R/plot_smcmc.R

In synlik: Synthetic Likelihood Methods for Intractable Likelihoods

.plot.smcmc <- function(x, trans = NULL, addPlot1 = NULL, addPlot2 = NULL, ...)
{
  if(!is(x, "smcmc")) stop("object has to be of class \"smcmc\" ")
  chains <- x@chains
  colnames(chains) <- names(x@param)
  
  oldPar <- par(no.readonly = TRUE)
  
  if(nrow(chains) > 0 )
  {
    print("Plotting the MCMC chains")
    .plotIter(chains, trans, type = "line", addPlot = addPlot1, ...)
    
    readline(prompt = "Press <Enter> to see the next plot...")
    
    print("The posterior densities")
    .plotIter(chains, trans, type = "hist", addPlot = addPlot2, ...)
    
    readline(prompt = "Press <Enter> to see the next plot...")
    
    print("Plotting the log-likelihood chain")
    par(mfrow = c(1, 1))
    plot(1:nrow(chains), x@llkChain, xlab = "Iteration", ylab = "Log-likelihood", main = "Log-likelihood chain", type = 'l', ...)
  }
  
  readline(prompt = "Press <Enter> to see the next plot...")
  
  print("Plotting correlation structure of the posterior sample")
  .plotMatrix(cor(chains), title = "Posterior correlations", xLabels = names(x@param), yLabels = names(x@param), 
              scaleLab = "Correlation", correl = TRUE, ...)
  
  readline(prompt = "Press <Enter> to see the next plot...")
  
  par(oldPar)
  
  invisible( callNextMethod(x) )
}



##########
#' @name plot-smcmc
#' 
#' @title Plotting objects of class \code{smcmc}.
#' 
#' @description Method for plotting an object of class \code{smcmc}.
#' 
#' @param x An object of class \code{smcmc}.
#' @param trans Name list or vector containing names of transforms for some parameters (ex: \code{list("par1" = "exp", "par2" = "log")}).
#'              The transformations will be applied before plotting.
#' @param addPlot1 Name of additional plotting function that will be call after the MCMC chain have been plotted. It has
#'                 to have prototype \code{fun(nam, ...)} where \code{nam} will be the parameter name. See "examples".
#' @param addPlot2 Name of additional plotting function that will be call after the histograms have been plotted. It has
#'                 to have prototype \code{fun(nam, ...)} where \code{nam} will be the parameter name. See "examples".
#' @param ... additional arguments to be passed to the plotting functions.
#'
#' @return NULL
#' 
#' @seealso \code{\link{smcmc-class}}, \code{\link{plot}}.
#' @aliases plot,smcmc,missing-method
#' @examples
#' data(ricker_smcmc)
#' 
#' # Functions for additional annotations (true parameters)
#' addline1 <- function(parNam, ...){ 
#'                abline(h = exp(ricker_smcmc@@param[parNam]), lwd = 2, lty = 2, col = 3) 
#'                }
#' addline2 <- function(parNam, ...){ 
#'                abline(v = exp(ricker_smcmc@@param[parNam]), lwd = 2, lty = 2, col = 3)
#'                }
#' 
#' # Transformations (exponentials)
#' trans <- rep("exp", 3)
#' names(trans) <- names(ricker_smcmc@@param)
#' 
#' plot(ricker_smcmc, 
#'      trans = trans,
#'      addPlot1 = "addline1", 
#'      addPlot2 = "addline2")
#' @rdname plot-smcmc
#' 
setMethod("plot",
          signature = signature(x = "smcmc", y = "missing"),
          definition = .plot.smcmc)