Nothing
### DPraschpoisson.R
### Fit a Rasch Poisson model with a Dirichlet Process prior
### for the random effect distribution
###
### Copyright: Alejandro Jara, 2006-2012.
###
### Last modification: 04-09-2009.
###
### This program is free software; you can redistribute it and/or modify
### it under the terms of the GNU General Public License as published by
### the Free Software Foundation; either version 2 of the License, or (at
### your option) any later version.
###
### This program is distributed in the hope that it will be useful, but
### WITHOUT ANY WARRANTY; without even the implied warranty of
### MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
### General Public License for more details.
###
### You should have received a copy of the GNU General Public License
### along with this program; if not, write to the Free Software
### Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
###
### The author's contact information:
###
### Alejandro Jara
### Department of Statistics
### Facultad de Matematicas
### Pontificia Universidad Catolica de Chile
### Casilla 306, Correo 22
### Santiago
### Chile
### Voice: +56-2-3544506 URL : http://www.mat.puc.cl/~ajara
### Fax : +56-2-3547729 Email: atjara@uc.cl
###
DPraschpoisson <- function(y,prior,mcmc,offset,state,status,grid=seq(-10,10,length=1000),
data=sys.frame(sys.parent()),compute.band=FALSE)
UseMethod("DPraschpoisson")
DPraschpoisson.default<-
function(y,
prior,
mcmc,
offset=NULL,
state,
status,
grid=seq(-10,10,length=1000),
data=sys.frame(sys.parent()),
compute.band=FALSE)
{
#########################################################################################
# call parameters
#########################################################################################
cl <- match.call()
y <- as.matrix(y)
#########################################################################################
# data structure
#########################################################################################
nsubject <- nrow(y)
p <- ncol(y)
ywork <- y
datastrm <- NULL
nmissing <- 0
total <- 0
for(i in 1:nsubject)
{
for(j in 1:p)
{
if(is.na(y[i,j]))
{
nmissing <- nmissing+1
datastrm <- rbind(datastrm,c(i,j))
}
else
{
total <- total+y[i,j]
}
}
}
nrec <- nsubject*p-nmissing
if(nmissing>0)
{
imiss <- 1
for(i in 1:nmissing)
{
ywork[datastrm[i,1],datastrm[i,2]] <- rpois(1,total/nrec)
}
}
else
{
imiss <- 0
nmissing <- 1
datastrm <- matrix(0,nrow=1,ncol=2)
}
#########################################################################################
# prior information
#########################################################################################
if(is.null(prior$a0))
{
a0 <- -1
b0 <- -1
alpha <- prior$alpha
alpharand <- 0
}
else
{
a0 <- prior$a0
b0 <- prior$b0
alpha <- 1
alpharand <- 1
}
a0b0 <- c(a0,b0)
if(is.null(prior$tau1))
{
tau1 <- -1
tau2 <- -1
sigma2 <- prior$sigma2
sigmainv <- 1/sigma2
sigmarand <- 0
}
else
{
tau1 <- prior$tau1
tau2 <- prior$tau2
sigma2 <-1
sigmainv <- 1/sigma2
sigmarand <- 1
}
if(is.null(prior$mub))
{
psiinv <- -1
smu <- 0
mu <- prior$mu
murand <- 0
}
else
{
psiinv <- (1/prior$Sb)
smu <- psiinv*prior$mub
mu <- rnorm(1,prior$mub,sqrt(prior$Sb))
murand <- 1
}
b0 <- prior$beta0
prec <- solve(prior$Sbeta0)
sb <- prec%*%prior$beta0
if(dim(prec)[1] != (p-1)) stop("the dimension of beta0 and Sbeta0 must be p-1")
#########################################################################################
# mcmc specification
#########################################################################################
mcmcvec <- c(mcmc$nburn,mcmc$nskip,mcmc$ndisplay)
nsave <- mcmc$nsave
#########################################################################################
# output
#########################################################################################
acrate <- rep(0,2)
cpo <- matrix(0,nrow=nsubject,ncol=p)
cpov <- rep(0,nsubject)
ngrid <- length(grid)
cdfsave <- matrix(0,nrow=nsave,ncol=ngrid)
thetasave <- matrix(0,nrow=nsave,ncol=p+5)
randsave <- matrix(0,nrow=nsave,ncol=nsubject+1)
#########################################################################################
# MLE estimation
#########################################################################################
RaschMLE <- function(y,nitem,nsubject,offset)
{
ywork2 <- NULL
roffset <- NULL
id <- NULL
x <- NULL
count <- 0
for(i in 1:nsubject)
{
ywork2 <- c(ywork2,y[i,])
roffset <- c(roffset,offset[i,])
id <- c(id,rep(i,nitem))
aa <- diag(-1,nitem)
aa[,1] <- 1
x <- rbind(x,aa)
}
out <- NULL
#library(nlme)
# library(MASS)
fit0 <- glmmPQL(ywork2~x-1+offset(roffset),random = ~ 1 | id,family=poisson(log), verbose = FALSE)
beta <- as.vector(fit0$coeff$fixed[2:nitem])
b <- as.vector(fit0$coeff$fixed[1]+fit0$coeff$random$id)
out$beta <- beta
out$b <- b
out$mu <- fit0$coeff$fixed[1]
out$sigma2 <- getVarCov(fit0)[1]
return(out)
}
if(is.null(offset))
{
roffset <- matrix(0,nrow=nsubject,ncol=p)
}
else
{
roffset <- offset
}
fit0 <- RaschMLE(ywork,p,nsubject,roffset)
#########################################################################################
# parameters depending on status
#########################################################################################
if(status==TRUE)
{
beta <- fit0$beta
b <- fit0$b
bclus <- c(b,rep(0,100))
ncluster <- nsubject
ss <- seq(1,nsubject)
if(murand==1) mu <- fit0$mu
if(sigmarand==1) sigma2 <- fit0$sigma2
}
if(status==FALSE)
{
alpha <- state$alpha
b <- state$b
bclus <- state$bclus
beta <- state$beta
mu <- state$mu
ncluster <- state$ncluster
sigma2 <- state$sigma2
sigmainv <- 1/sigma2
ss <- state$ss
}
#########################################################################################
# working space
#########################################################################################
betac <- rep(0,(p-1))
ccluster <- rep(0,nsubject)
fsavet <- rep(0,ngrid)
iflagp <- rep(0,(p-1))
prob <- rep(0,nsubject+100)
seed1 <- sample(1:29000,1)
seed2 <- sample(1:29000,1)
seed <- c(seed1,seed2)
workmhp <- rep(0,(p-1)*p/2)
workvp <- rep(0,p-1)
xtx <- matrix(0,nrow=p-1,ncol=p-1)
xty <- rep(0,p-1)
cstrt <- matrix(0,nrow=nsubject,ncol=nsubject)
workcpo <- matrix(0,nrow=nsubject,ncol=p)
if(is.null(offset))
{
roffset <- matrix(0,nrow=nsubject,ncol=p)
}
else
{
roffset <- offset
}
#########################################################################################
# calling the fortran code
#########################################################################################
foo <- .Fortran("spraschpoi",
datastrm =as.integer(datastrm),
imiss =as.integer(imiss),
ngrid =as.integer(ngrid),
nmissing =as.integer(nmissing),
nsubject =as.integer(nsubject),
p =as.integer(p),
y =as.integer(ywork),
roffset =as.double(roffset),
a0b0 =as.double(a0b0),
b0 =as.double(b0),
prec =as.double(prec),
psiinv =as.double(psiinv),
sb =as.double(sb),
smu =as.double(smu),
tau1 =as.double(tau1),
tau2 =as.double(tau2),
mcmc =as.integer(mcmcvec),
nsave =as.integer(nsave),
acrate =as.double(acrate),
cpo =as.double(cpo),
cpov =as.double(cpov),
cdfsave =as.double(cdfsave),
randsave =as.double(randsave),
thetasave =as.double(thetasave),
alpha =as.double(alpha),
b =as.double(b),
bclus =as.double(bclus),
beta =as.double(beta),
mu =as.double(mu),
ncluster =as.integer(ncluster),
sigma2 =as.double(sigma2),
sigmainv =as.double(sigmainv),
ss =as.integer(ss),
betac =as.double(betac),
ccluster =as.integer(ccluster),
cstrt =as.integer(cstrt),
fsavet =as.double(fsavet),
iflagp =as.integer(iflagp),
prob =as.double(prob),
seed =as.integer(seed),
workmhp =as.double(workmhp),
workvp =as.double(workvp),
xtx =as.double(xtx),
xty =as.double(xty),
grid =as.double(grid),
workcpo =as.double(workcpo),
PACKAGE ="DPpackage")
#########################################################################################
# save state
#########################################################################################
hpdf <- function(x)
{
alpha <- 0.05
vec <- x
n <- length(x)
alow <- rep(0,2)
aupp <- rep(0,2)
a <-.Fortran("hpd",n=as.integer(n),alpha=as.double(alpha),x=as.double(vec),
alow=as.double(alow),aupp=as.double(aupp),PACKAGE="DPpackage")
return(c(a$alow[1],a$aupp[1]))
}
pdf <- function(x)
{
alpha <- 0.05
vec <- x
n <- length(x)
alow<-rep(0,2)
aupp<-rep(0,2)
a<-.Fortran("hpd",n=as.integer(n),alpha=as.double(alpha),x=as.double(vec),
alow=as.double(alow),aupp=as.double(aupp),PACKAGE="DPpackage")
return(c(a$alow[2],a$aupp[2]))
}
model.name <- "Bayesian semiparametric Rasch Poisson Model"
state <- list(alpha=foo$alpha,
b=foo$b,
bclus=foo$bclus,
beta=foo$beta,
mu=foo$mu,
ncluster=foo$ncluster,
sigma2=foo$sigma2,
ss=foo$ss)
cpo <- matrix(foo$cpo,nrow=nsubject,ncol=p)
cdfsave <- matrix(foo$cdfsave,nrow=nsave,ncol=ngrid)
randsave <- matrix(foo$randsave,nrow=nsave,ncol=nsubject+1)
thetasave <- matrix(foo$thetasave,nrow=nsave,ncol=p+5)
cdf.m <- apply(cdfsave,2,mean)
cdf.l <- NULL
cdf.u <- NULL
if(compute.band)
{
limm <- apply(cdfsave, 2, hpdf)
cdf.l <- limm[1,]
cdf.u <- limm[2,]
}
pnames <- NULL
for(i in 2:p)
{
pnames <- c(pnames,paste("beta",i,sep=""))
}
pnames <- c(pnames,"mean","variance","mu","sigma2","ncluster","alpha")
colnames(thetasave) <- pnames
qnames <- NULL
for(i in 1:nsubject)
{
temp <- paste("theta(ID=",i,sep="")
temp <- paste(temp,")",sep="")
qnames <- c(qnames,temp)
}
qnames <- c(qnames,"theta(Prediction)")
dimnames(randsave) <- list(NULL,qnames)
coeff <- apply(thetasave, 2, mean)
save.state <- list(thetasave=thetasave,randsave=randsave,cdfsave=cdfsave)
z <- list(call=cl,
y=y,
modelname=model.name,
cpo=cpo,
prior=prior,
mcmc=mcmc,
state=state,
save.state=save.state,
nrec=nrec,
nsubject=nsubject,
p=p,
alpharand=alpharand,
murand=murand,
sigmarand=sigmarand,
acrate=foo$acrate,
coefficients=coeff,
cdf=cdf.m,
cdf.l=cdf.l,
cdf.u=cdf.u,
grid=grid,
cpov=foo$cpov)
cat("\n\n")
class(z)<-"DPraschpoisson"
return(z)
}
###
### Tools
###
### Copyright: Alejandro Jara Vallejos, 2006
### Last modification: 10-08-2006.
###
"print.DPraschpoisson"<-function (x, digits = max(3, getOption("digits") - 3), ...)
{
cat("\n",x$modelname,"\n\nCall:\n", sep = "")
print(x$call)
cat("\n")
if (length(x$coefficients)) {
cat("Posterior Inference of Parameters:\n")
if(x$alpharand==1){
print.default(format(x$coefficients, digits = digits), print.gap = 2,
quote = FALSE)}
if(x$alpharand==0){
print.default(format(x$coefficients[1:(length(x$coefficients)-1)], digits = digits), print.gap = 2,
quote = FALSE)}
}
cat("\nAcceptance Rate for Metropolis Steps = ",x$acrate,"\n")
cat("\nNumber of Observations:",x$nrec)
cat("\nNumber of Groups:",x$nsubject,"\n")
cat("\n\n")
invisible(x)
}
"summary.DPraschpoisson"<-function(object, hpd=TRUE, ...)
{
stde<-function(x)
{
n<-length(x)
return(sd(x)/sqrt(n))
}
hpdf<-function(x)
{
alpha<-0.05
vec<-x
n<-length(x)
alow<-rep(0,2)
aupp<-rep(0,2)
a<-.Fortran("hpd",n=as.integer(n),alpha=as.double(alpha),x=as.double(vec),
alow=as.double(alow),aupp=as.double(aupp),PACKAGE="DPpackage")
return(c(a$alow[1],a$aupp[1]))
}
pdf<-function(x)
{
alpha<-0.05
vec<-x
n<-length(x)
alow<-rep(0,2)
aupp<-rep(0,2)
a<-.Fortran("hpd",n=as.integer(n),alpha=as.double(alpha),x=as.double(vec),
alow=as.double(alow),aupp=as.double(aupp),PACKAGE="DPpackage")
return(c(a$alow[2],a$aupp[2]))
}
#nsave<-object$nsave
#dimen<-length(object$coefficients)
#thetasave<-matrix(object$save.state$thetasave,nrow=nsave, ncol=dimen)
thetasave<-object$save.state$thetasave
### Difficulty parameters
dimen1 <- object$p-1
mat <- thetasave[,1:dimen1]
coef.p <- object$coefficients[1:dimen1]
coef.m <- apply(mat, 2, median)
coef.sd <- apply(mat, 2, sd)
coef.se <- apply(mat, 2, stde)
if(hpd)
{
limm <- apply(mat, 2, hpdf)
coef.l <- limm[1,]
coef.u <- limm[2,]
}
else
{
limm <- apply(mat, 2, pdf)
coef.l <- limm[1,]
coef.u <- limm[2,]
}
names(coef.m) <- names(object$coefficients[1:dimen1])
names(coef.sd) <- names(object$coefficients[1:dimen1])
names(coef.se) <- names(object$coefficients[1:dimen1])
names(coef.l) <- names(object$coefficients[1:dimen1])
names(coef.u) <- names(object$coefficients[1:dimen1])
coef.table <- cbind(coef.p, coef.m, coef.sd, coef.se , coef.l , coef.u)
if(hpd)
{
dimnames(coef.table) <- list(names(coef.p), c("Mean", "Median", "Std. Dev.", "Naive Std.Error",
"95%HPD-Low","95%HPD-Upp"))
}
else
{
dimnames(coef.table) <- list(names(coef.p), c("Mean", "Median", "Std. Dev.", "Naive Std.Error",
"95%CI-Low","95%CI-Upp"))
}
ans <- c(object[c("call", "modelname")])
ans$coefficients<-coef.table
### Functionals
mat <- thetasave[,(dimen1+1):(dimen1+2)]
coef.p <- object$coefficients[(dimen1+1):(dimen1+2)]
coef.m <- apply(mat, 2, median)
coef.sd <- apply(mat, 2, sd)
coef.se <- apply(mat, 2, stde)
if(hpd)
{
limm <- apply(mat, 2, hpdf)
coef.l <- limm[1,]
coef.u <- limm[2,]
}
else
{
limm <- apply(mat, 2, pdf)
coef.l <- limm[1,]
coef.u <- limm[2,]
}
names(coef.m) <- names(object$coefficients[(dimen1+1):(dimen1+2)])
names(coef.sd) <- names(object$coefficients[(dimen1+1):(dimen1+2)])
names(coef.se) <- names(object$coefficients[(dimen1+1):(dimen1+2)])
names(coef.l) <- names(object$coefficients[(dimen1+1):(dimen1+2)])
names(coef.u) <- names(object$coefficients[(dimen1+1):(dimen1+2)])
coef.table <- cbind(coef.p, coef.m, coef.sd, coef.se , coef.l , coef.u)
if(hpd)
{
dimnames(coef.table) <- list(names(coef.p), c("Mean", "Median", "Std. Dev.", "Naive Std.Error",
"95%HPD-Low","95%HPD-Upp"))
}
else
{
dimnames(coef.table) <- list(names(coef.p), c("Mean", "Median", "Std. Dev.", "Naive Std.Error",
"95%CI-Low","95%CI-Upp"))
}
ans <- c(object[c("call", "modelname")])
ans$functionals <- coef.table
dimen1 <- dimen1 + 2
### CPO
ans$cpo<-object$cpo
### Baseline Information
dimen2 <- object$murand+object$sigmarand
if(dimen2>0)
{
if(dimen2==1)
{
if(object$murand==1)
{
mat<-matrix(thetasave[,dimen1+1],ncol=1)
coef.p<-object$coefficients[dimen1+1]
}
else
{
mat<-matrix(thetasave[,dimen1+2],ncol=1)
coef.p<-object$coefficients[dimen1+2]
}
}
else
{
mat<-thetasave[,(dimen1+1):(dimen1+2)]
coef.p<-object$coefficients[(dimen1+1):(dimen1+2)]
}
coef.m <-apply(mat, 2, median)
coef.sd<-apply(mat, 2, sd)
coef.se<-apply(mat, 2, stde)
if(hpd){
limm<-apply(mat, 2, hpdf)
coef.l<-limm[1,]
coef.u<-limm[2,]
}
else
{
limm<-apply(mat, 2, pdf)
coef.l<-limm[1,]
coef.u<-limm[2,]
}
coef.table <- cbind(coef.p, coef.m, coef.sd, coef.se , coef.l , coef.u)
if(hpd)
{
dimnames(coef.table) <- list(names(coef.p), c("Mean", "Median", "Std. Dev.", "Naive Std.Error",
"95%HPD-Low","95%HPD-Upp"))
}
else
{
dimnames(coef.table) <- list(names(coef.p), c("Mean", "Median", "Std. Dev.", "Naive Std.Error",
"95%CI-Low","95%CI-Upp"))
}
ans$base<-coef.table
}
### Precision parameter
if(is.null(object$prior$a0))
{
dimen3<-1
coef.p<-object$coefficients[(dimen1+2+1)]
mat<-matrix(thetasave[,(dimen1+2+1)],ncol=1)
}
else
{
dimen3<-2
coef.p<-object$coefficients[(dimen1+2+1):(dimen1+2+2)]
mat<-thetasave[,(dimen1+2+1):(dimen1+2+2)]
}
coef.m <-apply(mat, 2, median)
coef.sd<-apply(mat, 2, sd)
coef.se<-apply(mat, 2, stde)
if(hpd){
limm<-apply(mat, 2, hpdf)
coef.l<-limm[1,]
coef.u<-limm[2,]
}
else
{
limm<-apply(mat, 2, pdf)
coef.l<-limm[1,]
coef.u<-limm[2,]
}
coef.table <- cbind(coef.p, coef.m, coef.sd, coef.se , coef.l , coef.u)
if(hpd)
{
dimnames(coef.table) <- list(names(coef.p), c("Mean", "Median", "Std. Dev.", "Naive Std.Error",
"95%HPD-Low","95%HPD-Upp"))
}
else
{
dimnames(coef.table) <- list(names(coef.p), c("Mean", "Median", "Std. Dev.", "Naive Std.Error",
"95%CI-Low","95%CI-Upp"))
}
ans$prec<-coef.table
ans$nrec<-object$nrec
ans$nsubject<-object$nsubject
ans$acrate<-object$acrate
class(ans) <- "summaryDPraschpoisson"
return(ans)
}
"print.summaryDPraschpoisson"<-function (x, digits = max(3, getOption("digits") - 3), ...)
{
cat("\n",x$modelname,"\n\nCall:\n", sep = "")
print(x$call)
cat("\n")
cat("Posterior Predictive Distributions (log):\n")
print.default(format(summary(log(as.vector(x$cpo))), digits = digits), print.gap = 2,
quote = FALSE)
if (length(x$coefficients)) {
cat("\nDifficulty parameters:\n")
print.default(format(x$coefficients, digits = digits), print.gap = 2,
quote = FALSE)
}
if (length(x$functionals)) {
cat("\nFunctionals of the Random Effects:\n")
print.default(format(x$functionals, digits = digits), print.gap = 2,
quote = FALSE)
}
if (length(x$base)) {
cat("\nBaseline distribution:\n")
print.default(format(x$base, digits = digits), print.gap = 2,
quote = FALSE)
}
else cat("No baseline parameters\n")
if (length(x$prec)) {
cat("\nPrecision parameter:\n")
print.default(format(x$prec, digits = digits), print.gap = 2,
quote = FALSE)
}
cat("\nAcceptance Rate for Metropolis Steps = ",x$acrate,"\n")
cat("\nNumber of Observations:",x$nrec)
cat("\nNumber of Groups:",x$nsubject,"\n")
cat("\n\n")
invisible(x)
}
"plot.DPraschpoisson"<-function(x, hpd=TRUE, ask=TRUE, nfigr=2, nfigc=2, param=NULL, col="#bdfcc9", ...)
{
fancydensplot1<-function(x, hpd=TRUE, npts=200, xlab="", ylab="", main="",col="#bdfcc9", ...)
# Author: AJV, 2006
#
{
dens <- density(x,n=npts)
densx <- dens$x
densy <- dens$y
meanvar <- mean(x)
densx1 <- max(densx[densx<=meanvar])
densx2 <- min(densx[densx>=meanvar])
densy1 <- densy[densx==densx1]
densy2 <- densy[densx==densx2]
ymean <- densy1 + ((densy2-densy1)/(densx2-densx1))*(meanvar-densx1)
if(hpd==TRUE)
{
alpha<-0.05
alow<-rep(0,2)
aupp<-rep(0,2)
n<-length(x)
a<-.Fortran("hpd",n=as.integer(n),alpha=as.double(alpha),x=as.double(x),
alow=as.double(alow),aupp=as.double(aupp),PACKAGE="DPpackage")
xlinf<-a$alow[1]
xlsup<-a$aupp[1]
}
else
{
xlinf <- quantile(x,0.025)
xlsup <- quantile(x,0.975)
}
densx1 <- max(densx[densx<=xlinf])
densx2 <- min(densx[densx>=xlinf])
densy1 <- densy[densx==densx1]
densy2 <- densy[densx==densx2]
ylinf <- densy1 + ((densy2-densy1)/(densx2-densx1))*(xlinf-densx1)
densx1 <- max(densx[densx<=xlsup])
densx2 <- min(densx[densx>=xlsup])
densy1 <- densy[densx==densx1]
densy2 <- densy[densx==densx2]
ylsup <- densy1 + ((densy2-densy1)/(densx2-densx1))*(xlsup-densx1)
plot(0.,0.,xlim = c(min(densx), max(densx)), ylim = c(min(densy), max(densy)),
axes = F,type = "n" , xlab=xlab, ylab=ylab, main=main, cex=1.2)
xpol<-c(xlinf,xlinf,densx[densx>=xlinf & densx <=xlsup],xlsup,xlsup)
ypol<-c(0,ylinf,densy[densx>=xlinf & densx <=xlsup] ,ylsup,0)
polygon(xpol, ypol, border = FALSE,col=col)
lines(c(min(densx), max(densx)),c(0,0),lwd=1.2)
segments(min(densx),0, min(densx),max(densy),lwd=1.2)
lines(densx,densy,lwd=1.2)
segments(meanvar, 0, meanvar, ymean,lwd=1.2)
segments(xlinf, 0, xlinf, ylinf,lwd=1.2)
segments(xlsup, 0, xlsup, ylsup,lwd=1.2)
axis(1., at = round(c(xlinf, meanvar,xlsup), 2.), labels = T,pos = 0.)
axis(1., at = round(seq(min(densx),max(densx),length=15), 2.), labels = F,pos = 0.)
axis(2., at = round(seq(0,max(densy),length=5), 2.), labels = T,pos =min(densx))
}
if(is(x, "DPraschpoisson"))
{
if(is.null(param))
{
coef.p <- x$coefficients[1:(x$p+1)]
n <- length(coef.p)
pnames <- names(coef.p)
par(ask = ask)
layout(matrix(seq(1,nfigr*nfigc,1), nrow=nfigr , ncol=nfigc ,byrow=TRUE))
for(i in 1:n)
{
title1 <- paste("Trace of",pnames[i],sep=" ")
title2 <- paste("Density of",pnames[i],sep=" ")
plot(ts(x$save.state$thetasave[,i]),main=title1,xlab="MCMC scan",ylab=" ")
fancydensplot1(x$save.state$thetasave[,i],hpd=hpd,main=title2,xlab="values", ylab="density",col=col)
}
if(x$murand==1)
{
title1<-paste("Trace of","mu",sep=" ")
title2<-paste("Density of","mu",sep=" ")
plot(ts(x$save.state$thetasave[,x$p+2]),main=title1,xlab="MCMC scan",ylab=" ")
fancydensplot1(x$save.state$thetasave[,x$p+2],hpd=hpd,main=title2,xlab="values", ylab="density",col=col)
}
if(x$sigmarand==1)
{
title1<-paste("Trace of","sigma2",sep=" ")
title2<-paste("Density of","sigma2",sep=" ")
plot(ts(x$save.state$thetasave[,x$p+3]),main=title1,xlab="MCMC scan",ylab=" ")
fancydensplot1(x$save.state$thetasave[,x$p+3],hpd=hpd,main=title2,xlab="values", ylab="density",col=col)
}
title1<-paste("Trace of","ncluster",sep=" ")
title2<-paste("Density of","ncluster",sep=" ")
plot(ts(x$save.state$thetasave[,x$p+4]),main=title1,xlab="MCMC scan",ylab=" ")
hist(x$save.state$thetasave[,x$p+4],main=title2,xlab="values", ylab="probability",probability=TRUE)
if(x$alpharand==1)
{
title1<-paste("Trace of","alpha",sep=" ")
title2<-paste("Density of","alpha",sep=" ")
plot(ts(x$save.state$thetasave[,x$p+5]),main=title1,xlab="MCMC scan",ylab=" ")
fancydensplot1(x$save.state$thetasave[,x$p+5],hpd=hpd,main=title2,xlab="values", ylab="density",col=col)
}
title1 <- c("Density Estimate")
title2 <- c("CDF Estimate")
#fancydensplot1(x$save.state$randsave[,(x$nsubject+1)],hpd=hpd,main=title1,xlab="theta",col=col)
plot(x$grid,x$cdf,ylab="probability",main=title2,lty=1,type='l',lwd=2,ylim=c(0,1),xlab="theta")
}
else
{
coef.p<-x$coefficients
n<-length(coef.p)
pnames<-names(coef.p)
poss<-0
for(i in 1:n)
{
if(pnames[i]==param)poss=i
}
if(poss==0 && param !="predictive")
{
stop("This parameter is not present in the original model.\n")
}
par(ask = ask)
layout(matrix(seq(1,nfigr*nfigc,1), nrow=nfigr, ncol=nfigc, byrow = TRUE))
if(param !="predictive")
{
title1<-paste("Trace of",pnames[poss],sep=" ")
title2<-paste("Density of",pnames[poss],sep=" ")
plot(ts(x$save.state$thetasave[,poss]),main=title1,xlab="MCMC scan",ylab=" ")
if(param=="ncluster")
{
hist(x$save.state$thetasave[,poss],main=title2,xlab="values", ylab="probability",probability=TRUE)
}
else
{
fancydensplot1(x$save.state$thetasave[,poss],hpd=hpd,main=title2,xlab="values", ylab="density",col=col)
}
}
else
{
title1<-c("Density Estimate")
title2<-c("CDF Estimate")
#fancydensplot1(x$save.state$randsave[,(x$nsubject+1)],hpd=hpd,main=title1,xlab="theta",col=col)
plot(x$grid,x$cdf,ylab="probability",main=title2,lty=1,type='l',lwd=2,ylim=c(0,1),xlab="theta")
}
}
}
}
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