BTSPAS (version 2024.5.9)

plot_trace: Creates trace plots of specified parameters showing the multiple chains and the value of Rhat

Description

Takes the MCMC object returned from a split and produces trace_plots for the listed parameters. It shows a separate line on the plot for each chain and also shows the value of Rhat

Usage

plot_trace(
  title = " ",
  results = NULL,
  parms_to_plot = NULL,
  nrow = 2,
  ncol = 2
)

Value

List of ggplot2 objects using facet_wrap_paginate (...., page=...) with each element of the list corresponding to one page of the plot.

Arguments

title

A character string used for a title on reports and graphs

results

The MCMC object containing the results from the call to JAGS

parms_to_plot

A character vector of names of parameters to plot. These must match exactly to the parameter names used in the simulation.

ncol, nrow

How many plots to put on a page (number of rows and columns)

Author

Bonner, S.J. and Schwarz, C. J. .

Examples

if (FALSE) {
# Create trace plots of the logitP parameters
# 
# Trace plots of logitP
varnames <- names(results$sims.array[1,1,])  # extract the names of the variables 
trace.plot <- plot_trace(title=title, 
                         results=results, 
                         parms_to_plot=varnames[grep("^logitP", varnames)])
if(save.output.to.files){
  pdf(file=paste(prefix,"-trace-logitP.pdf",sep=""))
  plyr::l_ply(trace.plot, function(x){plot(x)})
  dev.off()
}
} # end of dontrun