statalign.base
Class Mcmc

java.lang.Object
  statalign.base.thread.Stoppable
      statalign.base.Mcmc

public class Mcmc
extends Stoppable

This class handles an MCMC run. The class extends Stoppable, it may be terminated/suspended in graphical mode.

Author:

miklos, novak, herman

Field Summary

boolean	burnin True while the MCMC is in the burn-in phase.
McmcModule	coreModel McmcModule containing the moves for the core components of the model, i.e. the indel parameters, substitution model parameters, alignment, topology and edge lengths.
boolean	firstHalfBurnin True while the MCMC is in the first half of burn-in phase.
MCMCPars	mcmcpars MCMC parameters including the number of burn-in steps, the total number of steps in the MCMC and the sampling rate.
McmcStep	mcmcStep
ModelExtManager	modelExtMan Manager that handles model extension plugins
CNetwork	network
PostprocessManager	postprocMan PostprocessManager that handles the postprocessing modules.
Tree	tree Current tree in the MCMC chain.

Constructor Summary

Mcmc(Tree tree, MCMCPars pars, PostprocessManager ppm, ModelExtManager modelExtMan)

Mcmc(Tree tree, MCMCPars pars, PostprocessManager ppm, ModelExtManager modelExtMan, int noOfProcesses, int rank, double heat)

Method Summary

boolean	acceptanceDecision(double oldLogLikelihood, double newLogLikelihood, double logProposalRatio, boolean acceptMoveIfPossible)
int	doMCMC() Starts an MCMC run.
java.lang.String	getInfoString() Returns a string representation describing the acceptance ratios of the current MCMC run.
State	getState() Returns a State object that describes the current state of the MCMC.
boolean	isParamChangeAccepted(double logProposalRatio, McmcMove m) This function is called by the McmcMove objects in order to determine whether the proposed moves are to be accepted.
static void	main2(java.lang.String[] args) Code to test that various samplers are working correctly.
static void	main3(java.lang.String[] args) Code to test that the moves are being sampled according to the correct weights (i.e. that there is not some bias arising from the choose function and/or random number generator).
static void	main4(java.lang.String[] args)
static void	main5(java.lang.String[] args)

Methods inherited from class statalign.base.thread.Stoppable

pausable, stoppable

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

network

public CNetwork network

tree

public Tree tree

Current tree in the MCMC chain.

mcmcpars

public MCMCPars mcmcpars

MCMC parameters including the number of burn-in steps, the total number of steps in the MCMC and the sampling rate.

mcmcStep

public McmcStep mcmcStep

postprocMan

public PostprocessManager postprocMan

PostprocessManager that handles the postprocessing modules.

modelExtMan

public ModelExtManager modelExtMan

Manager that handles model extension plugins

coreModel

public McmcModule coreModel

McmcModule containing the moves for the core components of the model, i.e. the indel parameters, substitution model parameters, alignment, topology and edge lengths. The coreModel also decides whether to execute MCMC moves from the ModelExtension modules.

burnin

public boolean burnin

True while the MCMC is in the burn-in phase.

firstHalfBurnin

public boolean firstHalfBurnin

True while the MCMC is in the first half of burn-in phase.

Constructor Detail

Mcmc

public Mcmc(Tree tree,
            MCMCPars pars,
            PostprocessManager ppm,
            ModelExtManager modelExtMan)

Mcmc

public Mcmc(Tree tree,
            MCMCPars pars,
            PostprocessManager ppm,
            ModelExtManager modelExtMan,
            int noOfProcesses,
            int rank,
            double heat)

Method Detail

isParamChangeAccepted

public boolean isParamChangeAccepted(double logProposalRatio,
                                     McmcMove m)

This function is called by the McmcMove objects in order to determine whether the proposed moves are to be accepted.

Parameters:

logProposalRatio - This also includes the contribution from the prior densities. It is assumed that any dependencies between the priors and other parameters will be handled inside the McmcMove objects.

Returns:

true if the move is accepted

acceptanceDecision

public boolean acceptanceDecision(double oldLogLikelihood,
                                  double newLogLikelihood,
                                  double logProposalRatio,
                                  boolean acceptMoveIfPossible)

getInfoString

public java.lang.String getInfoString()

Returns a string representation describing the acceptance ratios of the current MCMC run.

Returns:

a string describing the acceptance ratios.

getState

public State getState()

Returns a State object that describes the current state of the MCMC. This can then be passed on to other classes such as postprocessing plugins.

doMCMC

public int doMCMC()

Starts an MCMC run. If AutomateParameters.shouldAutomateProposalVariances() = true then the proposal distributions will be automatically adjusted during the burnin. If AutomateParameters.shouldAutomateNumberOfSamples() = true or AutomateParameters.shouldAutomateStepRate() = true or AutomateParameters.shouldAutomateBurnin() = true then these parameters will be adjusted automatically, although this approach may affect the theoretical convergence properties of the MCMC chain, so this type of automation should be regarded more as a quick way of getting some initial results without tweaking the parameters. This function also calls the appropriate functions of the PostpocessManager postprocMan to trigger data transfer to postprocessing modules when necessary

main5

public static void main5(java.lang.String[] args)

main4

public static void main4(java.lang.String[] args)

main3

public static void main3(java.lang.String[] args)

Code to test that the moves are being sampled according to the correct weights (i.e. that there is not some bias arising from the choose function and/or random number generator).

main2

public static void main2(java.lang.String[] args)

Code to test that various samplers are working correctly.