Defines functions plot_trend

Documented in plot_trend

#' Plot estimated trend and credible intervals
#' Plot posterior median of trend parameters and associated credible intervals.
#' @param theta A list generated by \code{extract_theta} function.  If \code{theta} is specified, do not specify a value for \code{mfit}.
#' @param mfit An object containing posterior draws from a \code{spmrf} or \code{stan} model fit.  The object can be of class \code{stanfit}, \code{array}, \code{matrix}, or \code{data.frame}.  Do not specify \code{theta} if \code{mfit} is specified.
#' @param obstype Name of probability distribution of observations.  This controls the back-transformation of the process parameters.  Possible obstypes are 'normal', 'poisson', 'binomial', or 'coalescent'. Assumed link functions are the log for 'poisson' and 'coalescent', and logit for 'binomial'.
#' @param alpha Controls level for 100*(1-\code{alpha})\% Bayesian credible intervals.
#' @param obsvar Vector of observations. Assumed to be ordered by time with one observation per time point. If \code{obsvar} is NULL, then data are not plotted. Note if plotting observations you must also specify a matching \code{xvar} of the same length.
#' @param uxvar vector of unique values of the grid locations of the trend parameters. This can be a numeric or integer vector. Must be the same length as \code{theta} and must be sorted to match order of locations of \code{theta} elements. If not specified and no \code{xvar} is specified, then a sequence from 1 to the length of \code{theta} with unit spacing will be used.  If \code{xvar} and \code{obsvar} are specified, then \code{uxvar} does not need to be specified.   
#' @param xvar x-variable for plotting observations \code{obsvar}. Should be a numeric integer vector.  Must be the same length as observation vector (\code{obsvar}). Must be specified if \code{obsvar} is specified.  
#' @param colset Color set for trend and credible intervals.  These are presets chosen with common color combinations.  Choices are 'blue', 'purple', 'red', 'green', and 'gray'. This parameter is overridden If \code{trend.col} and \code{bci.col} are specified.
#' @param trend.col Color of the trend line.  Any standard \code{R} plotting colors are allowed. Use this along with \code{bci.col} if color choices other than the presets provided by colset are desired.
#' @param bci.col Color of the credible interval band. Any standard \code{R} colors are allowed.
#' @param pt.col  Color of data points if plotted with \code{obsvec} specified.
#' @param pt.pch  Type of points to use if data plotted with \code{obsvec} specified (see \code{points} for details.
#' @param pt.cex  Size of points to use if data plotted with \code{obsvec} specified (see \code{points} for details.
#' @param xlab Character string describing label for x-axis.  Default is "x" if unspecified.
#' @param ylab Character string describing label for y-axis.  Default is "y" if unspecified.
#' @param main Character string describing label for main title.  Default is "" empty string.
#' @param xlim Numeric vector with two elements describing limits of x-variable. Default is \code{range} of sequence from 1 to max length of elements in \code{theta} or number of rows in \code{mfit}.
#' @param ylim Numeric vector with two elements describing limits of y-variable. Default is \code{range} of combined vector of \code{obsvec} and extreme values of BCI's if unspecified.
#' @param ... Additional parameters passed to the \code{plot} function.
#' @details  The input can be either in the form of a list generated by the \code{extract_theta} function (passed in as the \code{theta} variable) or as a raw model fit object from \code{spmrf} or \code{rstan} (passed in as \code{mfit}).  Note that using \code{mfit} is more computationally costly than using \code{theta} because the \code{extract_theta} function is called when \code{mfit} is specified.
#' @return Returns a \code{plot} object.
#' @seealso \code{\link[graphics]{plot}}, \code{\link[graphics]{points}}, \code{\link{extract_theta}}, \code{\link{spmrf}}, \code{\link[rstan]{stanfit}}, \code{\link[base]{array}}, \code{\link[base]{matrix}}, \code{\link[base]{data.frame}}
#' @export
plot_trend <- function(theta=NULL, mfit=NULL,  obstype="normal", alpha=0.05, obsvar=NULL, uxvar=NULL, xvar=NULL, colset="blue", trend.col=NULL, trend.lwd=3, bci.col=NULL, pt.col="gray60", pt.pch=1, pt.cex=1, ylab, xlab, main, ylim, xlim, ...){

	if (is.null(theta) & is.null(mfit)) stop("Must specify either a list with theta summary or a stan model fit object.")
	if (is.null(theta) & !is.null(mfit))	thp <- extract_theta(mfit, obstype, alpha)
  if (!is.null(theta) & !is.null(mfit)) stop("Must specify either a list with theta summary or a stan model fit object, but not both.")
	if (!is.null(theta) & is.null(mfit)) {
		  if (class(theta)!="list") stop("Argument theta must be a list.")
		  thp <- theta
	if (!is.null(obsvar) & is.null(xvar)) stop("Must specify xvar if using obsvar")

	if (is.null(trend.col) & is.null(bci.col)) {
		if (!(colset %in% c('blue','green','purple','red','gray')) ) stop("Preset colors for colset are 'blue', 'green', 'red', 'purple', and 'gray'.")
		if (colset=="blue"){
			tcol <- "blue"
			bcol <- "lightblue"
		if (colset=="green"){
			tcol <- "green3"
			bcol <- "lightgreen"
		if (colset=="red"){
			tcol <- "red"
			bcol <- "pink"
		if (colset=="purple") {
			tcol <- "purple"
			bcol <- "lavender"
		if (colset=="gray"){
			tcol <- "black"
			bcol <- "gray80"

	if (is.null(trend.col) & !is.null(bci.col)) stop("Must specify trend.col if specifying bci.col")
	if (!is.null(trend.col) & is.null(bci.col)) stop("Must specify bci.col if specifying trend.col")
	if (!is.null(trend.col) & !is.null(bci.col) ) {
		tcol <- trend.col
		bcol <- bci.col

	nn <- length(thp$postmed)

	if (is.null(uxvar) & !is.null(xvar)) uxvar <- sort(unique(xvar))
	if (is.null(uxvar) & is.null(xvar)) uxvar <- 1:nn

	prng <- range(c(thp$bci.lower, thp$bci.upper, obsvar))
  dum <- seq(prng[1], prng[2], length=nn)

  if (missing(ylim)) ylim <- prng
  if (missing(xlim)) xlim <- range(uxvar)
  if (missing(ylab)) ylab <- "y"
  if (missing(xlab)) xlab <- "x"
  if (missing(main)) main <- ""

	plot(uxvar, dum, type="n", ylim=ylim, xlim=xlim,ylab=ylab,xlab=xlab,main=main,  ...)
	  polygon(c(uxvar, rev(uxvar)), c(thp$bci.lower , rev(thp$bci.upper)), border=NA, col=bcol)
	  if (!is.null(obsvar)) points(xvar, obsvar, pch=pt.pch, col=pt.col,  cex=pt.cex)
	  lines(uxvar, thp$postmed, col=tcol, lwd=trend.lwd)

faulknerjam/bnps documentation built on Oct. 18, 2018, 12:03 p.m.