tlynx-0.0.1: Handle phylogenetic trees

Copyright	(c) Dominik Schrempf 2019
License	GPL-3
Maintainer	dominik.schrempf@gmail.com
Stability	unstable
Portability	portable
Safe Haskell	None
Language	Haskell2010

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 :: Maybe [Word32]
}
type Simulate = LoggingT (ReaderT SimulateArguments IO)
simulateArguments :: Parser SimulateArguments
reportSimulateArguments :: SimulateArguments -> String
simulateDesc :: String
simulateFooter :: String

Documentation

data SimulateArguments Source #

Arguments need to simulate phylogenetic trees.

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 :: Maybe [Word32]
Seed of NRG, random if Nothing.

type Simulate = LoggingT (ReaderT SimulateArguments IO) Source #

Logger and reader data type.

simulateArguments :: Parser SimulateArguments Source #

Command line parser.

reportSimulateArguments :: SimulateArguments -> String Source #

Print useful information about the provided arguments.

simulateDesc :: String Source #

Simulation is a little more involved, so we provide a description.

simulateFooter :: String Source #

And a footer.