Copyright | (c) 2015 Jared Tobin |
---|---|
License | MIT |
Maintainer | Jared Tobin <jared@jtobin.ca> |
Stability | unstable |
Portability | ghc |
Safe Haskell | None |
Language | Haskell2010 |
This implementation performs Hamiltonian Monte Carlo using an identity mass matrix.
The mcmc
function streams a trace to stdout to be processed elsewhere,
while the slice
transition can be used for more flexible purposes, such as
working with samples in memory.
See Neal, 2012 for the definitive reference of the algorithm.
Synopsis
- mcmc :: (MonadIO m, PrimMonad m, Num (IxValue (t Double)), Show (t Double), Traversable t, FunctorWithIndex (Index (t Double)) t, Ixed (t Double), IxValue (t Double) ~ Double) => Int -> Double -> Int -> t Double -> Target (t Double) -> Gen (PrimState m) -> m ()
- chain :: (PrimMonad m, Traversable f, FunctorWithIndex (Index (f Double)) f, Ixed (f Double), IxValue (f Double) ~ Double) => Int -> Double -> Int -> f Double -> Target (f Double) -> Gen (PrimState m) -> m [Chain (f Double) b]
- hamiltonian :: (Num (IxValue (t Double)), Traversable t, FunctorWithIndex (Index (t Double)) t, Ixed (t Double), PrimMonad m, IxValue (t Double) ~ Double) => Double -> Int -> Transition m (Chain (t Double) b)
- data Target a = Target {}
- create :: PrimMonad m => m (Gen (PrimState m))
- createSystemRandom :: IO GenIO
- withSystemRandom :: PrimBase m => (Gen (PrimState m) -> m a) -> IO a
- asGenIO :: (GenIO -> IO a) -> GenIO -> IO a
Documentation
mcmc :: (MonadIO m, PrimMonad m, Num (IxValue (t Double)), Show (t Double), Traversable t, FunctorWithIndex (Index (t Double)) t, Ixed (t Double), IxValue (t Double) ~ Double) => Int -> Double -> Int -> t Double -> Target (t Double) -> Gen (PrimState m) -> m () Source #
Trace n
iterations of a Markov chain and stream them to stdout.
>>>
withSystemRandom . asGenIO $ mcmc 10000 0.05 20 [0, 0] target
chain :: (PrimMonad m, Traversable f, FunctorWithIndex (Index (f Double)) f, Ixed (f Double), IxValue (f Double) ~ Double) => Int -> Double -> Int -> f Double -> Target (f Double) -> Gen (PrimState m) -> m [Chain (f Double) b] Source #
Trace n
iterations of a Markov chain and collect the results in a list.
>>>
results <- withSystemRandom . asGenIO $ chain 1000 0.05 20 [0, 0] target
hamiltonian :: (Num (IxValue (t Double)), Traversable t, FunctorWithIndex (Index (t Double)) t, Ixed (t Double), PrimMonad m, IxValue (t Double) ~ Double) => Double -> Int -> Transition m (Chain (t Double) b) Source #
A Hamiltonian transition operator.
Re-exported
A Target
consists of a function from parameter space to the reals, as
well as possibly a gradient.
Most implementations assume a log-target, so records are named accordingly.
createSystemRandom :: IO GenIO #
Seed a PRNG with data from the system's fast source of pseudo-random numbers.
withSystemRandom :: PrimBase m => (Gen (PrimState m) -> m a) -> IO a #
Seed a PRNG with data from the system's fast source of pseudo-random numbers, then run the given action.
This function is unsafe and for example allows STRefs or any other mutable data structure to escape scope:
>>>
ref <- withSystemRandom $ \_ -> newSTRef 1
>>>
withSystemRandom $ \_ -> modifySTRef ref succ >> readSTRef ref
2>>>
withSystemRandom $ \_ -> modifySTRef ref succ >> readSTRef ref
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