BEASTObject that performs calculations based on the State.
Probabilistic representation that can produce a log probability for instance for running an MCMC chain.
A class that produces a distribution chaining values in a parameter through the Gamma distribution. The value of a parameter is assumed to be Gamma distributed with mean as the previous value in the parameter. If useLogNormal is set, a log normal distribution is used instead of a Gamma. If a Jeffrey's prior is used, the first value is assumed to be distributed as 1/x, otherwise it is assumed to be uniform. Handy for population parameters.
Logable: yes, this can be used in a log.
jeffreys, reverse, uselog, shape, parameter, initialMean, useLogNormal
| type: java.lang.Boolean |
| use Jeffrey's prior (default false) |
| Optional input. Default: false |
| type: java.lang.Boolean |
| parameter in reverse (default false) |
| Optional input. Default: false |
| type: java.lang.Boolean |
| use logarithm of parameter values (default false) |
| Optional input. Default: false |
| type: java.lang.Double |
| shape parameter of the Gamma distribution (default 1.0 = exponential distribution) or precision parameter if the log normal is used. |
| Optional input. Default: 1.0 |
| type: beast.core.Function |
| chain parameter to calculate distribution over |
| Required input |
| type: beast.core.Function |
| the mean of the prior distribution on the first element. This is an alternative boundary condition to Jeffrey's on the first value. |
| Optional input |
| type: java.lang.Boolean |
| use Log Normal distribution instead of Gamma (default false) |
| Optional input. Default: false |