)canberra
Shannon's Conditional-Entropy H(X | Y)CE
Chebyshev distance (lowlevel function)chebyshev
Clark squared distance (lowlevel function)clark_sq
Cosine distance (lowlevel function)cosine_dist
Czekanowski distance (lowlevel function)czekanowski
Dice distance (lowlevel function)dice_dist
Distances and Similarities between Many Probability Density Functionsdist_many_many
Distances and Similarities between One and Many Probability Density Functionsdist_one_many
Distances and Similarities between Two Probability Density Functionsdist_one_one
Distance Diversity between Probability Density Functionsdist.diversity
Distances and Similarities between Probability Density Functionsdistance
Divergence squared distance (lowlevel function)divergence_sq
Estimate Probability Vectors From Count Vectorsestimate.probability
Euclidean distance (lowlevel function)euclidean
Fidelity distance (lowlevel function)fidelity
Get method names for 'distance'getDistMethods
Generalized Jensen-Shannon DivergencegJSD
Gower distance (lowlevel function)gower
Shannon's Entropy H(X)H
Harmonic mean distance (lowlevel function)harmonic_mean_dist
Hellinger distance (lowlevel function)hellinger
Inner product distance (lowlevel function)inner_product
Intersection distance (lowlevel function)intersection_dist
Jaccard distance (lowlevel function)jaccard
Shannon's Joint-Entropy H(X,Y)JE
Jeffreys distance (lowlevel function)jeffreys
Jensen difference (lowlevel function)jensen_difference
Jensen-Shannon distance (lowlevel function)jensen_shannon
Jensen-Shannon DivergenceJSD
K-Divergence (lowlevel function)k_divergence
Kullback-Leibler DivergenceKL
Kulczynski_d distance (lowlevel function)kulczynski_d
kullback-Leibler distance (lowlevel function)kullback_leibler_distance
Kumar hassebrook distance (lowlevel function)kumar_hassebrook
Kumar-Johnson distance (lowlevel function)kumar_johnson
Linear Correlationlin.cor
Lorentzian distance (lowlevel function)lorentzian
Manhattan distance (lowlevel function)manhattan
Matusita distance (lowlevel function)matusita
Shannon's Mutual Information I(X,Y)MI
Minkowski distance (lowlevel function)minkowski
Motyka distance (lowlevel function)motyka
Neyman chi-squared distance (lowlevel function)neyman_chi_sq
Pearson chi-squared distance (lowlevel function)pearson_chi_sq
Probability symmetric chi-squared distance (lowlevel function)prob_symm_chi_sq
Ruzicka distance (lowlevel function)ruzicka
Soergel distance (lowlevel function)soergel
Sorensen distance (lowlevel function)sorensen
Squared chi-squared distance (lowlevel function)squared_chi_sq
Squared chord distance (lowlevel function)squared_chord
Squared euclidean distance (lowlevel function)squared_euclidean
Taneja difference (lowlevel function)taneja
Tanimoto distance (lowlevel function)tanimoto
Topsoe distance (lowlevel function)topsoe
Wave hedges distance (lowlevel function)wave_hedges