BEAST v2.6.7 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.


Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, Alexei J. Drummond BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS computational biology 15, no. 4 (2019): e1006650.



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


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


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


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


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


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


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


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


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


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


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


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