Nothing
`plot.bgpd` <-
function( x, which.plots=1:3, density.adjust=2,
print.seed = FALSE , ...){
varnames <- names(coef(x))
if ( 1 %in% which.plots ){
kdes <- list()
if (is.R()){
for (i in 1:length(varnames)){
kdes[[ i ]] <- density(x$param[, i], n=200, adjust=density.adjust)
}
}
else {
for (i in 1:length(varnames)){
bw <- bandwidth.hb(x$param[, i]) * density.adjust
kdes[[i]] <- density(x$param[, i], n=200, width=bw)
}
}
for( i in 1:length(kdes)){
plot(kdes[[i]], type = "l" , xlab = varnames[i] , ylab="Density" ,
main = paste("Posterior for", varnames[i]))
polygon( c( rev( kdes[[i]]$x ), kdes[[i]]$x ),
c( rep( 0 , length( kdes[[i]]$y ) ) , kdes[[i]]$y ),
col=6
)
m <- mean( x$param[, i] )
ym <- kdes[[i]]$y[abs(kdes[[i]]$x - m) == min( abs(kdes[[i]]$x - m ) ) ]
if( is.R()){
segments( x0=m, y0=0, y1=ym , x1=m )
}
else{ segments( m, y1=0, y2=ym ) }
if ( print.seed )
title( sub = paste( c( "Seed: ", x$seed ) , collapse = " " ),
adj=0 )
}
}
if( 2 %in% which.plots ){
# Trace plots and moving averages
for (i in 1:length(varnames)){
plot( x$chains[ , i], type = "l" , xlab = "Step number", ylab = paste(varnames[i], "& cumulative mean"))
lines( cumsum( x$chains[ , i] ) / (1:nrow( x$chains)), lwd=3, col=8 )
axis( 4 )
abline( v = x$burn, lty=4, lwd=3, col=2 )
if ( print.seed )
title( sub = paste( c( "Seed: ", x$seed ) , collapse = " " ), adj=0 )
}
}
if(3 %in% which.plots){
# Plot ACFs
for(i in 1:length(varnames)){
acf( x$param[ , i] , main = paste("ACF for", varnames[i], "\n(thin =",x$thin,")"))
if ( print.seed )
title( sub = paste( c( "Seed: ", x$seed ) , collapse = " " ), adj=0 )
}
}
invisible()
}
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