Copyright	(c) Dominik Schrempf 2020
License	GPL-3.0-or-later
Maintainer	dominik.schrempf@gmail.com
Stability	unstable
Portability	portable
Safe Haskell	None
Language	Haskell2010

TLynx.Simulate.Options

Description

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

Synopsis

data SimulateArguments = SimulateArguments {
- argsNTrees :: Int
- argsNLeaves :: Int
- argsHeight :: Maybe Double
- argsConditionMRCA :: Bool
- argsLambda :: Double
- argsMu :: Double
- argsRho :: Double
- argsSubSample :: Bool
- argsSumStat :: Bool
- argsSeed :: Seed
}
simulateArguments :: Parser SimulateArguments
reportSimulateArguments :: SimulateArguments -> String
simulateFooter :: [String]

Documentation

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.
argsHeight :: Maybe Double
Tree height (time to origin or MRCA).
argsConditionMRCA :: Bool
False: condition on origin; True: condition on MRCA.
argsLambda :: Double
Birth rate.
argsMu :: Double
Death rate.
argsRho :: Double
Smapling rate.
argsSubSample :: Bool
Perform actual sub-sampling.
argsSumStat :: Bool
Only print summary statistics?
argsSeed :: Seed
Seed of NRG, random if Nothing.

Instances

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 Seed # setSeed :: SimulateArguments -> Vector Word32 -> 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-0.3.2-I41YUX7QtfkBLX5ZeepvaY" 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 "argsHeight") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe Double)) :: (S1 (MetaSel (Just "argsConditionMRCA") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Bool) :: S1 (MetaSel (Just "argsLambda") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Double)))) :: ((S1 (MetaSel (Just "argsMu") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Double) :: S1 (MetaSel (Just "argsRho") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Double)) :: (S1 (MetaSel (Just "argsSubSample") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Bool) :: (S1 (MetaSel (Just "argsSumStat") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Bool) :*: S1 (MetaSel (Just "argsSeed") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Seed))))))

simulateArguments :: Parser SimulateArguments Source #

Command line parser.

reportSimulateArguments :: SimulateArguments -> String Source #

Print useful information about the provided arguments.

simulateFooter :: [String] Source #

And a footer.