DistributionDiversitySpec.hs

{- |
Module      :  ELynx.Data.Alphabet.DistributionDiversitySpec
Copyright   :  (c) Dominik Schrempf 2019
License     :  GPL-3

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

Creation date: Mon Feb 25 13:41:12 2019.

-}

module ELynx.Data.Alphabet.DistributionDiversitySpec
  (spec
  ) where

import qualified Data.Vector.Unboxed                       as V
import           Test.Hspec

import           ELynx.Data.Alphabet.DistributionDiversity
import           ELynx.Tools.Equality

testArr1 :: V.Vector Double
testArr1 = V.replicate 20 0.0

testArr2 :: V.Vector Double
testArr2 = V.fromList [0, 0, 0, 1, 0]

-- Compare results from random array tested with Python functions.
testArr3 :: V.Vector Double
testArr3 = V.fromList [0.3, 0.4, 0.7]

spec :: Spec
spec = do
  describe "entropy" $
    it "calculates entropy of vectors" $ do
    entropy testArr1 `shouldBe` 0.0
    entropy testArr2 `shouldBe` 0.0
    entropy testArr3 `shouldSatisfy` nearlyEq 0.9773805948045555

  describe "kEffEntropy" $
    it "calculates the effective number of used states using entropy" $ do
    kEffEntropy testArr1 `shouldBe` 1.0
    kEffEntropy testArr2 `shouldBe` 1.0
    kEffEntropy testArr3 `shouldSatisfy` nearlyEq 2.6574860842252765

  describe "homoplasy" $
    it "calculates homoplasy of vectors" $ do
    homoplasy testArr1 `shouldBe` 0.0
    homoplasy testArr2 `shouldBe` 1.0
    homoplasy testArr3 `shouldSatisfy` nearlyEq 0.74

  describe "kEffHomoplasy" $
    it "calculates the effective number of used states using homoplasy" $ do
    kEffHomoplasy testArr1 `shouldSatisfy` isInfinite
    kEffHomoplasy testArr2 `shouldBe` 1.0
    kEffHomoplasy testArr3 `shouldSatisfy` nearlyEq 1.3513513513513513