ELynx.Tree.Distribution.TimeOfOriginNearCritical

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 TimeOfOriginNearCriticalDistribution

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

TONCD

Fields

• todTN :: Int

  Number of leaves of the tree.

• todLa :: Rate

  Birth rate.

• todMu :: Rate

  Death rate.

Instances

Eq TimeOfOriginNearCriticalDistribution

Defined in ELynx.Tree.Distribution.TimeOfOriginNearCritical

Methods

(==) :: TimeOfOriginNearCriticalDistribution -> TimeOfOriginNearCriticalDistribution -> Bool

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

Data TimeOfOriginNearCriticalDistribution

Defined in ELynx.Tree.Distribution.TimeOfOriginNearCritical

Methods

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

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

toConstr :: TimeOfOriginNearCriticalDistribution -> Constr

dataTypeOf :: TimeOfOriginNearCriticalDistribution -> DataType

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

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

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

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

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

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

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

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

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

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

Generic TimeOfOriginNearCriticalDistribution

Defined in ELynx.Tree.Distribution.TimeOfOriginNearCritical

Associated Types

type Rep TimeOfOriginNearCriticalDistribution :: Type -> Type

Methods

from :: TimeOfOriginNearCriticalDistribution -> Rep TimeOfOriginNearCriticalDistribution x

to :: Rep TimeOfOriginNearCriticalDistribution x -> TimeOfOriginNearCriticalDistribution

Distribution TimeOfOriginNearCriticalDistribution

Defined in ELynx.Tree.Distribution.TimeOfOriginNearCritical

Methods

cumulative :: TimeOfOriginNearCriticalDistribution -> Double -> Double

complCumulative :: TimeOfOriginNearCriticalDistribution -> Double -> Double

ContDistr TimeOfOriginNearCriticalDistribution

Defined in ELynx.Tree.Distribution.TimeOfOriginNearCritical

Methods

density :: TimeOfOriginNearCriticalDistribution -> Double -> Double

quantile :: TimeOfOriginNearCriticalDistribution -> Double -> Double

complQuantile :: TimeOfOriginNearCriticalDistribution -> Double -> Double

logDensity :: TimeOfOriginNearCriticalDistribution -> Double -> Double

ContGen TimeOfOriginNearCriticalDistribution

Defined in ELynx.Tree.Distribution.TimeOfOriginNearCritical

Methods

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

type Rep TimeOfOriginNearCriticalDistribution

Defined in ELynx.Tree.Distribution.TimeOfOriginNearCritical

type Rep TimeOfOriginNearCriticalDistribution = D1 ('MetaData "TimeOfOriginNearCriticalDistribution" "ELynx.Tree.Distribution.TimeOfOriginNearCritical" "elynx-tree-0.6.0.0-FQkEU9t6m33732ommPyIXg" 'False) (C1 ('MetaCons "TONCD" '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 :: TimeOfOriginNearCriticalDistribution -> Time -> Double

Cumulative distribution function; see Mathematica notebook.

density :: TimeOfOriginNearCriticalDistribution -> Time -> Double

The density function Eq. (5).

quantile :: TimeOfOriginNearCriticalDistribution -> Double -> Time

The inverted cumulative probability distribution cumulative. See also ContDistr.