mcmcOutputConvert 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.
mcmcOutput(object, ...)# S3 method for default
mcmcOutput(object, ...)
# S3 method for mcmc.list
mcmcOutput(object, header, ...)
# S3 method for mcmc
mcmcOutput(object, header, ...)
# S3 method for jagsUI
mcmcOutput(object, header, ...)
# S3 method for bugs
mcmcOutput(object, header, ...)
# S3 method for rjags
mcmcOutput(object, header, ...)
# S3 method for runjags
mcmcOutput(object, header, ...)
# S3 method for matrix
mcmcOutput(object, nChains=1, header, ...)
# S3 method for data.frame
mcmcOutput(object, nChains=1, header, ...)
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. |
an object containing the MCMC chains; see Details.
text to use as the header by print and summary methods.
the number of chains.
named arguments to be passed to other methods (currently not used).
Mike Meredith.
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. |