merge default into stable

1 files changed, 54 insertions, 0 deletions

diff --git a/tests/examplefiles/example.bug b/tests/examplefiles/example.bug
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+# Alligators: multinomial - logistic regression 
+#  http://www.openbugs.info/Examples/Aligators.html
+model {
+   # PRIORS    
+   alpha[1] <- 0; # zero contrast for baseline food
+   for (k in 2 : K) { 
+     alpha[k] ~ dnorm(0, 0.00001) # vague priors
+   } 
+   # Loop around lakes:
+   for (k in 1 : K){ 
+      beta[1, k] <- 0 
+   } # corner-point contrast with first lake 
+   for (i in 2 : I) { 
+     beta[i, 1] <- 0 ; # zero contrast for baseline food
+     for (k in 2 : K){ 
+       beta[i, k] ~ dnorm(0, 0.00001) # vague priors
+     } 
+   }
+   # Loop around sizes:
+   for (k in 1 : K){ 
+     gamma[1, k] <- 0 # corner-point contrast with first size 
+   } 
+   for (j in 2 : J) { 
+     gamma[j, 1] <- 0 ; # zero contrast for baseline food
+     for ( k in 2 : K){ 
+       gamma[j, k] ~ dnorm(0, 0.00001) # vague priors
+     } 
+   }
+
+   # LIKELIHOOD   
+   for (i in 1 : I) { # loop around lakes
+     for (j in 1 : J) { # loop around sizes
+
+       # Fit standard Poisson regressions relative to baseline
+       lambda[i, j] ~ dflat()   # vague priors 
+       for (k in 1 : K) { # loop around foods
+           X[i, j, k] ~ dpois(mu[i, j, k])
+           log(mu[i, j, k]) <- lambda[i, j] + alpha[k] + beta[i, k] + gamma[j, k]
+           culmative.X[i, j, k] <- culmative(X[i, j, k], X[i, j, k])
+       }
+     }
+   }
+
+   # TRANSFORM OUTPUT TO ENABLE COMPARISON 
+   # WITH AGRESTI'S RESULTS
+   for (k in 1 : K) { # loop around foods
+       for (i in 1 : I) { # loop around lakes
+         b[i, k] <- beta[i, k] - mean(beta[, k]); # sum to zero constraint
+       }
+       for (j in 1 : J) { # loop around sizes
+         g[j, k] <- gamma[j, k] - mean(gamma[, k]); # sum to zero constraint
+       }
+   }
+}