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.
MCMC that can tune the treelikelihood for efficiency
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.
doi:10.1371/journal.pcbi.1006650
useThreads, minThreads, maxThreads, switchCount, reconfigCount, stopAfterSamerResults, includeMPTL, includeSPTL, chainLength, state, init, storeEvery, preBurnin, numInitializationAttempts, distribution, operator, logger, sampleFromPrior, operatorschedule
| type: java.lang.Boolean |
| calculated the distributions in parallel using threads (default true)-- only used if no SelfTuningCompoundDistribution specified. |
| Optional input. Default: true |
| type: java.lang.Integer |
| minimum number of threads to use (default 1)-- only used if no SelfTuningCompoundDistribution specified. |
| Optional input. Default: 1 |
| type: java.lang.Integer |
| maximum number of threads to use, if less than 1 the number of threads in BeastMCMC is used (default -1)-- only used if no SelfTuningCompoundDistribution specified. |
| Optional input. Default: -1 |
| type: java.lang.Long |
| number of milli seconds to calculate likelihood before switching configuration-- only used if no SelfTuningCompoundDistribution specified. |
| Optional input |
| type: java.lang.Long |
| number of times to calculate likelihood before self tuning again-- only used if no SelfTuningCompoundDistribution specified. |
| Optional input |
| type: java.lang.Integer |
| number of times the same configuration is optimal in a row before stopping to tune-- only used if no SelfTuningCompoundDistribution specified. |
| Optional input. Default: 3 |
| type: java.lang.Boolean |
| include multi-partition (BEAGLE 3) tree likelihood in configurations-- only used if no SelfTuningCompoundDistribution specified. |
| Optional input. Default: true |
| type: java.lang.Boolean |
| include single-partition (BEAGLE 2) tree likelihood in configurations-- only used if no SelfTuningCompoundDistribution specified. |
| Optional input. Default: true |
| type: java.lang.Long |
| Length of the MCMC chain i.e. number of samples taken in main loop |
| Required input |
| type: beast.base.inference.State |
| elements of the state space |
| Optional input |
| type: beast.base.inference.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.base.inference.Distribution |
| probability distribution to sample over (e.g. a posterior) |
| Required input |
| type: beast.base.inference.Operator*** |
| operator for generating proposals in MCMC state space |
| Optional input |
| type: beast.base.inference.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.base.inference.OperatorSchedule |
| specify operator selection and optimisation schedule |
| Required input |