Wednesday, 5 December 2007

Focus on DIC


This is something that's only of interest to Bayesians, so the rest of you can look away.
In a couple of analyses with BUGS, I've seen comparisons of DIC from different models, and the values have been almost exactly the same. This sort of thing is suspicious, and eventually I worked out why. I thought it was worth posting about this, so that everyone else can share The Secret.

It's best to explain the problem with an example (the complete R code for this is below). I simulated a couple of simple hierarchical models, so

Yij ~ N(θi, σy2)
θi ~ N(μi, σθ2)

(j =1,...,n, i=1,...,m. There are m groups, each with n observations). I then had two models for μi:

Model 1
μi = φ + β (i-5.5)

Model 2
μi = φ

The first model has a covariate (cunningly equal to the identity of the group), and the second has none. The data are plotted below. The effect of the covariate is clear, so DIC should be able to pick it up.


Now, I fit each of the models to each data set. This is easy running it through the R2WinBUGS package in R. From this I can extract the DIC:

Data 1
Model 1 DIC: 1464.0 pD: 10.9
Model 2 DIC: 1464.4 pD: 11.2

Data 2
Model 1 DIC: 1407.7 pD: 10.9
Model 2 DIC: 1407.7 pD: 10.9

So, in both cases the DIC is the same (for Data 2 the difference is in the third decimal place!). But for Data 1, Model 1 should be better - hey, we can see it on the figure! So, what's going on?

We can get a clue from plotting the posteriors for μi from the groups, from the two models:


Only the error bars are plotted (i.e. plus/minus 1 posterior standard deviation), and the 1:1 line is drawn in a fetching shade called "hotpink". Obviously the models are predicting the same means for the groups, and hence we will get the same deviance. We can see why this is happening from the group-level standard deviations (σθ2, posterior means and standard errors in parentheses):

Data 1
Model 1: 0.87 (0.280)
Model 2: 4.4 (1.31)

Data 2
Model 1: 1.1 (0.34)
Model 2: 1.1 (0.31)

So, for the data where there is a trend, but none is fitted, σθ2 is much larger - essentially, the lack of the linear trend is compensated by the increase in variance. The difference is not in the model for θ at all, but higher in the hierarchy (or hier in the higherarchy?).

Of course, this is obvious from looking at the models. The solution is to change the focus, from θ to φ and &beta. This then means calculating the marginal deviance, marginalising over θ, i.e. looking at P(Y | φ, β) and integrating over P(θ | Y). This can be done analytically (Hat-tip to David Spiegelhalter for correcting my errors, and refraining from making any justified comments about my mathematical ability!), whence we find that the deviance can be calculated because

barYi. ~ N(μi, σy2/n + σθ2) )

when we do this, we get these results:

Data 1
Model 1 DIC: 26.9 pD: 2.7
Model 2 DIC: 57.8 pD: 1.7

Data 2
Model 1 DIC: 30.9 pD: 2.6
Model 2 DIC: 30.3 pD: 1.7


Now this makes more sense, for the data with an effect, the DIC massively favours the correct model. Without the effect in the data, the DIC is pretty similar. In both cases, also note that pD is larger by 1 for the model with 1 extra parameter. Which is what should happen!

What lessons can we draw from this? Firstly, that DIC is not an automatic panacea - you do have to focus it on the right part of the model. If the focus is not at the level immediately above the data (i.e. θ here), then you can't use the DIC given by BUGS. The correctly focussed DIC is more complex to get at: you have to calculate it yourself. For more complex models this might be awkward, if there are no analytical results, then the parameters to be integrated out have to be simulated, for example by MCMC. But this requires some further thought...



library(R2WinBUGS)
# Simulate data
Cov=1:10
Group = rep(Cov, each=50)
beta = 1
# With covariate
GrpMean1=rnorm(length(Cov), beta*Cov, 1)
Value1=rnorm(length(Group), GrpMean1[Group], 1)
DataToBUGS1=list(N=length(Value1), NGrp=length(Cov), Group=Group, Y=Value1)
# Without covariate
GrpMean2=rnorm(length(Cov), 5.5, 1)
Value2=rnorm(length(Group), GrpMean2[Group], 1)
DataToBUGS2=list(N=length(Value2), NGrp=length(Cov), Group=Group, Y=Value2)

# Plot the data
# png("C:/Bob/Blog/Data.png", width = 960, height = 480)
par(mfrow=c(1,2), mar=c(2.1,2.1,1.1,1.1), oma=c(2,2,0,0), las=1)
plot(jitter(Group), Value1, pch=3, col="grey70")
points(Cov, GrpMean1, col=1, pch=3, cex=1.5)

plot(jitter(Group), Value2, pch=3, col="grey70")
points(Cov, GrpMean2, col=1, pch=3, cex=1.5)
mtext("Group", 1, outer=T)
mtext("Y", 2, outer=T)
#dev.off()

# Write BUGS models to files
model1 <- function(){
for (i in 1:N){ Y[i] ~ dnorm(muGrp[Group[i]], tau.y) }
for (j in 1:NGrp){
muGrp[j] ~ dnorm(muG[j], tau.Grp)
muG[j] <- mu0 + betaGrp*(j-5.5)
}
mu0 ~ dnorm (0.0, 1.0E-6)
betaGrp ~ dnorm (0.0, 1.0E-6)
tau.y <- pow(sigma.y, -2)
sigma.y ~ dunif (0, 1000)
tau.Grp <- pow(sigma.Grp, -2)
sigma.Grp ~ dunif (0, 1000)
}
write.model(model1, "C:/Bob/Blog/model1.txt")

model2 <- function(){
for (i in 1:N){ Y[i] ~ dnorm(muGrp[Group[i]], tau.y) }
for (j in 1:NGrp){ muGrp[j] ~ dnorm(mu0, tau.Grp) }
mu0 ~ dnorm (0.0, 1.0E-6)
tau.y <- pow(sigma.y, -2)
sigma.y ~ dunif (0, 1000)
tau.Grp <- pow(sigma.Grp, -2)
sigma.Grp ~ dunif (0, 1000)
}
write.model(model2, "C:/Bob/Blog/model2.txt")

# Initial values
Inits1=list(list(mu0=0, betaGrp=1, sigma.Grp=5, sigma.y=1), list(mu0=2, betaGrp=0, sigma.Grp=5, sigma.y=1) )
Inits2=list(list(mu0=0, sigma.Grp=5, sigma.y=1), list(mu0=2, sigma.Grp=5, sigma.y=1) )

# Fit the models
# Data 1, Model 1
Data1Model1.post=openbugs(DataToBUGS1, inits=Inits1, c("mu0", "muGrp", "betaGrp", "sigma.y", "sigma.Grp"), model.file = "C:/Bob/Blog/model1.txt", n.chains = 2, n.iter = 11000, n.burnin = 1000, n.thin = 10)
# Data 1, Model 2 (no slope in model)
Data1Model2.post=openbugs(DataToBUGS1, inits=Inits2, c("mu0", "muGrp", "sigma.y", "sigma.Grp"), model.file = "C:/Bob/Blog/model2.txt", n.chains = 2, n.iter = 11000, n.burnin = 1000, n.thin = 10)
# Data 2, Model 1
Data2Model1.post=openbugs(DataToBUGS2, inits=Inits1, c("mu0", "muGrp", "betaGrp", "sigma.y", "sigma.Grp"), model.file = "C:/Bob/Blog/model1.txt", n.chains = 2, n.iter = 11000, n.burnin = 1000, n.thin = 10)
# Data 2, Model 2 (no slope in model)
Data2Model2.post=openbugs(DataToBUGS2, inits=Inits2, c("mu0", "muGrp", "betaGrp", "sigma.y", "sigma.Grp"), model.file = "C:/Bob/Blog/model2.txt", n.chains = 2, n.iter = 11000, n.burnin = 1000, n.thin = 10)
print(Data1Model1.post)
print(Data1Model2.post)
print(Data2Model1.post)
print(Data2Model2.post)

# Plot mu
# png("C:/Bob/Blog/Theta.png", width = 960, height = 480)
par(mfrow=c(1,2), mar=c(2.1,2.1,1.1,1.1), oma=c(2,2,1,0), las=1)
plot(Data1Model1.post$mean$muGrp, Data1Model2.post$mean$muGrp, type="n", main="Data 1")
segments(Data1Model1.post$mean$muGrp,Data1Model2.post$mean$muGrp-Data1Model2.post$sd$muGrp, Data1Model1.post$mean$muGrp, Data1Model2.post$mean$muGrp+Data1Model2.post$sd$muGrp)
segments(Data1Model1.post$mean$muGrp-Data1Model1.post$sd$muGrp, Data1Model2.post$mean$muGrp, Data1Model1.post$mean$muGrp+Data1Model1.post$sd$muGrp, Data1Model2.post$mean$muGrp)
abline(0,1, col="hotpink")

plot(Data2Model1.post$mean$muGrp, Data2Model2.post$mean$muGrp, type="n", main="Data 2")
segments(Data2Model1.post$mean$muGrp, Data2Model2.post$mean$muGrp-Data2Model2.post$sd$muGrp, Data2Model1.post$mean$muGrp, Data2Model2.post$mean$muGrp+Data2Model2.post$sd$muGrp)
segments(Data2Model1.post$mean$muGrp-Data2Model1.post$sd$muGrp, Data2Model2.post$mean$muGrp, Data2Model1.post$mean$muGrp+Data2Model1.post$sd$muGrp, Data2Model2.post$mean$muGrp)
abline(0,1, col="hotpink")
mtext(expression(paste(theta[i], ", Model 1", sep="")), 1, outer=T)
mtext(expression(paste(theta[i], ", Model 2", sep="")), 2, outer=T, las=0)
#dev.off()

####################################################################### DevCalc1=function(mcmc, data) {
NamesGrp=paste("muGrp[", data$Group, "]", sep="")
-2*sum(dnorm(data$Y, mcmc[NamesGrp], mcmc["sigma.y"], log=TRUE))
}
DevCalc2=function(mcmc, data) {
Mean=unlist(tapply(data$Y, list(data$Group), mean))
Mu=mcmc["mu0"]
N=length(data$Group)/length(unique(data$Group))
-2*sum(dnorm(Mean, Mu, sqrt((mcmc["sigma.y"]^2)/N + mcmc["sigma.Grp"]^2), log=TRUE)) }
DevCalc2beta=function(mcmc, data) {
Mean=unlist(tapply(data$Y, list(data$Group), mean))
Mu=mcmc["mu0"] + mcmc["betaGrp"]*(as.numeric(names(Mean)) - 5.5)
N=length(data$Group)/length(unique(data$Group))
-2*sum(dnorm(Mean, Mu, sqrt((mcmc["sigma.y"]^2)/N + mcmc["sigma.Grp"]^2), log=TRUE))
}
DIC.calc=function(dat, mcmc, func) {
Dev=apply(mcmc$sims.array, c(1,2), func, data=dat)
mean=apply(mcmc$sims.array, 3, mean)
pD=mean(Dev) - func(mean, dat)
DIC=mean(Dev) + pD
return(list(DIC=DIC, pD=pD, Dbar=mean(Dev)))
}
PrintDIC=function(DIC, Label) { cat(Label, " DIC:", DIC$DIC, " pD:", DIC$pD, "\n")}

# Focus on theta
DIC.D1M1=DIC.calc(DataToBUGS1, Data1Model1.post, DevCalc1) DIC.D1M2=DIC.calc(DataToBUGS1, Data1Model2.post, DevCalc1)
DIC.D2M1=DIC.calc(DataToBUGS2, Data2Model1.post, DevCalc1)
DIC.D2M2=DIC.calc(DataToBUGS2, Data2Model2.post, DevCalc1)
PrintDIC(DIC.D1M1, "Data 1, Model 1")
PrintDIC(DIC.D1M2, "Data 1, Model 2")
PrintDIC(DIC.D2M1, "Data 2, Model 1")
PrintDIC(DIC.D2M2, "Data 2, Model 2")

# Focus on phi
DIC2.D1M1=DIC.calc(DataToBUGS1, Data1Model1.post, DevCalc2beta)
DIC2.D1M2=DIC.calc(DataToBUGS1, Data1Model2.post, DevCalc2)
DIC2.D2M1=DIC.calc(DataToBUGS2, Data2Model1.post, DevCalc2beta)
DIC2.D2M2=DIC.calc(DataToBUGS2, Data2Model2.post, DevCalc2)
PrintDIC(DIC2.D1M1, "Data 1, Model 1")
PrintDIC(DIC2.D1M2, "Data 1, Model 2")
PrintDIC(DIC2.D2M1, "Data 2, Model 1")
PrintDIC(DIC2.D2M2, "Data 2, Model 2")


3 comments:

Mahima Hada said...

Great post! Extremely useful for us winbugs users. A related Q: the DIC option in a multivariate probit model that am running in bugs is not accessible (its grayed out). Any idea why?

GrrlScientist said...

hey bob, sorry to leave my bird droppings on your wonderful blog, but I tagged you!

GrrlScientist

Panic Attacks said...

That extra parameter works! Thanks for taking the time and effort to sort it out, and providing the detailed explanation.