BirthDeathCriticalNoTime.hs

{-# LANGUAGE DeriveDataTypeable #-}
{-# LANGUAGE DeriveGeneric      #-}

{- |
   Module      :  ELynx.Distribution.BirthDeathCriticalNoTime
   Description :  Birth and death distribution
   Copyright   :  (c) Dominik Schrempf 2018
   License     :  GPL-3

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

Creation date: Tue Feb 13 13:16:18 2018.

See Gernhard, T. (2008). The conditioned reconstructed process. Journal of
Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005.

Distribution of the values of the point process such that it corresponds to
reconstructed trees under the birth and death process; critical birth and death
process with lambda=mu.

-}

module ELynx.Distribution.BirthDeathCriticalNoTime
  ( BirthDeathCriticalNoTimeDistribution(..)
  , cumulative
  , density
  , quantile
  ) where

import           Data.Data                (Data, Typeable)
import           GHC.Generics             (Generic)
import qualified Statistics.Distribution  as D

import           ELynx.Distribution.Types

-- | Distribution of the values of the point process such that it corresponds to
-- a reconstructed tree of the birth and death process.
newtype BirthDeathCriticalNoTimeDistribution = BDCNTD
  { bdcntdLa  :: Rate    -- ^ Birth and death rate.
  } deriving (Eq, Typeable, Data, Generic)

instance D.Distribution BirthDeathCriticalNoTimeDistribution where
    cumulative = cumulative

-- | Cumulative distribution function section 2.1.2, second formula.
cumulative :: BirthDeathCriticalNoTimeDistribution -> Time -> Double
cumulative (BDCNTD l) x
  | x <= 0    = 0
  | otherwise = x * l / (1.0 + x * l)

instance D.ContDistr BirthDeathCriticalNoTimeDistribution where
  density  = density
  quantile = quantile

-- | Density function section 2.1.2, first formula; t cancels out because it is
-- expected to be much larger than 1.0; because t \in [0, \infty].
density :: BirthDeathCriticalNoTimeDistribution -> Time -> Double
density (BDCNTD l) x
  | x < 0     = 0
  | otherwise = l / ((1.0 + x * l)**2)

-- | Inverted cumulative probability distribution 'cumulative'. See also
-- 'D.ContDistr'.
quantile :: BirthDeathCriticalNoTimeDistribution -> Double -> Time
quantile (BDCNTD l) p
  | p >= 0 && p <= 1 = p / (l - l*p)
  | otherwise        =
    error $ "PointProcess.quantile: p must be in [0,1]. Got: " ++ show p ++ "."

instance D.ContGen BirthDeathCriticalNoTimeDistribution where
  genContVar = D.genContinuous