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Calculate Kullback-Leibler Divergence

Source: R/entropy.R
calculate_kl_divergence.Rd

Calculate the Kullback-Leibler (KL) divergence between two codon frequency distributions. This measures how one distribution diverges from a second, expected distribution.

Usage

calculate_kl_divergence(observed, reference, epsilon = 1e-10)

Arguments

observed

Named numeric vector of observed codon frequencies

reference

Named numeric vector of reference codon frequencies

epsilon

Small value to avoid log(0) (default: 1e-10)

Value

Numeric value of KL divergence

Examples

sequence1 <- "ATGATGATGTTATTATTACGCCGCCGCC"
sequence2 <- "TTATTATTACGCCGCCGCCATGATGATG"
freqs1 <- calculate_codon_frequencies(sequence1)
freqs2 <- calculate_codon_frequencies(sequence2)
kl_div <- calculate_kl_divergence(freqs1, freqs2)