tlynx-0.8.0.0: Handle phylogenetic trees
Copyright2021 Dominik Schrempf
LicenseGPL-3.0-or-later
Maintainer[email protected]
Stabilityunstable
Portabilityportable
Safe HaskellNone
LanguageHaskell2010

TLynx.Simulate.Options

Description

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

Synopsis

Documentation

data Process Source #

Process to be used for simulation.

Constructors

BirthDeath 

Fields

Coalescent 

Instances

Instances details
FromJSON Process Source # 
Instance details

Defined in TLynx.Simulate.Options

Methods

parseJSON :: Value -> Parser Process #

parseJSONList :: Value -> Parser [Process] #

omittedField :: Maybe Process #

ToJSON Process Source # 
Instance details

Defined in TLynx.Simulate.Options

Methods

toJSON :: Process -> Value #

toEncoding :: Process -> Encoding #

toJSONList :: [Process] -> Value #

toEncodingList :: [Process] -> Encoding #

omitField :: Process -> Bool #

Generic Process Source # 
Instance details

Defined in TLynx.Simulate.Options

Associated Types

type Rep Process 
Instance details

Defined in TLynx.Simulate.Options

type Rep Process = D1 ('MetaData "Process" "TLynx.Simulate.Options" "tlynx-0.8.0.0-JHadlx080MyGliqJ0mTjDo" '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))

Methods

from :: Process -> Rep Process x #

to :: Rep Process x -> Process #

Show Process Source # 
Instance details

Defined in TLynx.Simulate.Options

Methods

showsPrec :: Int -> Process -> ShowS #

show :: Process -> String #

showList :: [Process] -> ShowS #

Eq Process Source # 
Instance details

Defined in TLynx.Simulate.Options

Methods

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

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

type Rep Process Source # 
Instance details

Defined in TLynx.Simulate.Options

type Rep Process = D1 ('MetaData "Process" "TLynx.Simulate.Options" "tlynx-0.8.0.0-JHadlx080MyGliqJ0mTjDo" '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

Instances

Instances details
FromJSON SimulateArguments Source # 
Instance details

Defined in TLynx.Simulate.Options

Methods

parseJSON :: Value -> Parser SimulateArguments #

parseJSONList :: Value -> Parser [SimulateArguments] #

omittedField :: Maybe SimulateArguments #

ToJSON SimulateArguments Source # 
Instance details

Defined in TLynx.Simulate.Options

Methods

toJSON :: SimulateArguments -> Value #

toEncoding :: SimulateArguments -> Encoding #

toJSONList :: [SimulateArguments] -> Value #

toEncodingList :: [SimulateArguments] -> Encoding #

omitField :: SimulateArguments -> Bool #

Generic SimulateArguments Source # 
Instance details

Defined in TLynx.Simulate.Options

Associated Types

type Rep SimulateArguments 
Instance details

Defined in TLynx.Simulate.Options

type Rep SimulateArguments = D1 ('MetaData "SimulateArguments" "TLynx.Simulate.Options" "tlynx-0.8.0.0-JHadlx080MyGliqJ0mTjDo" '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)))))

Methods

from :: SimulateArguments -> Rep SimulateArguments x #

to :: Rep SimulateArguments x -> SimulateArguments #

Show SimulateArguments Source # 
Instance details

Defined in TLynx.Simulate.Options

Methods

showsPrec :: Int -> SimulateArguments -> ShowS #

show :: SimulateArguments -> String #

showList :: [SimulateArguments] -> ShowS #

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] #

Eq SimulateArguments Source # 
Instance details

Defined in TLynx.Simulate.Options

Methods

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

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

type Rep SimulateArguments Source # 
Instance details

Defined in TLynx.Simulate.Options

type Rep SimulateArguments = D1 ('MetaData "SimulateArguments" "TLynx.Simulate.Options" "tlynx-0.8.0.0-JHadlx080MyGliqJ0mTjDo" '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

FromJSON TimeSpec Source # 
Instance details

Methods

parseJSON :: Value -> Parser TimeSpec #

parseJSONList :: Value -> Parser [TimeSpec] #

omittedField :: Maybe TimeSpec #

ToJSON TimeSpec Source # 
Instance details

Methods

toJSON :: TimeSpec -> Value #

toEncoding :: TimeSpec -> Encoding #

toJSONList :: [TimeSpec] -> Value #

toEncodingList :: [TimeSpec] -> Encoding #

omitField :: TimeSpec -> Bool #

Generic TimeSpec Source # 
Instance details

Associated Types

type Rep TimeSpec 
Instance details

Defined in TLynx.Simulate.Options

type Rep TimeSpec = D1 ('MetaData "TimeSpec" "ELynx.Tree.Simulate.PointProcess" "elynx-tree-0.7.2.2-32z0E9LMYChDaU1tPYV1F3" 'False) (C1 ('MetaCons "Random" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Origin" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Time)) :+: C1 ('MetaCons "Mrca" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Time))))

Methods

from :: TimeSpec -> Rep TimeSpec x #

to :: Rep TimeSpec x -> TimeSpec #

Show TimeSpec Source # 
Instance details

Methods

showsPrec :: Int -> TimeSpec -> ShowS #

show :: TimeSpec -> String #

showList :: [TimeSpec] -> ShowS #

Eq TimeSpec Source # 
Instance details

Methods

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

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