ELynx.Data.Alphabet.DistributionDiversity

Creation date: Mon Feb 25 13:32:56 2019.

Entropy

entropy :: Vector Double -> Double

Entropy of vector.

kEffEntropy :: Vector Double -> Double

Effective number of used characters measured using entropy. The result only makes sense when the sum of the array is 1.0.

Homoplasy

homoplasy :: Vector Double -> Double

Probability of homoplasy of vector. The result is the probability of binomially sampling the same character twice and only makes sense when the sum of the array is 1.0.

kEffHomoplasy :: Vector Double -> Double

Effective number of used characters measured using homoplasy. The result only makes sense when the sum of the array is 1.0.

Count characters

frequencyCharacters :: AlphabetSpec -> Vector Character -> Vector Double

For a given code vector of characters, calculate frequency of characters. The input vector has arbitrary length (most often the number of sequences in an alignment), the length of the output vector is the number of characters in the alphabet.