ELynx.Tree.Distribution.TimeOfOrigin

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 time of origin for birth and death trees. See corollary 3.3 in the paper cited above.

Documentation

data TimeOfOriginDistribution

Distribution of the time of origin for a phylogenetic tree evolving under the birth and death process and conditioned on observing n leaves today.

Constructors

TOD

Fields

• todTN :: Int

  Number of leaves of the tree.

• todLa :: Rate

  Birth rate.

• todMu :: Rate

  Death rate.

Instances

Eq TimeOfOriginDistribution

Defined in ELynx.Tree.Distribution.TimeOfOrigin

Methods

(==) :: TimeOfOriginDistribution -> TimeOfOriginDistribution -> Bool

(/=) :: TimeOfOriginDistribution -> TimeOfOriginDistribution -> Bool

Data TimeOfOriginDistribution

Defined in ELynx.Tree.Distribution.TimeOfOrigin

Methods

gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> TimeOfOriginDistribution -> c TimeOfOriginDistribution

gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c TimeOfOriginDistribution

toConstr :: TimeOfOriginDistribution -> Constr

dataTypeOf :: TimeOfOriginDistribution -> DataType

dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c TimeOfOriginDistribution)

dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c TimeOfOriginDistribution)

gmapT :: (forall b. Data b => b -> b) -> TimeOfOriginDistribution -> TimeOfOriginDistribution

gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> TimeOfOriginDistribution -> r

gmapQr :: forall r r'. (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> TimeOfOriginDistribution -> r

gmapQ :: (forall d. Data d => d -> u) -> TimeOfOriginDistribution -> [u]

gmapQi :: Int -> (forall d. Data d => d -> u) -> TimeOfOriginDistribution -> u

gmapM :: Monad m => (forall d. Data d => d -> m d) -> TimeOfOriginDistribution -> m TimeOfOriginDistribution

gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> TimeOfOriginDistribution -> m TimeOfOriginDistribution

gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> TimeOfOriginDistribution -> m TimeOfOriginDistribution

Generic TimeOfOriginDistribution

Defined in ELynx.Tree.Distribution.TimeOfOrigin

Associated Types

type Rep TimeOfOriginDistribution :: Type -> Type

Methods

from :: TimeOfOriginDistribution -> Rep TimeOfOriginDistribution x

to :: Rep TimeOfOriginDistribution x -> TimeOfOriginDistribution

Distribution TimeOfOriginDistribution

Defined in ELynx.Tree.Distribution.TimeOfOrigin

Methods

cumulative :: TimeOfOriginDistribution -> Double -> Double

complCumulative :: TimeOfOriginDistribution -> Double -> Double

ContDistr TimeOfOriginDistribution

Defined in ELynx.Tree.Distribution.TimeOfOrigin

Methods

density :: TimeOfOriginDistribution -> Double -> Double

quantile :: TimeOfOriginDistribution -> Double -> Double

complQuantile :: TimeOfOriginDistribution -> Double -> Double

logDensity :: TimeOfOriginDistribution -> Double -> Double

ContGen TimeOfOriginDistribution

Defined in ELynx.Tree.Distribution.TimeOfOrigin

Methods

genContVar :: PrimMonad m => TimeOfOriginDistribution -> Gen (PrimState m) -> m Double

type Rep TimeOfOriginDistribution

Defined in ELynx.Tree.Distribution.TimeOfOrigin

type Rep TimeOfOriginDistribution = D1 ('MetaData "TimeOfOriginDistribution" "ELynx.Tree.Distribution.TimeOfOrigin" "elynx-tree-0.6.0.0-FQkEU9t6m33732ommPyIXg" 'False) (C1 ('MetaCons "TOD" 'PrefixI 'True) (S1 ('MetaSel ('Just "todTN") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :*: (S1 ('MetaSel ('Just "todLa") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Rate) :*: S1 ('MetaSel ('Just "todMu") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Rate))))

cumulative :: TimeOfOriginDistribution -> Time -> Double

Cumulative distribution function Corollary 3.3.

density :: TimeOfOriginDistribution -> Time -> Double

The density function Eq. (5).

quantile :: TimeOfOriginDistribution -> Double -> Time

The inverted cumulative probability distribution cumulative. See also ContDistr.