plot.dream: Visualising DREAM results

In dream: DiffeRential Evolution Adaptive Metropolis

Description

Plots various visualisation of MCMC chain results

Usage

## S3 method for class 'dream'
plot(x,interactive=TRUE,...)

Arguments

x	A dream object
interactive	whether to use devAskNewPage (the default) or print all at once
...	Placeholder for S3method

Details

Extracts the second half of the MCMC chains as a coda object

Calls:

• coda's plot

• coda's xyplot

• coda's densityplot

• Plots the distribution of acceptance rates

• coda's gelman.plot (may fail depending on characteristics of MCMC chains)

• Plots the evolution of the Gelman R statistic, using previously internally compueted results

• Plots the multi-variate density of the first chain

Examples

## Not run: 
  ##To run the equivalent coda visualisations:

    ss <- window(dream.obj$Sequences, start = end(dream.obj$Sequences)/2 + 1)
    plot(ss)
    print(xyplot(ss))

    ## Lattice graphics parameter density plots
    ## Each chain is superposed
    print(densityplot(ss))

    ## All chains combined (treated as one)
    print(densityplot(as.mcmc(as.matrix(ss))))

    ## Alternatively, specify burn-in within the call
    print(densityplot(dream.obj$Sequences, start = end(dream.obj$Sequences)/2 + 1))

    ## Base graphics parameter density plots
    plot(ss,trace=F)

    ## Uses densplot behind the scenes, e.g.
    densplot(ss[,1])

  
## End(Not run)

dream documentation built on May 2, 2019, 5:21 p.m.