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Tip revision: e59f1fc3b0389804e671d681b7fc639e687d4154 authored by Tracy Sweet on 01 March 2020, 06:00:06 UTC
version 0.8.2
Tip revision: e59f1fc

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

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


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


	object or list of objects of class 'HLSM' returned by \code{HLSMrandomEf()} or \code{HLSMfixedEF()}

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

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

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

    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.
      the matched call.    
       list of matrices of suggested niters, burnin, and thinning for each chain.
      list containing \code{psrf}, a matrix of psrf estimates and upper limits for variable, and \code{mpsrf} the multivariate psrf estimate.

    Christian Meyer

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