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#Get traceplots for series of parameters
traceplot <- function(x, parameters=NULL, Rhat_min=NULL,
per_plot=9, ask=NULL){
#Check input class and get basic plot settings
check_class(x)
if(is.null(ask))
ask <- grDevices::dev.interactive(orNone = TRUE)
plot_info <- get_plot_info(x, parameters, per_plot, ask, Rhat_min)
#Handle par()
old_par <- graphics::par(plot_info$new_par)
on.exit(graphics::par(old_par))
#Generate plot
n <- length(plot_info$params)
for (i in 1:n){
m_labels <- (i %% plot_info$per_plot == 0) || (i==n)
param_trace(x, plot_info$params[i], m_labels=m_labels)
}
}
#Traceplot for single parameter
param_trace <- function(x, parameter, m_labels=FALSE){
#Get samples and Rhat values
vals <- mcmc_to_mat(x$samples, parameter)
Rhat <- sprintf("%.3f",round(x$summary[parameter, 'Rhat'],3))
#Draw plot
cols <- grDevices::rainbow(ncol(vals))
graphics::matplot(1:nrow(vals), vals, type='l', lty=1, col=cols,
xlab='Iterations', ylab='Value',
main=paste('Trace of',parameter))
# graphics::plot(1:nrow(vals), vals[,1], type='l', col=cols[1],
# ylim=range(vals), xlab='Iterations', ylab='Value',
# main=paste('Trace of',parameter))
# for (i in 2:ncol(vals)) graphics::lines(1:nrow(vals), vals[,i], col=cols[i]) # this fails with 1 chain
#Add Rhat value
graphics::legend('bottomright', legend=bquote(hat(R) == .(Rhat)),
bty='o', bg='white', cex=1.2)
#Add margin labels if necessary
if(m_labels){
graphics::mtext("Iteration", side=1, line=1.5, outer=TRUE)
graphics::mtext("Value", side=2, line=1.5, outer=TRUE)
}
}
#General function for setting up plots
# get_plot_info now has its own file
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