MCMC settings class — SCAMCMC • FLa4a

Class definition (slots), constructors, accessors, replacement (when relevant) and common methods.

SCAMCMC(object, ...)

# S4 method for class 'missing'
SCAMCMC(object, ...)

getADMBCallArgs(object, ...)

getN(object, ...)

# S4 method for class 'SCAMCMC'
getN(object, ...)

Arguments

object: a SCAMCMC object
...: extra arguments

Slot

mcmc N: Run N MCMC iterations
mcsave N: Save every N th MCMC iteration
mcscale N: Rescale step size for first N iterations
mcmult N: Rescale the covariance matrix
mcrb N: Reduce high parameter correlations
mcprobe X: Use a fat-tailed proposal distribution
mcdiag: Use a diagonal covariance matrix
mcnoscale: Do not scale the algorithm during
mcu: Use a uniform distribution as proposal distribution
hybrid: Use the hybrid method
hynstep N: Mean number of steps for the leapfrog method
hyeps X: The stepsize for the leapfrog method [X numeric and > 0]

Accessors

All slots in the class have accessor and replacement methods defined that allow retrieving and substituting individual slots.

The values passed for replacement need to be of the class of that slot. A numeric vector can also be used when replacing FLQuant slots, and the vector will be used to substitute the values in the slot, but not its other attributes.

Constructor

A construction method exists for this class that can take named arguments for any of its slots. All slots are then created to match the requirements of the class validity. If an unnamed FLQuant object is provided, this is used for sizing, but not for populating any slot.