ELynx.MarkovProcess.SubstitutionModel

Creation date: Tue Jan 29 19:10:46 2019.

To be imported qualified.

Types

type Name = String

Name of substitution model; abstracted and subject to change.

type Params = [Double]

Parameters of substitution model. May be the empty list.

data SubstitutionModel

Complete definition of a substitution model. Create instances with substitutionModel. A substitution model has an alphabet, a name, and a list of parameters (e.g., the kappa value for the HKY model). Further, the transition rate matrix is defined by a stationary distribution and a set of exchangeabilities.

Instances

Read SubstitutionModel

Defined in ELynx.MarkovProcess.SubstitutionModel

Methods

readsPrec :: Int -> ReadS SubstitutionModel

readList :: ReadS [SubstitutionModel]

readPrec :: ReadPrec SubstitutionModel

readListPrec :: ReadPrec [SubstitutionModel]

Show SubstitutionModel

Defined in ELynx.MarkovProcess.SubstitutionModel

Methods

showsPrec :: Int -> SubstitutionModel -> ShowS

show :: SubstitutionModel -> String

showList :: [SubstitutionModel] -> ShowS

Accessors

alphabet :: SubstitutionModel -> Alphabet

Alphabet

name :: SubstitutionModel -> Name

Name

params :: SubstitutionModel -> Params

List of parameters

stationaryDistribution :: SubstitutionModel -> StationaryDistribution

Stationary distribution

exchangeabilityMatrix :: SubstitutionModel -> ExchangeabilityMatrix

Exchangeability matrix

rateMatrix :: SubstitutionModel -> RateMatrix

Calculate rate matrix from substitution model.

totalRate :: SubstitutionModel -> Double

Get scale of substitution model.

Building substitution models

data Normalize

Should the substitution model be normalized?

Constructors

DoNormalize

DoNotNormalize

Instances

Read Normalize

Defined in ELynx.MarkovProcess.SubstitutionModel

Methods

readsPrec :: Int -> ReadS Normalize

readList :: ReadS [Normalize]

readPrec :: ReadPrec Normalize

readListPrec :: ReadPrec [Normalize]

Show Normalize

Defined in ELynx.MarkovProcess.SubstitutionModel

Methods

showsPrec :: Int -> Normalize -> ShowS

show :: Normalize -> String

showList :: [Normalize] -> ShowS

Eq Normalize

Defined in ELynx.MarkovProcess.SubstitutionModel

Methods

(==) :: Normalize -> Normalize -> Bool

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

substitutionModel :: Alphabet -> Name -> Params -> Normalize -> StationaryDistribution -> ExchangeabilityMatrix -> SubstitutionModel

Create normalized SubstitutionModel. See normalize.

Transformations

scale :: Double -> SubstitutionModel -> SubstitutionModel

Scale the rate of a substitution model by given factor.

normalize :: SubstitutionModel -> SubstitutionModel

Normalize a substitution model, so that, on average, one substitution happens per unit time.

appendName :: Name -> SubstitutionModel -> SubstitutionModel

Abbend to name.