Copyright	(c) Dominik Schrempf 2021
License	GPL-3.0-or-later
Maintainer	dominik.schrempf@gmail.com
Stability	unstable
Portability	portable
Safe Haskell	None
Language	Haskell2010

TLynx.Simulate.Options

Contents

Orphan instances

Description

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

Synopsis

data Process
- = BirthDeath {
  - bdLambda :: Double
  - bdMu :: Double
  - bdRho :: Maybe Double
  - bdHeight :: TimeSpec
  }
- | Coalescent
data SimulateArguments = SimulateArguments {
- argsNTrees :: Int
- argsNLeaves :: Int
- argsProcess :: Process
- argsSubSample :: Maybe Double
- argsSumStat :: Bool
- argsSeed :: SeedOpt
}
simulateArguments :: Parser SimulateArguments
reportSimulateArguments :: SimulateArguments -> String

Documentation

data Process Source #

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

Instances details

Eq Process Source #
Instance details Defined in TLynx.Simulate.Options Methods (==) :: Process -> Process -> Bool # (/=) :: Process -> Process -> Bool #
Show Process Source #
Instance details Defined in TLynx.Simulate.Options Methods showsPrec :: Int -> Process -> ShowS # show :: Process -> String # showList :: [Process] -> ShowS #
Generic Process Source #
Instance details 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 Source #
Instance details Defined in TLynx.Simulate.Options Methods toJSON :: Process -> Value # toEncoding :: Process -> Encoding # toJSONList :: [Process] -> Value # toEncodingList :: [Process] -> Encoding #
FromJSON Process Source #
Instance details Defined in TLynx.Simulate.Options Methods parseJSON :: Value -> Parser Process # parseJSONList :: Value -> Parser [Process] #
type Rep Process Source #
Instance details 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 Source #

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

Instances details

Eq SimulateArguments Source #
Instance details Defined in TLynx.Simulate.Options Methods (==) :: SimulateArguments -> SimulateArguments -> Bool # (/=) :: SimulateArguments -> SimulateArguments -> Bool #
Show SimulateArguments Source #
Instance details Defined in TLynx.Simulate.Options Methods showsPrec :: Int -> SimulateArguments -> ShowS # show :: SimulateArguments -> String # showList :: [SimulateArguments] -> ShowS #
Generic SimulateArguments Source #
Instance details 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 Source #
Instance details Defined in TLynx.Simulate.Options Methods toJSON :: SimulateArguments -> Value # toEncoding :: SimulateArguments -> Encoding # toJSONList :: [SimulateArguments] -> Value # toEncodingList :: [SimulateArguments] -> Encoding #
FromJSON SimulateArguments Source #
Instance details Defined in TLynx.Simulate.Options Methods parseJSON :: Value -> Parser SimulateArguments # parseJSONList :: Value -> Parser [SimulateArguments] #
Reproducible SimulateArguments Source #
Instance details 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 Source #
Instance details 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 Source #

Command line parser.

reportSimulateArguments :: SimulateArguments -> String Source #

Print useful information about the provided arguments.

Orphan instances

Eq TimeSpec Source #
Instance details Methods (==) :: TimeSpec -> TimeSpec -> Bool # (/=) :: TimeSpec -> TimeSpec -> Bool #
Show TimeSpec Source #
Instance details Methods showsPrec :: Int -> TimeSpec -> ShowS # show :: TimeSpec -> String # showList :: [TimeSpec] -> ShowS #
Generic TimeSpec Source #
Instance details Associated Types type Rep TimeSpec :: Type -> Type # Methods from :: TimeSpec -> Rep TimeSpec x # to :: Rep TimeSpec x -> TimeSpec #
ToJSON TimeSpec Source #
Instance details Methods toJSON :: TimeSpec -> Value # toEncoding :: TimeSpec -> Encoding # toJSONList :: [TimeSpec] -> Value # toEncodingList :: [TimeSpec] -> Encoding #
FromJSON TimeSpec Source #
Instance details Methods parseJSON :: Value -> Parser TimeSpec # parseJSONList :: Value -> Parser [TimeSpec] #