TLynx.Simulate.Options

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

Documentation

data Height

Condition on tree height (origin or most recent common ancestor).

Constructors

Origin Double

Mrca Double

Instances

Eq Height

Defined in TLynx.Simulate.Options

Methods

(==) :: Height -> Height -> Bool

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

Show Height

Defined in TLynx.Simulate.Options

Methods

showsPrec :: Int -> Height -> ShowS

show :: Height -> String

showList :: [Height] -> ShowS

Generic Height

Defined in TLynx.Simulate.Options

Associated Types

type Rep Height :: Type -> Type

Methods

from :: Height -> Rep Height x

to :: Rep Height x -> Height

ToJSON Height

Defined in TLynx.Simulate.Options

Methods

toJSON :: Height -> Value

toEncoding :: Height -> Encoding

toJSONList :: [Height] -> Value

toEncodingList :: [Height] -> Encoding

FromJSON Height

Defined in TLynx.Simulate.Options

Methods

parseJSON :: Value -> Parser Height

parseJSONList :: Value -> Parser [Height]

type Rep Height

Defined in TLynx.Simulate.Options

type Rep Height = D1 (MetaData "Height" "TLynx.Simulate.Options" "tlynx-0.4.0-8tcIvrUCDfo4d2N61gOzrk" False) (C1 (MetaCons "Origin" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Double)) :+: C1 (MetaCons "Mrca" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Double)))

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 :: Maybe Height

  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-0.4.0-8tcIvrUCDfo4d2N61gOzrk" 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 (Maybe Height)))) :+: 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 :: Seed

  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 Seed

setSeed :: SimulateArguments -> Vector Word32 -> 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-0.4.0-8tcIvrUCDfo4d2N61gOzrk" 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 Seed)))))

simulateArguments :: Parser SimulateArguments

Command line parser.

reportSimulateArguments :: SimulateArguments -> String

Print useful information about the provided arguments.