# R/GQD.plot.R In DiffusionRgqd: Inference and Analysis for Generalized Quadratic Diffusions

``` GQD.plot=function(x,thin=1,burns,h=FALSE,palette='mono')
{
if(class(x)=='GQD.mcmc')
{
par.matrix=t(x\$par.matrix)
prop.matrix=t(x\$prop.matrix)
theta=par.matrix[,1]
acc=x\$acceptance.rate
tt = seq(1,dim(x\$par.matrix)[1],thin)

nper=length(theta)
if(nper==1){par(mfrow=c(1,2));d1=1;d2=1;}
if(nper==2){par(mfrow=c(2,2));d1=1;d2=2;}
if(nper==3){par(mfrow=c(2,2));d1=2;d2=2;}
if(nper>3)
{
d1=1:((nper)+1)
d2=d1
O=outer(d1,d2)
test=O-((nper)+1)
test[test<0]=100
test=test[1:4,1:4]
test
wh=which(test==min(test))

d1=d1[col(test)[wh[1]]]
d2=d2[row(test)[wh[1]]]
par(mfrow=c(d1,d2))
}
if(palette=='mono')
{
cols =rep('#222299',nper)
}else{
cols=rainbow_hcl(nper, start = 10, end = 275,c=100,l=70)
}
ylabs=paste0('theta[',1:nper,']')
for(i in 1:nper)
{
if(h)
{
hist(par.matrix[i,tt],col=cols[i],main=ylabs[i],freq=F)
}else
{
plot(prop.matrix[i,tt]~tt,col='gray90',type='s',main=ylabs[i],xlab='Iteration',ylab='')
lines(par.matrix[i,tt]~tt,col=cols[i],type='s')
if(!missing(burns)){abline(v=burns,lty='dotdash')}
}
}
plot(acc,type='l',ylim=c(0,1),col='darkblue',main='Accept. Rate',xlab='Iteration',ylab='%/100')
abline(h=seq(0,1,1/10),lty='dotted')
if(!missing(burns)){abline(v=burns,lty='dotdash')}
abline(h=0.4,lty='solid',col='red',lwd=1.2)
abline(h=0.2,lty='solid',col='red',lwd=1.2)

box()
}

if(class(x)=='GQD.mle')
{
stop('Nothing to plot!')
}

if(class(x)=='GQD.density')
{
if(requireNamespace('rgl', quietly = TRUE))
{

open3d(windowRect=c(50,50,640+50,50+640),zoom=0.95)
persp3d(x=x\$Xt,y=x\$time,z=x\$density,col='white',box=F,xlab='State (X_t)',ylab='Time (t)',zlab='Density f(X_t|X_s)')
play3d(spin3d(axis=c(0,0,1), rpm=3), duration=10)
}else
{

}
}

if(class(x)=='BiGQD.density')
{
colpal=function(n){rev(sequential_hcl(n,power=0.8,l=c(40,100)))}
for(i in 1:dim(x\$density)[3])
{

# Now illustrate the density:
filled.contour(x\$Xt,x\$Yt,x\$density[,,i],
main=paste0('Transition Density \n (t = ',x\$time[i],')'),
color.palette=colpal
,xlab='Xt',ylab='Yt')
}
}
}
```

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DiffusionRgqd documentation built on May 2, 2019, 3:26 a.m.