Hierarchical Dirichlet regression (jags)... overfitting - r

Question

Good Morning, please I need community help in order to understand some problems that occurred writing this model.
I aim at modeling causes of death proportion using as predictors "log_GDP" (Gross domestic product in log scale), and "log_h" (hospital beds per 1,000 people on log scale)
y: 3 columns that are observed proportions of deaths over the years.
x1: "log_GDP" (Gross domestic product in log scale)
x2: "log_h" (hospital beds per 1,000 people in log scale)
As you can see from the estimation result in the last plot, I got a high noise level. Where I worked using just one covariate i.e. log_GDP, I obtained smoothed results
Here the model specification:
Here simulated data:
library(reshape2)
library(tidyverse)
library(ggplot2)
library(runjags)
CIRC <- c(0.3685287, 0.3675516, 0.3567829, 0.3517274, 0.3448940, 0.3391031, 0.3320184, 0.3268640,
0.3227445, 0.3156360, 0.3138515,0.3084506, 0.3053657, 0.3061224, 0.3051044)
NEOP <- c(0.3602199, 0.3567355, 0.3599409, 0.3591258, 0.3544591, 0.3566269, 0.3510974, 0.3536156,
0.3532980, 0.3460948, 0.3476183, 0.3475634, 0.3426035, 0.3352433, 0.3266048)
OTHER <-c(0.2712514, 0.2757129, 0.2832762, 0.2891468, 0.3006468, 0.3042701, 0.3168842, 0.3195204,
0.3239575, 0.3382691, 0.3385302, 0.3439860, 0.3520308, 0.3586342, 0.3682908)
log_h <- c(1.280934, 1.249902, 1.244155, 1.220830, 1.202972, 1.181727, 1.163151, 1.156881, 1.144223,
1.141033, 1.124930, 1.115142, 1.088562, 1.075002, 1.061257)
log_GDP <- c(29.89597, 29.95853, 29.99016, 30.02312, 30.06973, 30.13358, 30.19878, 30.25675, 30.30184,
30.31974, 30.30164, 30.33854, 30.37460, 30.41585, 30.45150)
D <- data.frame(CIRC=CIRC, NEOP=NEOP, OTHER=OTHER,
log_h=log_h, log_GDP=log_GDP)
cause.y <- as.matrix((data.frame(D[,1],D[,2],D[,3])))
cause.y <- cause.y/rowSums(cause.y)
mat.x<- D$log_GDP
mat.x2 <- D$log_h
n <- 15
Jags Model
dirlichet.model = "
model {
#setup priors for each species
for(j in 1:N.spp){
m0[j] ~ dnorm(0, 1.0E-3) #intercept prior
m1[j] ~ dnorm(0, 1.0E-3) # mat.x prior
m2[j] ~ dnorm(0, 1.0E-3)
}
#implement dirlichet
for(i in 1:N){
y[i,1:N.spp] ~ ddirch(a0[i,1:N.spp])
for(j in 1:N.spp){
log(a0[i,j]) <- m0[j] + m1[j] * mat.x[i]+ m2[j] * mat.x2[i] # m0 = intercept; m1= coeff log_GDP; m2= coeff log_h
}
}} #close model loop.
"
jags.data <- list(y = cause.y,mat.x= mat.x,mat.x2= mat.x2, N = nrow(cause.y), N.spp = ncol(cause.y))
jags.out <- run.jags(dirlichet.model,
data=jags.data,
adapt = 5000,
burnin = 5000,
sample = 10000,
n.chains=3,
monitor=c('m0','m1','m2'))
out <- summary(jags.out)
head(out)
Gather coefficient and I make estimation of proportions
coeff <- out[c(1,2,3,4,5,6,7,8,9),4]
coef1 <- out[c(1,4,7),4] #coeff (interc and slope) caus 1
coef2 <- out[c(2,5,8),4] #coeff (interc and slope) caus 2
coef3 <- out[c(3,6,9),4] #coeff (interc and slope) caus 3
pred <- as.matrix(cbind(exp(coef1[1]+coef1[2]*mat.x+coef1[3]*mat.x2),
exp(coef2[1]+coef2[2]*mat.x+coef2[3]*mat.x2),
exp(coef3[1]+coef3[2]*mat.x+coef3[3]*mat.x2)))
pred <- pred / rowSums(pred)
Predicted and Obs. values DB
Obs <- data.frame(Circ=cause.y[,1],
Neop=cause.y[,2],
Other=cause.y[,3],
log_GDP=mat.x,
log_h=mat.x2)
Obs$model <- "Obs"
Pred <- data.frame(Circ=pred[,1],
Neop=pred[,2],
Other=pred[,3],
log_GDP=mat.x,
log_h=mat.x2)
Pred$model <- "Pred"
tot60<-as.data.frame(rbind(Obs,Pred))
tot <- melt(tot60,id=c("log_GDP","log_h","model"))
tot$variable <- as.factor(tot$variable)
Plot
tot %>%filter(model=="Obs") %>% ggplot(aes(log_GDP,value))+geom_point()+
geom_line(data = tot %>%
filter(model=="Pred"))+facet_wrap(.~variable,scales = "free")

Answer 1

The problem for the non-smoothness is that you are calculating Pr(y=m|X) = f(x1, x2) - that is the predicted probability is a function of x1 and x2. Then you are plotting Pr(y=m|X) as a function of a single x variable - log of GDP. That result will almost certainly not be smooth. The log_GDP and log_h variables are highly negatively correlated which is why the result is not much more variable than it is.
In my run of the model, the average coefficient for log_GDP is actually positive for NEOP and Other, suggesting that the result you see in the plot is quite misleading. If you were to plot these in two dimensions, you would see that the result is again, smooth.
mx1 <- seq(min(mat.x), max(mat.x), length=25)
mx2 <- seq(min(mat.x2), max(mat.x2), length=25)
eg <- expand.grid(mx1 = mx1, mx2 = mx2)
pred <- as.matrix(cbind(exp(coef1[1]+coef1[2]*eg$mx1 + coef1[3]*eg$mx2),
exp(coef2[1]+coef2[2]*eg$mx1 + coef2[3]*eg$mx2),
exp(coef3[1]+coef3[2]*eg$mx1 + coef3[3]*eg$mx2)))
pred <- pred / rowSums(pred)
Pred <- data.frame(Circ=pred[,1],
Neop=pred[,2],
Other=pred[,3],
log_GDP=mx1,
log_h=mx2)
lattice::wireframe(Neop ~ log_GDP + log_h, data=Pred, drape=TRUE)
A couple of other things to watch out for.
Usually in hierarchical Bayesian models, your the parameters of your coefficients would themselves be distributions with hyperparameters. This enables shrinkage of the coefficients toward the global mean which is a hallmark of hierarhical models.
Not sure if this is what your data really look like or not, but the correlation between the two independent variables is going to make it difficult for the model to converge. You could try using a multivariate normal distribution for the coefficients - that might help.