BEAST v2.5.0 Documentation: beast.core.MCMC

Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc.
MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results.

Reference:

Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537

doi:10.1371/journal.pcbi.1003537

Inputs:

chainLength, state, init, storeEvery, preBurnin, numInitializationAttempts, distribution, operator, logger, sampleFromPrior, operatorschedule

 

chainLength
type: java.lang.Long
Length of the MCMC chain i.e. number of samples taken in main loop
Required input

 

state
type: beast.core.State
elements of the state space
Optional input

 

init
type: beast.core.StateNodeInitialiser***
one or more state node initilisers used for determining the start state of the chain
Optional input

 

storeEvery
type: java.lang.Integer
store the state to disk every X number of samples so that we can resume computation later on if the process failed half-way.
Optional input. Default: -1

 

preBurnin
type: java.lang.Integer
Number of burn in samples taken before entering the main loop
Optional input. Default: 0

 

numInitializationAttempts
type: java.lang.Integer
Number of initialization attempts before failing (default=10)
Optional input. Default: 10

 

distribution
type: beast.core.Distribution
probability distribution to sample over (e.g. a posterior)
Required input

 

operator
type: beast.core.Operator***
operator for generating proposals in MCMC state space
Optional input

 

logger
type: beast.core.Logger***
loggers for reporting progress of MCMC chain
Required input

 

sampleFromPrior
type: java.lang.Boolean
whether to ignore the likelihood when sampling (default false). The distribution with id 'likelihood' in the posterior input will be ignored when this flag is set.
Optional input. Default: false

 

operatorschedule
type: beast.core.OperatorSchedule
specify operator selection and optimisation schedule
Optional input