| Copyright | (c) Dominik Schrempf 2021 |
|---|---|
| License | GPLv3 |
| Maintainer | dominik.schrempf@gmail.com |
| Stability | unstable |
| Portability | non-portable (not tested) |
| Safe Haskell | None |
| Language | Haskell2010 |
ELynx.Simulate.MarkovProcessAlongTree
Description
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.
Synopsis
- simulate :: PrimMonad m => Int -> StationaryDistribution -> ExchangeabilityMatrix -> Tree Double -> Gen (PrimState m) -> m (Tree [State])
- simulateAndFlatten :: PrimMonad m => Int -> StationaryDistribution -> ExchangeabilityMatrix -> Tree Double -> Gen (PrimState m) -> m [[State]]
- simulateAndFlattenPar :: Int -> StationaryDistribution -> ExchangeabilityMatrix -> Tree Double -> GenIO -> IO [[State]]
- simulateMixtureModel :: PrimMonad m => Int -> Vector Double -> Vector StationaryDistribution -> Vector ExchangeabilityMatrix -> Tree Double -> Gen (PrimState m) -> m (Tree [State])
- simulateAndFlattenMixtureModel :: PrimMonad m => Int -> Vector Double -> Vector StationaryDistribution -> Vector ExchangeabilityMatrix -> Tree Double -> Gen (PrimState m) -> m ([Int], [[State]])
- simulateAndFlattenMixtureModelPar :: Int -> Vector Double -> Vector StationaryDistribution -> Vector ExchangeabilityMatrix -> Tree Double -> GenIO -> IO ([Int], [[State]])
Single rate matrix.
simulate :: PrimMonad m => Int -> StationaryDistribution -> ExchangeabilityMatrix -> Tree Double -> Gen (PrimState m) -> m (Tree [State]) Source #
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]] Source #
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]] Source #
See simulateAndFlatten, parallel version.
Mixture models.
simulateMixtureModel :: PrimMonad m => Int -> Vector Double -> Vector StationaryDistribution -> Vector ExchangeabilityMatrix -> Tree Double -> Gen (PrimState m) -> m (Tree [State]) Source #
Simulate a number of sites for a given set of substitution models with
corresponding weights. Keep states at internal nodes. See also
simulate.
simulateAndFlattenMixtureModel Source #
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]]) Source #
See simulateAndFlattenMixtureModel, parallel version.