NucleotideSpec.hs

{- |
Module      :  ELynx.Data.MarkovProcess.NucleotideSpec
Copyright   :  (c) Dominik Schrempf 2020
License     :  GPL-3.0-or-later

Maintainer  :  dominik.schrempf@gmail.com
Stability   :  unstable
Portability :  portable

Creation date: Fri Jan 25 16:47:28 2019.

-}

module ELynx.Data.MarkovProcess.NucleotideSpec
  ( spec
  )
where

import           Data.Vector.Generic
import           Test.Hspec

import           ELynx.Tools

import           ELynx.Data.MarkovProcess.Nucleotide
import           ELynx.Data.MarkovProcess.RateMatrix
import           ELynx.Data.MarkovProcess.SubstitutionModel

stationaryDist :: StationaryDistribution
stationaryDist = fromList [0.2, 0.3, 0.3, 0.2]

hkyModel :: SubstitutionModel
hkyModel = hky 6.0 stationaryDist

spec :: Spec
spec =
  describe "getStationaryDistribution"
    $ it "extracts the stationary distribution from a rate matrix"
    $ do
        let sd = getStationaryDistribution (rateMatrix hkyModel)
        sd `nearlyEqVec` stationaryDist `shouldBe` True