Nothing
summaryRMD <- function(fit, fit2, pathout, numTrials=1, thisTrial){
dir.create(paste(pathout, "/", thisTrial, sep=""));
cmPat <- fit$data$n.subj # number of subjects that has non-mising values
# beta and sigma2;
parms <- mcmc(cbind(fit$beta.dose, fit$beta.other, fit$s2.gamma, fit$s2.epsilon))
if (ncol(fit$beta.other) == 2) {
varnames(parms) <- c("beta.dose", "beta.intercept", "beta.cycle", "s2.gamma", "s2.epsilon")
}else{
varnames(parms) <- c("beta.dose", "beta.intercept", "s2.gamma", "s2.epsilon")
}
parms2 <- mcmc(cbind(fit2$beta.dose, fit2$beta.other, fit2$s2.gamma, fit2$s2.epsilon))
if (ncol(fit2$beta.other) == 2) {
varnames(parms2) <- c("beta.dose", "beta.intercept", "beta.cycle", "s2.gamma", "s2.epsilon")
}else{
varnames(parms2) <- c("beta.dose", "beta.intercept", "s2.gamma", "s2.epsilon")
}
combined=mcmc.list(mcmc(parms),mcmc(parms2));
res = summary(parms)
write.table(res$statistics, file=paste(pathout, "/", thisTrial, "/statsParms", cmPat, ".txt", sep=""))
write.table(res$quantile, file=paste(pathout, "/", thisTrial, "/quanParms", cmPat, ".txt", sep=""))
write.table(effectiveSize(parms), file=paste(pathout, "/", thisTrial, "/sizeParms", cmPat, ".txt", sep=""))
# gamma
gamma.mc <- mcmc(fit$gamma)
colnames.gamma <- NULL
for (i in 1:cmPat)
colnames.gamma <- c(colnames.gamma, paste("gamma", i, sep=''))
varnames(gamma.mc) <- colnames.gamma
res = summary(gamma.mc)
write.table(res$statistics, file=paste(pathout, "/", thisTrial, "/statsGamma", cmPat, ".txt", sep=""))
write.table(res$quantile, file=paste(pathout, "/", thisTrial, "/quanGamma", cmPat, ".txt", sep=""))
write.table(effectiveSize(gamma.mc), file=paste(pathout, "/", thisTrial, "/sizeGamma", cmPat, ".txt", sep=""))
#pdf(file=paste(pathout, "/", thisTrial, "/traceParms", cmPat, ".pdf", sep=""))
#plot(parms)
#dev.off()
#pdf(file=paste(pathout, "/", thisTrial, "/traceGamma", cmPat, ".pdf", sep=""))
#plot(gamma.mc)
#dev.off()
#if (numTrials == 1){
if (thisTrial ==1 ){ #plot all
# traceplots
#pdf(file=paste(pathout, "/", thisTrial, "/gelmanParms", cmPat, ".pdf", sep=""))
#gelman.plot(combined)
#dev.off();
}
}
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