# http://data.princeton.edu/pop510/hospBUGS.html
library(MASS)
library(R2WinBUGS)
library(plyr)
load("C:/Users/ngreen1/Dropbox/small-area & chlamydia/R_code/scripts/mrp/data/cleaned-regn-input-mrpNatsal.RData")
Natsal$gor_factor <- as.factor(Natsal$gor)
Natsal$gor_factor <- as.numeric(Natsal$gor_factor)
WinBUGSdata <- data.frame(cttestly=Natsal$cttestly, gor_factor=Natsal$gor_factor, rsex=as.numeric(Natsal$rsex)-1)
# WinBUGSdata <- rbind(WinBUGSdata, c(NA,NA,NA))
setwd("C:/Users/ngreen1/Dropbox/small-area & chlamydia/R_code/scripts")
sink("model.txt")
cat("
model
{
# Priors
alpha ~ dnorm(0,0.005)
b.sex ~ dnorm(0,0.005)
# Hyperprior
tau ~ dgamma(0.001, 0.001)
# Likelihood
for(i in 1:n) {
cttestly[i] ~ dbin(p[i], N)
logit(p[i]) <- alpha + b.sex*rsex[i] + u[gor_factor[i]]
}
# Regions
for(j in 1:m) {
u[j] ~ dnorm(0, tau)
}
}
", fill=TRUE)
sink()
# Bundle data
win.data <- list(rsex = WinBUGSdata$rsex,
gor_factor = WinBUGSdata$gor_factor,
cttestly = WinBUGSdata$cttestly,
n = nrow(WinBUGSdata), m = 9, N = 1)
# Inits function
# inits <- function(){ list(alpha=rlnorm(1), b.age=rlnorm(1), b.sex=rlnorm(1))}
inits <- list(
list(alpha=0, b.sex=1, tau=0.5),
list(alpha=0, b.sex=1, tau=0.5),
list(alpha=0, b.sex=1, tau=0.5))
# Parameters to estimate
params <- c("alpha", "b.sex", "tau")
# MCMC settings
nc <- 3 #Number of Chains
ni <- 1000 #Number of draws from posterior
nb <- 200 #Number of draws to discard as burn-in
nt <- 5 #Thinning rate
# Start Gibbs sampling
out <- bugs(data=win.data, inits=inits, parameters.to.save=params,
model.file="model.txt", n.thin=nt, n.chains=nc, n.burnin=nb,
n.iter=ni, debug = TRUE,
DIC = TRUE, working.directory = getwd(), bugs.directory = 'C:/Program Files/WinBUGS14')
outmcmc <- read.bugs(out)
summary(outmcmc)
traceplot(outmcmc)
densityplot(outmcmc)
library(mcmcplots)
caterplot(out, lwd=c(1,4), style = "plain", col="black", pch=19, parms = c("b.age","b.sex"))
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