HLSMdiag: Function to conduct diagnostics the MCMC chain from a random effect HLSM (and HLSMfixedEF for fixed effects model)

Description

Function to compute and report diagnostic plots and statistics for a single or multiple HLSM objects.

Usage

HLSMdiag(object, burnin = 0,
         diags = c('psrf', 'raftery', 'traceplot', 'autocorr'),
         col = 1:6, lty = 1)

Arguments

object

object or list of objects of class 'HLSM' returned by HLSMrandomEf() or HLSMfixedEF()

burnin

numeric value to burn the chain while extracting results from the 'HLSM'object. Default is burnin = 0.

diags

a character vector that is a subset of c('psrf', 'raftery', 'traceplot', 'autocorr'). Default returns all diagnostics. If only a single chain is supplied in object, 'psrf' throws a warning if explicitly requested by user.

col

a character or integer vector specifying the colors for the traceplot and autocorr plot

lty

a character or integer vector specifying the linetype for the traceplot and autocorr plot

Value

Returns an object of class "HLSMdiag". It is a list that contains variable-level diagnostic tables from either or both of the raftery diagnostic and psrf diagnostic. When returned to the console, a summary table of the diagnostics will be printed instead of the list representation of the object.

call

the matched call.

raftery

list of matrices of suggested niters, burnin, and thinning for each chain.

psrf

list containing psrf, a matrix of psrf estimates and upper limits for variable, and mpsrf the multivariate psrf estimate.