ELynx.Simulate.MarkovProcessAlongTree

Calculate transition probability matrices, map rate matrices on trees, populate a tree with states according to a stationary distribution, etc.

The implementation of the Markov process is more than basic and can be improved in a lot of ways.

Single rate matrix.

simulate :: PrimMonad m => Int -> StationaryDistribution -> ExchangeabilityMatrix -> Tree Double -> Gen (PrimState m) -> m (Tree [State])

Simulate a number of sites for a given substitution model. Keep states at internal nodes. The result is a tree with the list of simulated states as node labels.

simulateAndFlatten :: PrimMonad m => Int -> StationaryDistribution -> ExchangeabilityMatrix -> Tree Double -> Gen (PrimState m) -> m [[State]]

Simulate a number of sites for a given substitution model. Only the states at the leafs are retained. The states at internal nodes are removed. This has a lower memory footprint.

simulateAndFlattenPar :: Int -> StationaryDistribution -> ExchangeabilityMatrix -> Tree Double -> GenIO -> IO [[State]]

See simulateAndFlatten, parallel version.

Mixture models.

simulateMixtureModel :: PrimMonad m => Int -> Vector Double -> Vector StationaryDistribution -> Vector ExchangeabilityMatrix -> Tree Double -> Gen (PrimState m) -> m (Tree [State])

Simulate a number of sites for a given set of substitution models with corresponding weights. Keep states at internal nodes. See also simulate.

simulateAndFlattenMixtureModel

Arguments

:: PrimMonad m

=> Int

-> Vector Double

-> Vector StationaryDistribution

-> Vector ExchangeabilityMatrix

-> Tree Double

-> Gen (PrimState m)

-> m ([Int], [[State]])

(IndicesOfComponents, [SimulatedSequenceForEachTip])

Simulate a number of sites for a given set of substitution models with corresponding weights. Forget states at internal nodes. See also simulateAndFlatten.

simulateAndFlattenMixtureModelPar :: Int -> Vector Double -> Vector StationaryDistribution -> Vector ExchangeabilityMatrix -> Tree Double -> GenIO -> IO ([Int], [[State]])

See simulateAndFlattenMixtureModel, parallel version.