# R/joint.pr.plot.R In LaplacesDemon: Complete Environment for Bayesian Inference

#### Documented in joint.pr.plot

```###########################################################################
# joint.pr.plot                                                           #
#                                                                         #
# The purpose of the joint.pr.plot function is to plot a joint            #
# probability region. The joint.pr.plot function uses modified forms of   #
# the ellipse and dataEllipse functions from the car package.             #
###########################################################################

joint.pr.plot <- function(x, y, quantiles=c(0.25,0.50,0.75,0.95))
{
### Function from car package for ellipses
ellipse <- function(center, shape, radius, log="", center.pch=19,
ylab="", col=palette()[2], lwd=2, fill=FALSE, fill.alpha=0.3,
...)
{
trans.colors <- function(col, alpha=0.5, names=NULL) {
# this function by Michael Friendly
nc <- length(col)
na <- length(alpha)
# make lengths conform, filling out to the longest
if(nc != na) {
col <- rep(col, length.out=max(nc,na))
alpha <- rep(alpha, length.out=max(nc,na))}
clr <-rbind(col2rgb(col)/255, alpha=alpha)
col <- rgb(clr[1,], clr[2,], clr[3,], clr[4,], names=names)
return(col)}
logged <- function(axis=c("x", "y")){
axis <- match.arg(axis)
0 != length(grep(axis, log))}
if(!(is.vector(center) && 2==length(center)))
stop("center must be a vector of length 2")
if(!(is.matrix(shape) && all(2==dim(shape))))
stop("shape must be a 2 by 2 matrix")
if(max(abs(shape - t(shape)))/max(abs(shape)) > 1e-10)
stop("shape must be a symmetric matrix")
angles <- (0:segments)*2*pi/segments
unit.circle <- cbind(cos(angles), sin(angles))
Q <- chol(shape, pivot=TRUE)
order <- order(attr(Q, "pivot"))
ellipse <- t(center + radius*t( unit.circle %*% Q[,order]))
colnames(ellipse) <- c("x", "y")
if(logged("x")) ellipse[, "x"] <- exp(ellipse[, "x"])
if(logged("y")) ellipse[, "y"] <- exp(ellipse[, "y"])
fill.col <- trans.colors(col, fill.alpha)
if(draw) {
lines(ellipse, col=col, lwd=lwd, ...)
if(fill) polygon(ellipse, col=fill.col, border=NA)
}
else {
plot(ellipse, type="n", xlab=xlab, ylab=ylab, ...)
lines(ellipse, col=col, lwd=lwd, ... )
if(fill) polygon(ellipse, col=fill.col, border=NA)
}
if((center.pch != FALSE) && (!is.null(center.pch)))
points(center[1], center[2], pch=center.pch,
cex=center.cex, col=col)}
invisible(ellipse)
}
### Function from car package for ellipses
dataEllipse <- function(x, y, weights, log="", quantiles=c(0.5, 0.95),
center.pch=19, center.cex=1.5, draw=TRUE, plot.points=draw,
ylab=deparse(substitute(y)), col=palette()[1:2], lwd=1,
fill=FALSE, fill.alpha=0.3, ...)
{
if(length(col) == 1) col <- rep(col, 2)
if(missing(y)) {
if(is.matrix(x) && ncol(x) == 2) {
if(missing(xlab)) xlab <- colnames(x)[1]
if(missing(ylab)) ylab <- colnames(x)[2]
y <- x[,2]
x <- x[,1]
}
else stop("x and y must be vectors, or x must be a 2 column matrix.")
}
else if(!(is.vector(x) && is.vector(y) && length(x) == length(y)))
stop("x and y must be vectors of the same length")
if(missing(weights)) weights <- rep(1, length(x))
if(length(weights) != length(x))
stop("weights must be of the same length as x and y")
if(draw) {
mycol <- rgb(0, 100, 0, 50, maxColorValue=255)
plot(x, y, type="n", col=mycol, pch=16, xlab=xlab,
ylab=ylab, ...)
if(plot.points) points(x, y, col=mycol, pch=16, ...)}}
dfn <- 2
dfd <- length(x) - 1
v <- cov.wt(cbind(x, y), wt=weights)
shape <- v\$cov
center <- v\$center
result <- vector("list", length=length(quantiles))
names(result) <- quantiles
for (i in seq(along=quantiles)) {
level <- quantiles[i]
radius <- sqrt(dfn * qf(level, dfn, dfd))
result[[i]] <- ellipse(center, shape, radius, log=log,
center.pch=center.pch, center.cex=center.cex,
segments=segments, col=col[1], lwd=lwd, fill=fill,
fill.alpha=fill.alpha, draw=draw, ...)}
invisible(if(length(quantiles) == 1) result[[1]] else result)
}
dataEllipse(x, y, quantiles=quantiles)
}

#End
```

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LaplacesDemon documentation built on July 1, 2018, 9:02 a.m.