###############################################################
# A simulated data: spatial Copula Cox PH
###############################################################
rm(list=ls())
library(survival)
library(spBayesSurv)
library(coda)
library(MASS)
## True parameters
betaT = c(-1);
theta1 = 0.98; theta2 = 0.1;
## generate coordinates:
## npred is the # of locations for prediction
n = 50; npred = 3; ntot = n + npred;
ldist = 100; wdist = 40;
s1 = runif(ntot, 0, wdist); s2 = runif(ntot, 0, ldist);
s = rbind(s1,s2); #plot(s[1,], s[2,]);
## Covariance matrix
corT = matrix(1, ntot, ntot);
for (i in 1:(ntot-1)){
for (j in (i+1):ntot){
dij = sqrt(sum( (s[,i]-s[,j])^2 ));
corT[i,j] = theta1*exp(-theta2*dij);
corT[j,i] = theta1*exp(-theta2*dij);
}
}
## Generate x
x = runif(ntot,-1.5,1.5);
## Generate transformed log of survival times
z = mvrnorm(1, rep(0, ntot), corT);
## The CDF of Ti:
Lambda = function(t) t;
Fi = function(t, xi){
res = 1-exp(-Lambda(t)*exp(sum(xi*betaT)));
res[which(t<0)] = 0;
res
}
## The pdf of Ti:
fi = function(t, xi){
res=(1-Fi(t,xi))*(1)*exp(sum(xi*betaT));
res[which(t<0)] = 0;
res
}
#integrate(function(x) fi(x, 0), -Inf, Inf)
## true plot
xx = seq(0, 5, 0.1)
#plot(xx, fi(xx, -1), "l", lwd=2, col=2)
#lines(xx, fi(xx, 1), "l", lwd=2, col=3)
## The inverse for CDF of Ti
Finvsingle = function(u, xi) {
res = uniroot(function (x) Fi(x, xi)-u, lower=0, upper=5000,
tol=.Machine$double.eps^0.5);
res$root
}
Finv = function(u, xi) {sapply(u, Finvsingle, xi)};
## Generate survival times t
u = pnorm(z);
t = rep(0, ntot);
for (i in 1:ntot){
t[i] = Finv(u[i], x[i]);
}
tTrue = t; #plot(x,t);
## Censoring scheme
Centime = runif(ntot, 1, 5);
Centime = 10000;
delta = (t<=Centime) +0 ;
sum(delta)/ntot;
cen = which(delta==0);
t[cen] = Centime[cen];
## make a data frame
dtotal = data.frame(s1=s1, s2=s2, t=t, logt=log(t), x=x, delta=delta,
tTrue=tTrue, logtTrue=log(tTrue));
## Hold out npred=3 for prediction purpose
predindex = sample(1:ntot, npred);
dpred = dtotal[predindex,];
dtrain = dtotal[-predindex,];
# Prediction settings
xpred = dpred$x;
s0 = cbind( dpred$s1, dpred$s2 );
prediction = list(spred=s0, xpred=xpred);
###############################################################
# spatial Copula Cox PH
###############################################################
# rename the variables
d = dtrain;n=nrow(d); n;
s = cbind(d$s1, d$s2);
t = d$t;
x = d$x;
X = cbind(x);
p = ncol(X); # number of covariates + 1
delta =d$delta;
# Initial Exp Cox PH
fit0 = survreg( Surv(t, delta) ~ x, dist="weibull", data=d );
h0 = as.vector( exp( -fit0$coefficients[1] ) );
beta = as.vector( -fit0$coefficients[-1]/fit0$scale ); beta;
# Prior information
prior = list(M = 10);
# current state values
state <- list(theta = c(0.98, 0.5));
# MCMC parameters
nburn <- 500
nsave <- 500
nskip <- 0
ndisplay <- 1000
mcmc <- list(nburn=nburn,
nsave=nsave,
nskip=nskip,
ndisplay=ndisplay)
# Note larger nburn, nsave and nskip should be used in practice.
# Fit the spatial Cox PH model
res2 = spCopulaCoxph( y = t,
delta =delta,
s = s,
x = X,
RandomIntervals=FALSE,
prediction=prediction,
prior=prior,
mcmc=mcmc,
state=state);
par(mfrow = c(2,2))
#traceplot(mcmc(res2$hcen), main="hcen")
beta.save = res2$beta; rowMeans(beta.save);
traceplot(mcmc(beta.save[1,]), main="beta")
traceplot(mcmc(res2$theta1), main="theta1")
traceplot(mcmc(res2$theta2), main="theta2")
res2$ratebeta;
res2$ratetheta;
## LPML
LPML2 = sum(log(res2$cpo)); LPML2;
## MSPE
mean((dpred$tTrue-apply(res2$Tpred, 1, median))^2);
## plots
par(mfrow = c(2,1))
xnew = c(-1, 1)
xpred = cbind(xnew);
nxpred = nrow(xpred);
ygrid = seq(-5, 1.1, 0.4);tgrid = exp(ygrid);
ngrid = length(ygrid);
estimates = GetCurves(res2, xpred, ygrid, CI=c(0.05, 0.95));
fhat = estimates$fhat;
Shat = estimates$Shat;
## density in t
plot(tgrid, fi(tgrid, xnew[1]), "l", lwd=2, xlim=c(0,6), main="density in y")
for(i in 1:nxpred){
lines(tgrid, fi(tgrid, xnew[i]), lwd=2)
lines(tgrid, fhat[,i], lty=2, lwd=2, col=4);
}
## survival in t
plot(tgrid, 1-Fi(tgrid, xnew[1]), "l", lwd=2, xlim=c(0,6), main="survival in y")
for(i in 1:nxpred){
lines(tgrid, 1-Fi(tgrid, xnew[i]), lwd=2)
lines(tgrid, Shat[,i], lty=2, lwd=2, col=4);
lines(tgrid, estimates$Shatup[,i], lty=2, lwd=1, col=4);
lines(tgrid, estimates$Shatlow[,i], lty=2, lwd=1, col=4);
}
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