mcmc.control: Control options for MCMC after ADMB fitting
In bbolker/glmmadmb: Generalized Linear Mixed Models using 'AD Model Builder'

Description Usage Arguments Details Value Note 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	mcmcControl(mcmc = 1000, mcmc2=0, mcsave, mcnoscale = FALSE, mcgrope = FALSE, mcmult = 1)

`mcmc`	Total number of MCMC steps
`mcmc2`	MCMC2 steps (see ADMB-RE manual)
`mcsave`	Thinning interval. Default is `pmax(1,floor(mcmc/1000))`, i.e. aim to save 1000 steps
`mcnoscale`
`mcgrope`
`mcmult`

See the AD Model Builder reference manual

Returns a list of options suitable for passing as the mcmc.opts argument to glmmadmb

Some options (mcmc2, etc.) that can be used in AD Model Builder and ADMB-RE may not be available

The functions in the coda and plotMCMC packages are useful for diagnosing convergence and other problems, summarizing, and displaying the results of MCMC runs.

The tools for working with MCMC output in glmmADMB are limited at the moment (sorry!) — in particular, the fixed-effect parameter estimates are given in terms of the internally fitted variables (which uses an orthogonalized version of the original design matrix), not the original coefficients. If you need to use the MCMC output, please contact the maintainers and encourage them to work on them some more.

Ben Bolker