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