statalign.base
Class MCMCPars

java.lang.Object
  statalign.base.MCMCPars

public class MCMCPars
extends java.lang.Object

This is a container class containing the MCMC parameters described below.

Author:

miklos, novak

Field Summary

int	burnIn Number of burn-in steps
int	cycles Number of cycles total after burn-in period
boolean	doReportDuringBurnin If true then logging information is also printed during the burnin.
boolean	fixAlign
boolean	fixEdge
boolean	fixTopology
int	randomisationPeriod Length of the period in which the MCMC chain should be allowed to drift randomly, with all moves accepted, before starting the burnin.
int	sampRate One sampling after each sampRate cycles
long	seed The seed for the random number generator
int	swapRate How often to propose swaps between chains (per cycle).
long	swapSeed The swap seed for the swap random number generator.

Constructor Summary

MCMCPars(int burnIn, int cycles, int sampRate, long seed, long swapSeed, int swapRate)
This constructor sets the values in the class

MCMCPars(int burnIn, int cycles, int sampRate, long seed, long swapSeed, int swapRate, int randomisationPeriod)
This constructor sets the values in the class

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

burnIn

public int burnIn

Number of burn-in steps

cycles

public int cycles

Number of cycles total after burn-in period

sampRate

public int sampRate

One sampling after each sampRate cycles

seed

public long seed

The seed for the random number generator

swapSeed

public long swapSeed

The swap seed for the swap random number generator.

swapRate

public int swapRate

How often to propose swaps between chains (per cycle).

randomisationPeriod

public int randomisationPeriod

Length of the period in which the MCMC chain should be allowed to drift randomly, with all moves accepted, before starting the burnin. This can be useful for generating different starting configurations to test convergence.

fixAlign

public boolean fixAlign

fixTopology

public boolean fixTopology

fixEdge

public boolean fixEdge

doReportDuringBurnin

public boolean doReportDuringBurnin

If true then logging information is also printed during the burnin.

Constructor Detail

MCMCPars

public MCMCPars(int burnIn,
                int cycles,
                int sampRate,
                long seed,
                long swapSeed,
                int swapRate)

This constructor sets the values in the class

Parameters:

burnIn - this.burnIn is set to this value.

cycles - this.cycles is set to this value.

sampRate - this.sampRate is set to this value.

MCMCPars

public MCMCPars(int burnIn,
                int cycles,
                int sampRate,
                long seed,
                long swapSeed,
                int swapRate,
                int randomisationPeriod)

This constructor sets the values in the class

Parameters:

burnIn - this.burnIn is set to this value.

cycles - this.cycles is set to this value.

sampRate - this.sampRate is set to this value.

randomisationPeriod - this.randomisationPeriod is set to this value.