entropy (version 1.3.1)

KL.plugin: Plug-In Estimator of the Kullback-Leibler divergence and of the Chi-Squared Divergence

Description

KL.plugin computes the Kullback-Leiber (KL) divergence between two discrete random variables \(x_1\) and \(x_2\). The corresponding probability mass functions are given by freqs1 and freqs2. Note that the expectation is taken with regard to \(x_1\) using freqs1.

chi2.plugin computes the chi-squared divergence between two discrete random variables \(x_1\) and \(x_2\) with freqs1 and freqs2 as corresponding probability mass functions. Note that the denominator contains freqs2.

Usage

KL.plugin(freqs1, freqs2, unit=c("log", "log2", "log10"))
chi2.plugin(freqs1, freqs2, unit=c("log", "log2", "log10"))

Arguments

freqs1

frequencies (probability mass function) for variable \(x_1\).

freqs2

frequencies (probability mass function) for variable \(x_2\).

unit

the unit in which entropy is measured. The default is "nats" (natural units). For computing entropy in "bits" set unit="log2".

Value

KL.plugin returns the KL divergence.

chi2.plugin returns the chi-squared divergence.

Details

Kullback-Leibler divergence between the two discrete variables \(x_1\) to \(x_2\) is \( \sum_k p_1(k) \log (p_1(k)/p_2(k)) \) where \(p_1\) and \(p_2\) are the probability mass functions of \(x_1\) and \(x_2\), respectively, and \(k\) is the index for the classes.

The chi-squared divergence is given by \( \sum_k (p_1(k)-p_2(k))^2/p_2(k) \).

Note that both the KL divergence and the chi-squared divergence are not symmetric in \(x_1\) and \(x_2\). The chi-squared divergence can be derived as a quadratic approximation of twice the KL divergence.

See Also

KL.Dirichlet, KL.shrink, KL.empirical, mi.plugin, discretize2d.

Examples

# NOT RUN {
# load entropy library 
library("entropy")

# probabilities for two random variables
freqs1 = c(1/5, 1/5, 3/5)
freqs2 = c(1/10, 4/10, 1/2) 

# KL divergence between x1 to x2
KL.plugin(freqs1, freqs2)

# and corresponding (half) chi-squared divergence
0.5*chi2.plugin(freqs1, freqs2)

## relationship to Pearson chi-squared statistic

# Pearson chi-squared statistic and p-value
n = 30 # sample size (observed counts)
chisq.test(n*freqs1, p = freqs2) # built-in function

# Pearson chi-squared statistic from Pearson divergence
pcs.stat = n*chi2.plugin(freqs1, freqs2) # note factor n
pcs.stat

# and p-value
df = length(freqs1)-1 # degrees of freedom
pcs.pval = 1-pchisq(pcs.stat, df)
pcs.pval
# }