Nothing
.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)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.