Description Usage Arguments Details Value Note Author(s) Examples
Determines the options (number of steps, save interval, etc.) for running MCMC based on the estimated mode (maximum likelihood estimate) and parameter variance-covariance matrix
1 2 | mcmc.control(mcmc = 1000, mcmc2=0, mcsave, mcnoscale = FALSE, mcgrope =
FALSE, mcmult = 1, mcmcpars=NULL)
|
mcmc |
Total number of MCMC steps |
mcmc2 |
MCMC2 steps (see ADMB-RE manual) |
mcsave |
Thinning interval for values saved in the PSV file.
Default is |
mcnoscale |
don't rescale step size for mcmc depending on acceptance rate |
mcgrope |
(double) Use a candidate distribution that is a mixture
of a multivariate normal and a fatter-tailed distribution with a
proportion |
mcmult |
Multiplier for the MCMC candidate distribution |
mcmcpars |
(character) vector of parameters to track in MCMC run.
At least one must be specified.
ADMB produces two kinds of output for MCMC.
For any |
See the AD Model Builder reference manual. The mcrb
option
(reduce correlation of the Hessian when constructing the
candidate distribution) and the mcseed
options (seed
for random number generator) are not yet implemented; mcnoscale
above
may not work properly
Returns a list of options suitable for passing as the mcmc.opts
argument to do_admb
Some options (mcmc2
, etc.) that can be used in AD Model Builder
and ADMB-RE may not be available
Ben Bolker
1 | mcmc.control(mcmc=2000)
|
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