elynx-seq-0.5.1.1: Handle molecular sequences
Copyright(c) Dominik Schrempf 2021
LicenseGPL-3.0-or-later
Maintainerdominik.schrempf@gmail.com
Stabilityunstable
Portabilityportable
Safe HaskellNone
LanguageHaskell2010

ELynx.Data.Alphabet.DistributionDiversity

Description

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

Synopsis

Entropy

entropy :: Vector v Double => v Double -> Double Source #

Entropy of vector.

kEffEntropy :: Vector v Double => v Double -> Double Source #

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 v Double => v Double -> Double Source #

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 v Double => v Double -> Double Source #

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 :: (Vector v Character, Vector v Int, Vector v Double) => AlphabetSpec -> v Character -> v Double Source #

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.