BugsLexer, JagsLexer, StanLexer: fixed filenames, added analyse_text functions

1 files changed, 55 insertions, 0 deletions

diff --git a/tests/examplefiles/example.bug b/tests/examplefiles/example.bug
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index 00000000..b5b2fe7f
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+++ 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
+       }
+   }
+}