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.
A prototype for BEAST 2.0: The computational science of evolutionary software. Bouckaert, Drummond, Rambaut, Alekseyenko, Suchard & the BEAST Core Development Team. 2010
preBurnin, chainLength, storeEvery, posterior, operator, logger, init
| type: java.lang.Integer |
| Number of burn in samples taken before entering the main loop |
| Optional input. Default: 0 |
| type: java.lang.Integer |
| Length of the MCMC chain i.e. number of samples taken in main loop |
| Required 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: beastlabs.core.Posterior |
| posterior probability distribution to sample over |
| Required input |
| type: beast.base.inference.Operator*** |
| operator for generating proposals in MCMC state space |
| Required input |
| type: beast.base.inference.Logger*** |
| loggers for reporting progress of MCMC chain |
| Required input |
| type: beast.base.core.BEASTObject*** |
| list of plugins used for initialising StateNodes. Only initAndValidate is called on these plugins, but they are ignored once the chain is running |
| Optional input |