TLynx.Simulate.Options

Creation date: Fri May 3 11:51:07 2019.

Documentation

data Process

Process to be used for simulation.

Constructors

BirthDeath

Fields

• bdLambda :: Double

  Birth rate.

• bdMu :: Double

  Death rate.

• bdRho :: Maybe Double

  Sampling rate.

• bdHeight :: TimeSpec

  Condition on height?

Coalescent

Instances

Eq Process

Defined in TLynx.Simulate.Options

Methods

(==) :: Process -> Process -> Bool

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

Show Process

Defined in TLynx.Simulate.Options

Methods

showsPrec :: Int -> Process -> ShowS

show :: Process -> String

showList :: [Process] -> ShowS

Generic Process

Defined in TLynx.Simulate.Options

Associated Types

type Rep Process :: Type -> Type

Methods

from :: Process -> Rep Process x

to :: Rep Process x -> Process

ToJSON Process

Defined in TLynx.Simulate.Options

Methods

toJSON :: Process -> Value

toEncoding :: Process -> Encoding

toJSONList :: [Process] -> Value

toEncodingList :: [Process] -> Encoding

FromJSON Process

Defined in TLynx.Simulate.Options

Methods

parseJSON :: Value -> Parser Process

parseJSONList :: Value -> Parser [Process]

type Rep Process

Defined in TLynx.Simulate.Options

type Rep Process = D1 ('MetaData "Process" "TLynx.Simulate.Options" "tlynx-0.6.0.0-HofljkDb0GQAc1uqX5sBHh" 'False) (C1 ('MetaCons "BirthDeath" 'PrefixI 'True) ((S1 ('MetaSel ('Just "bdLambda") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Double) :*: S1 ('MetaSel ('Just "bdMu") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Double)) :*: (S1 ('MetaSel ('Just "bdRho") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Double)) :*: S1 ('MetaSel ('Just "bdHeight") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 TimeSpec))) :+: C1 ('MetaCons "Coalescent" 'PrefixI 'False) (U1 :: Type -> Type))

data SimulateArguments

Arguments need to simulate phylogenetic trees using birth and death processes.

Constructors

SimulateArguments

Fields

• argsNTrees :: Int

  Simulated trees.

• argsNLeaves :: Int

  Number of leaves.

• argsProcess :: Process

  Process.

• argsSubSample :: Maybe Double

  Perform sub-sampling with given probability.

• argsSumStat :: Bool

  Only print summary statistics?

• argsSeed :: SeedOpt

  Seed of NRG, random if Nothing.

Instances

Eq SimulateArguments

Defined in TLynx.Simulate.Options

Methods

(==) :: SimulateArguments -> SimulateArguments -> Bool

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

Show SimulateArguments

Defined in TLynx.Simulate.Options

Methods

showsPrec :: Int -> SimulateArguments -> ShowS

show :: SimulateArguments -> String

showList :: [SimulateArguments] -> ShowS

Generic SimulateArguments

Defined in TLynx.Simulate.Options

Associated Types

type Rep SimulateArguments :: Type -> Type

Methods

from :: SimulateArguments -> Rep SimulateArguments x

to :: Rep SimulateArguments x -> SimulateArguments

ToJSON SimulateArguments

Defined in TLynx.Simulate.Options

Methods

toJSON :: SimulateArguments -> Value

toEncoding :: SimulateArguments -> Encoding

toJSONList :: [SimulateArguments] -> Value

toEncodingList :: [SimulateArguments] -> Encoding

FromJSON SimulateArguments

Defined in TLynx.Simulate.Options

Methods

parseJSON :: Value -> Parser SimulateArguments

parseJSONList :: Value -> Parser [SimulateArguments]

Reproducible SimulateArguments

Defined in TLynx.Simulate.Options

Methods

inFiles :: SimulateArguments -> [FilePath]

outSuffixes :: SimulateArguments -> [String]

getSeed :: SimulateArguments -> Maybe SeedOpt

setSeed :: SimulateArguments -> SeedOpt -> SimulateArguments

parser :: Parser SimulateArguments

cmdName :: String

cmdDsc :: [String]

cmdFtr :: [String]

type Rep SimulateArguments

Defined in TLynx.Simulate.Options

type Rep SimulateArguments = D1 ('MetaData "SimulateArguments" "TLynx.Simulate.Options" "tlynx-0.6.0.0-HofljkDb0GQAc1uqX5sBHh" 'False) (C1 ('MetaCons "SimulateArguments" 'PrefixI 'True) ((S1 ('MetaSel ('Just "argsNTrees") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :*: (S1 ('MetaSel ('Just "argsNLeaves") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :*: S1 ('MetaSel ('Just "argsProcess") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Process))) :*: (S1 ('MetaSel ('Just "argsSubSample") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Double)) :*: (S1 ('MetaSel ('Just "argsSumStat") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Bool) :*: S1 ('MetaSel ('Just "argsSeed") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 SeedOpt)))))

simulateArguments :: Parser SimulateArguments

Command line parser.

reportSimulateArguments :: SimulateArguments -> String

Print useful information about the provided arguments.

Orphan instances

Eq TimeSpec

Methods

(==) :: TimeSpec -> TimeSpec -> Bool

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

Show TimeSpec

Methods

showsPrec :: Int -> TimeSpec -> ShowS

show :: TimeSpec -> String

showList :: [TimeSpec] -> ShowS

Generic TimeSpec

Associated Types

type Rep TimeSpec :: Type -> Type

Methods

from :: TimeSpec -> Rep TimeSpec x

to :: Rep TimeSpec x -> TimeSpec

ToJSON TimeSpec

Methods

toJSON :: TimeSpec -> Value

toEncoding :: TimeSpec -> Encoding

toJSONList :: [TimeSpec] -> Value

toEncodingList :: [TimeSpec] -> Encoding

FromJSON TimeSpec

Methods

parseJSON :: Value -> Parser TimeSpec

parseJSONList :: Value -> Parser [TimeSpec]