[This article was first published on Xi'an's Og » R, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

As a result of a corridor conversation in Warwick, I started looking at distributions on the IR³ simplex,

$\{(x_1,x_2,x_3)\in\mathbb{R}_+^3;\ x_1+x_2+x_3=1\},$

and wanted to plot the density in a nice way. As I could not find a proper package on CRAN, the closer being the BMAmevt (for Bayesian Model Averaging for Multivariate Extremes) R package developed by a former TSI Master student, Anne Sabourin, I ended up programming the thing myself. And producing the picture above. Here is the code, for all it is worth:

# setting the limits
par(mar=c(0,0,0,0),bg="black")
plot(c(0,1),col="white",axes=F,xlab="",ylab="",
xlim=c(-1,1)*1.1/sqrt(2),ylim=c(-.1,sqrt(3/2))*1.1)

# density on a grid with NAs outside, as in image()
gride=matrix(NA,ncol=520,nrow=520)
ww3=ww2=seq(.01,.99,le=520)
for (i in 1:520){
cur=ww2[i];op=1-cur
for (j in 1:(521-i))
gride[i,j]=mydensity(c(cur,ww3[j],op-ww3[j]))
}

# preparing the graph
subset=(1:length(gride))[!is.na(gride)]
logride=log(gride[subset])
grida=(logride-min(logride))/diff(range(logride))
grolor=terrain.colors(250)[1+trunc(as.vector(grida)*250)]
iis=(subset%%520)+520*(subset==520)
jis=(subset%/%520)+1

# plotting the value of the (log-)density
# at each point of the grid
points(x=(ww3[jis]-ww2[iis])/sqrt(2),
y=(1-ww3[jis]-ww2[iis])/sqrt(2/3),
pch=20,col=grolor,cex=.3)


Filed under: pictures, R, Statistics, University life Tagged: Bayesian inference, image(), posterior distribution, R, simplex, surface, terrain.colors()

To leave a comment for the author, please follow the link and comment on their blog: Xi'an's Og » R.

R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job.
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

# Never miss an update! Subscribe to R-bloggers to receive e-mails with the latest R posts.(You will not see this message again.)

Click here to close (This popup will not appear again)