mcmcOutput-class {mcmcOutput}

Conversion to class mcmcOutput

Description

Convert output containing MCMC chains to the class mcmcOutput. The function is generic, with methods for a range of input objects.

print, summary, plot and window methods are available for the class. See also postPlot, discrepancyPlot, crosscorrPlot, postPriorOverlap.

Usage

mcmcOutput(object, ...)

## Default S3 method:
mcmcOutput(object, ...)

## S3 method for class 'mcmc.list'
mcmcOutput(object, header, ...)

## S3 method for class 'mcmc'
mcmcOutput(object, header, ...)

## S3 method for class 'jagsUI'
mcmcOutput(object, header, ...)

## S3 method for class 'bugs'
mcmcOutput(object, header, ...)

## S3 method for class 'rjags'
mcmcOutput(object, header, ...)

## S3 method for class 'runjags'
mcmcOutput(object, header, ...)

## S3 method for class 'matrix'
mcmcOutput(object, nChains=1, header, ...)

## S3 method for class 'data.frame'
mcmcOutput(object, nChains=1, header, ...)

Arguments

object

an object containing the MCMC chains; see Details.

header

text to use as the header by print and summary methods.

nChains

the number of chains.

...

named arguments to be passed to other methods (currently not used).

Details

mcmcOutput objects store the output from MCMC estimation runs in a compact and easily accessible format. Several customised extraction methods are available:

$	: extracts arrays for individual parameters in the same way as a sims.list.
[ with 1 index	: returns a new mcmcOutput object with the selected node(s).
[ with 2 indices	: returns the selected row(s) and columns(s).
[ with 3 indices	: behaves as an iterations x chains x nodes array.

Value

An object of class mcmcOutput. This is a matrix with a column for the MCMC chain for each node monitored. The first 2 attributes in the list below must be present, the rest are optional but may be used by print or summary methods:

nChains	the number of chains.
simsList	a list specifying which columns correspond to each parameter.
header	text to be displayed as the first line when the object is printed.
call	the original function call.
modelFile	the name of the original model file.
timeTaken	the time taken in seconds for the MCMC run.
runDate	an object of class POSIXct with the date of the MCMC run.

Author(s)

Mike Meredith.