Manager for all the states and handle reading / writing from / to databse. More...

#include <chainarray.hpp>

Public Member Functions
	ChainArray (uint nStacks, uint nChains, double tempFactor, double initialSigma, double sigmaFactor, db::Database &db, uint cacheLength, bool recover)
	Create a chain array. More...

uint	length (uint id)
	Get the length of a chain. More...

bool	append (uint id, const State &proposedState)
	Append a state to a chain. More...

void	initialise (uint id, const State &state)
	Initialise a chain (by definitely accepting a new state). More...

State	lastState (uint id)
	Return the last state from a chain. More...

State	state (uint id, uint index)
	Return a particular state. More...

std::vector< State >	states (uint id)
	Return all states from a chain. More...

bool	swap (uint id1, uint id2)
	Attempt to swap the states in two different chains. More...

double	sigma (uint id) const
	Get the proposal width of a specific chain. More...

void	setSigma (uint id, double sigma)
	Set the proposal width of a specific chain. More...

double	beta (uint id) const
	Get the inverse temperature of a specific chain. More...

void	setBeta (uint id, double beta)
	Set the inverse temperature of a specific chain. More...

uint	numStacks () const
	Get the number of stacks. More...

uint	numChains () const
	Get the number of chains per stack. More...

uint	numTotalChains () const
	Get the total number of chains in every stack. More...

void	flushCache (uint id)
	Forcibly flush the cache for a particular chain. More...

void	recoverFromCache (uint id)
	Recover a particular chain from cached. More...

Detailed Description

Manager for all the states and handle reading / writing from / to databse.

The chain ID used by MCMC sampler.

This class works with Ids:

if nStacks = 2, nChains = 4
id 0 = stack 1 chain 1 // lowest temperature chain of stack 1
id 1 = stack 1 chain 2 // high temperature chain of stack 1
id 2 = stack 1 chain 3 // high temperature chain of stack 1
id 3 = stack 1 chain 4 // highest temperature chain of stack 1
id 4 = stack 2 chain 1 // lowest temperature chain of stack 2
id 5 = stack 2 chain 2 // high temperature chain of stack 2
id 6 = stack 2 chain 3 // high temperature chain of stack 2
id 7 = stack 2 chain 4 // highest temperature chain of stack 2

Constructor & Destructor Documentation

stateline::mcmc::ChainArray::ChainArray	(	uint	nStacks,
		uint	nChains,
		double	tempFactor,
		double	initialSigma,
		double	sigmaFactor,
		db::Database &	db,
		uint	cacheLength,
		bool	recover
	)

Create a chain array.

Parameters

nStacks	The number of stacks. Each stack have the same temperature sequence.
nChains	The number of chains in each stack.
tempFactor	The ratio between the temperatures of consecutive chains in a stack.
initialSigma	The initial step sizes of the chains.
sigmaFactor	The ratio between the temperatures of consectuive chains in a stack.
db	The database to store chain data.
cacheLength	The size of the memory cache used to store the chains.
recover	If set to true, chain data will be recovered from the database

Member Function Documentation

bool stateline::mcmc::ChainArray::append	(	uint	id,
		const State &	proposedState
	)

Append a state to a chain.

Parameters

id	The id of the chain (see The chain ID used by MCMC sampler.).
proposedState	The new state to append.

Returns: Whether the state accepted or rejected (in which case last state is reappended).

double stateline::mcmc::ChainArray::beta ( uint id ) const

Get the inverse temperature of a specific chain.

Parameters

id	The id of the second chain (see The chain ID used by MCMC sampler.).

Returns: The inverse temperature of the chain.

void stateline::mcmc::ChainArray::flushCache ( uint id )

Forcibly flush the cache for a particular chain.

Parameters

id	The id of the chain to flush.

void stateline::mcmc::ChainArray::initialise	(	uint	id,
		const State &	state
	)

Initialise a chain (by definitely accepting a new state).

Parameters

id	The id of the chain (see The chain ID used by MCMC sampler.).
state	the new state to append

State stateline::mcmc::ChainArray::lastState ( uint id )

Return the last state from a chain.

Parameters

id	The id of the chain (see The chain ID used by MCMC sampler.).

Returns: The most recent state in the chain.

uint stateline::mcmc::ChainArray::length ( uint id )

Get the length of a chain.

Parameters

id	The id of the chain (see The chain ID used by MCMC sampler.).

Returns: The number of elements in the chain.

uint stateline::mcmc::ChainArray::numChains ( ) const

Get the number of chains per stack.

Returns: The number of chains in each stack of the chain array.

uint stateline::mcmc::ChainArray::numStacks ( ) const

Get the number of stacks.

Returns: The number of stacks in the chain array.

uint stateline::mcmc::ChainArray::numTotalChains ( ) const

Get the total number of chains in every stack.

Returns: The total number of chains in the chain array.

void stateline::mcmc::ChainArray::recoverFromCache ( uint id )

Recover a particular chain from cached.

Parameters

id	The id of the chain to recover.

void stateline::mcmc::ChainArray::setBeta	(	uint	id,
		double	beta
	)

Set the inverse temperature of a specific chain.

Parameters

id	The id of the second chain (see The chain ID used by MCMC sampler.).
beta	The new inverse temperature of the chain.

void stateline::mcmc::ChainArray::setSigma	(	uint	id,
		double	sigma
	)

Set the proposal width of a specific chain.

Parameters

id	The id of the second chain (see The chain ID used by MCMC sampler.).
sigma	The new proposal width value.

double stateline::mcmc::ChainArray::sigma ( uint id ) const

Get the proposal width of a specific chain.

Parameters

id	The id of the second chain (see The chain ID used by MCMC sampler.).

Returns: The proposal width of the chain.

State stateline::mcmc::ChainArray::state	(	uint	id,
		uint	index
	)

Return a particular state.

Parameters

id	The id of the chain (see The chain ID used by MCMC sampler.).
index	The index of the state (0 for first state).

Returns: The most recent state in the chain.

std::vector< State > stateline::mcmc::ChainArray::states ( uint id )

Return all states from a chain.

Parameters

id	The id of the chain (see The chain ID used by MCMC sampler.).

Returns: The most recent state in the chain.

bool stateline::mcmc::ChainArray::swap	(	uint	id1,
		uint	id2
	)

Attempt to swap the states in two different chains.

Parameters

id1	The id of the first chain (see The chain ID used by MCMC sampler.).
id2	The id of the second chain (see The chain ID used by MCMC sampler.).

Returns: Whether the swap was successful.

The documentation for this class was generated from the following files:

/home/lb/code/GDF/src/infer/chainarray.hpp
/home/lb/code/GDF/src/infer/chainarray.cpp

Public Member Functions

Detailed Description

The chain ID used by MCMC sampler.

Constructor & Destructor Documentation

Member Function Documentation