BEASTObject that performs calculations based on the State.
Probabilistic representation that can produce a log probability for instance for running an MCMC chain.
Takes a collection of tree likelihoods and combines them into the compound of these distributions while tuning the number of threads, types of BEAGLE instances, andwhether to use BEAGLE 2 or 3 API (i.e. seperate TreeLikelihoods or MultiPartitionTreeLikelihood). Self tuning replacement of CompounDistribution with id=='likelihood'.
Logable: yes, this can be used in a log.
distribution, useThreads, minThreads, maxThreads, ignore, switchCount, reconfigCount, stopAfterSamerResults, includeMPTL, includeSPTL, *
| type: beast.base.inference.Distribution*** |
| individual probability distributions, e.g. the likelihood and prior making up a posterior |
| Optional input |
| type: java.lang.Boolean |
| calculated the distributions in parallel using threads (default true) |
| Optional input. Default: true |
| type: java.lang.Integer |
| minimum number of threads to use (default 1) |
| 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) |
| Optional input. Default: -1 |
| type: java.lang.Boolean |
| ignore all distributions and return 1 as distribution (default false) |
| Optional input. Default: false |
| type: java.lang.Long |
| number of milli seconds to calculate likelihood before switching configuration |
| Optional input |
| type: java.lang.Long |
| number of times to calculate likelihood before self tuning again |
| Optional input |
| type: java.lang.Integer |
| number of times the same configuration is optimal in a row before stopping to tune |
| Optional input. Default: 3 |
| type: java.lang.Boolean |
| include multi-partition (BEAGLE 3) tree likelihood in configurations |
| Optional input. Default: true |
| type: java.lang.Boolean |
| include single-partition (BEAGLE 2) tree likelihood in configurations |
| Optional input. Default: true |
| type: ? |
| Optional input |