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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.

Functions (57)

Shannon's Conditional-Entropy H(X | Y)

Shannon's Entropy H(X)

Shannon's Joint-Entropy H(X,Y)

JSD

Jensen-Shannon Divergence

Kullback-Leibler Divergence

Shannon's Mutual Information I(X,Y)

additive_symm_chi_sq

Additive symmetric chi-squared distance (lowlevel function)

avg

AVG distance (lowlevel function)

bhattacharyya

Bhattacharyya distance (lowlevel function)

binned.kernel.est

Kernel Density Estimation

canberra

Canberra distance (lowlevel function)

chebyshev

Chebyshev distance (lowlevel function)

clark_sq

Clark squared distance (lowlevel function)

cosine_dist

Cosine distance (lowlevel function)

czekanowski

Czekanowski distance (lowlevel function)

dice_dist

Dice distance (lowlevel function)

dist.diversity

Distance Diversity between Probability Density Functions

distance

Distances between Probability Density Functions

divergence_sq

Divergence squared distance (lowlevel function)

estimate.probability

Estimate Probability Vectors From Count Vectors

euclidean

Euclidean distance (lowlevel function)

fidelity

Fidelity distance (lowlevel function)

gJSD

Generalized Jensen-Shannon Divergence

getDistMethods

Get method names for distance

gower

Gower distance (lowlevel function)

harmonic_mean_dist

Harmonic mean distance (lowlevel function)

hellinger

Hellinger distance (lowlevel function)

inner_product

Inner product distance (lowlevel function)

intersection_dist

Intersection distance (lowlevel function)

jaccard

Jaccard distance (lowlevel function)

jeffreys

Jeffreys distance (lowlevel function)

jensen_difference

Jensen difference (lowlevel function)

jensen_shannon

Jensen-Shannon distance (lowlevel function)

k_divergence

K-Divergence (lowlevel function)

kulczynski_d

Kulczynski_d distance (lowlevel function)

kullback_leibler_distance

kullback-Leibler distance (lowlevel function)

kumar_hassebrook

Kumar hassebrook distance (lowlevel function)

kumar_johnson

Kumar-Johnson distance (lowlevel function)

lin.cor

Linear Correlation

lorentzian

Lorentzian distance (lowlevel function)

manhattan

Manhattan distance (lowlevel function)

matusita

Matusita distance (lowlevel function)

minkowski

Minkowski distance (lowlevel function)

motyka

Motyka distance (lowlevel function)

neyman_chi_sq

Neyman chi-squared distance (lowlevel function)

pearson_chi_sq

Pearson chi-squared distance (lowlevel function)

prob_symm_chi_sq

Probability symmetric chi-squared distance (lowlevel function)

ruzicka

Ruzicka distance (lowlevel function)

soergel

Soergel distance (lowlevel function)

sorensen

Sorensen distance (lowlevel function)

squared_chi_sq

Squared chi-squared distance (lowlevel function)

squared_chord

Squared chord distance (lowlevel function)

squared_euclidean

Squared euclidean distance (lowlevel function)

taneja

Taneja difference (lowlevel function)

tanimoto

Tanimoto distance (lowlevel function)

topsoe

Topsoe distance (lowlevel function)

wave_hedges

Wave hedges distance (lowlevel function)

philentropy

Similarity and Distance Quantification Between Probability Functions

v0.4.0

GPL-2

Authors

Hajk-Georg Drost [aut, cre] (<https://orcid.org/0000-0002-1567-306X>)

Initial release

2020-01-09

philentropy

Functions (57)

philentropy

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