lecture 13 new script

Author: rmcelreath

scripts/13_varying_features_bangladesh.R

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+# week 7
+# varying effects, clusters and features, non-centering
+
+library(rethinking)
+
+# simple varying intercepts model
+library(rethinking)
+data(bangladesh)
+d <- bangladesh
+
+dat <- list(
+    C = d$use.contraception,
+    D = as.integer(d$district) )
+
+mCD <- ulam(
+    alist(
+        C ~ bernoulli(p),
+        logit(p) <- a[D],
+        vector[61]:a ~ normal(abar,sigma),
+        abar ~ normal(0,1),
+        sigma ~ exponential(1)
+    ) , data=dat , chains=4 , cores=4 )
+
+
+# plot estimates
+p <- link( mCD , data=list(D=1:61) )
+# blank2(w=2)
+plot( NULL , xlab="district" , lwd=3 , col=2 , xlim=c(1,61), ylim=c(0,1) , ylab="prob use contraception" )
+
+points( 1:61 , apply(p,2,mean) , xlab="district" , lwd=3 , col=2 , ylim=c(0,1) , ylab="prob use contraception" )
+
+ for ( i in 1:61 ) lines( c(i,i) , PI(p[,i]) , lwd=8 , col=col.alpha(2,0.5) )
+
+# show raw proportions - have to skip 54
+n <- table(dat$D)
+Cn <- xtabs(dat$C ~ dat$D)
+pC <- as.numeric( Cn/n )
+pC <- c( pC[1:53] , NA , pC[54:60] )
+points( pC , lwd=2 )
+
+# only some labels via locator
+n <- table(dat$D)
+n <- as.numeric(n)
+n <- c( n[1:53] , 0 , n[54:60] )
+identify( 1:61 , pC , labels=n , cex=1 )
+
+
+
+
+#####################
+# add urban category
+
+dat <- list(
+    C = d$use.contraception,
+    D = as.integer(d$district),
+    U = ifelse(d$urban==1,1,0) )
+
+# total U
+mCDU <- ulam(
+    alist(
+        C ~ bernoulli(p),
+        logit(p) <- a[D] + b[D]*U,
+        vector[61]:a ~ normal(abar,sigma),
+        vector[61]:b ~ normal(bbar,tau),
+        c(abar,bbar) ~ normal(0,1),
+        c(sigma,tau) ~ exponential(1)
+    ) , data=dat , chains=4 , cores=4 )
+
+traceplot(mCDU,pars="tau",lwd=2,n_cols=1)
+trankplot(mCDU,pars="tau",lwd=3,n_cols=1)
+
+# non-centered version
+mCDUnc <- ulam(
+    alist(
+        C ~ bernoulli(p),
+        logit(p) <- a[D] + b[D]*U,
+        # define effects using other parameters
+        save> vector[61]:a <<- abar + za*sigma,
+        save> vector[61]:b <<- bbar + zb*tau,
+        # z-scored effects
+        vector[61]:za ~ normal(0,1),
+        vector[61]:zb ~ normal(0,1),
+        # ye olde hyper-priors
+        c(abar,bbar) ~ normal(0,1),
+        c(sigma,tau) ~ exponential(1)
+    ) , data=dat , chains=4 , cores=4 )
+
+# plot estimates
+
+Uval <- 0
+xcol <- ifelse(Uval==0,2,4)
+p <- link( mCDUnc , data=list(D=1:61,U=rep(Uval,61)) )
+# blank2(w=2,h=0.8)
+plot( NULL , xlab="district" , lwd=3 , col=2 , xlim=c(1,61), ylim=c(0,1) , ylab="prob use contraception" )
+abline(h=0.5,lty=2,lwd=0.5)
+
+points( 1:61 , apply(p,2,mean) , xlab="district" , lwd=3 , col=xcol , ylim=c(0,1) , ylab="prob use contraception" )
+
+ for ( i in 1:61 ) lines( c(i,i) , PI(p[,i]) , lwd=8 , col=col.alpha(xcol,0.5) )
+
+# show raw proportions - have to skip 54
+n <- table(dat$D,dat$U)
+Cn <- xtabs(dat$C ~ dat$D + dat$U)
+pC <- as.numeric( Cn[,Uval+1]/n[,Uval+1] )
+pC <- c( pC[1:53] , NA , pC[54:60] )
+points( pC , lwd=2 )
+
+# only some labels via locator
+nn <- as.numeric(n[,Uval+1])
+nn <- c( nn[1:53] , 0 , nn[54:60] )
+identify( 1:61 , pC , labels=nn , cex=1 )
+
+# show standard deviations
+post <- extract.samples(mCDUnc)
+dens(post$sigma,xlab="posterior standard deviation",lwd=3,col=2,xlim=c(0,1.2))
+dens(post$tau,lwd=3,col=4,add=TRUE,adj=0.2)
+curve(dexp(x,1),from=0,to=1.3,add=TRUE,lwd=2,lty=2)
+
+####
+# shrinkage plot now
+post <- extract.samples(mCDUnc)
+logitp0 <- post$a
+logitp1 <- post$a + post$b
+
+# blank2(w=1)
+#plot( NULL , xlab="log-odds C (rural)" , ylab="log-odds C (urban)" , xlim=c(-2,1), ylim=c(-1.5,1.5) )
+
+plot( NULL , xlab="prob C (rural)" , ylab="prob C (urban)" , xlim=c(0.1,0.7), ylim=c(0.2,0.75) )
+abline(h=0.5,lty=2,lwd=0.5)
+abline(v=0.5,lty=2,lwd=0.5)
+
+# plausibility ellipses
+library(ellipse)
+xxx <- sample(1:61,size=6)
+for ( i in xxx ) {
+    SIGMA <- cov( cbind( logitp0[,i] , logitp1[,i] ) )
+    MU <- c( mean(logitp0[,i]) , mean(logitp1[,i]) )
+    el <- ellipse( SIGMA , centre=MU , level=0.5 )
+    lines( inv_logit(el) , col=col.alpha(2,0.3) , lwd=2 )
+    #polygon( inv_logit(el) , col=col.alpha(2,0.2) , border=NA )
+}
+
+# posterior means
+p0 <- inv_logit(logitp0)
+p1 <- inv_logit(logitp1)
+points( apply(p0,2,mean) , apply(p1,2,mean) , lwd=6 , col="white" )
+points( apply(p0,2,mean) , apply(p1,2,mean) , lwd=3 , col=2 )
+
+n <- table(dat$D,dat$U)
+Cn <- xtabs(dat$C ~ dat$D + dat$U)
+pC0 <- as.numeric( Cn[,1]/n[,1] )
+pC1 <- as.numeric( Cn[,2]/n[,2] )
+
+points( (pC0) , (pC1) , lwd=2 , cex=2*apply(n,1,sum)/100 + 0.5 )
+
+for ( i in 1:61 ) {
+    lines( c(pC0[i],p0x[i])) , c(pC1[i],p1x[i]) )
+}
+