Changes made in revision 1 of wardClones.R

--- /tmp/cvx_RzsOTH	2012-02-07 18:56:53.000000000 -0800
+++ /tmp/cvx_pwXsZO	2012-02-07 18:56:53.000000000 -0800
@@ -8,7 +8,7 @@
 ###################################
 # STEP 1: SET PARAMETERS
 ###################################
-numClones<-25;  # must be at least 2
+numClones<-100;  # must be at least 2
 chainLength <- 5000;
 burn <- 5000; # should be at least 5000
 
@@ -23,7 +23,6 @@
 Y <- matrix(0,N,numClones);
 for(i in 1:numClones) Y[,i] <- dat[,1];
 
-
 ###################################
 # THIS SECTION WRITES THE BUGS CODE
 ###################################
@@ -31,14 +30,13 @@
 model {
    # first year
    for(j in 1:numClones) {
-      init[j] ~ dunif(0,10);
+      init[j] ~ dunif(0,12);
    }
    # parameter B
    B ~ dunif(-3,3);
    # Q is process error
-   logsigma2.Q ~ dunif(-13.81551,2);
-   sigma2.Q <- exp(logsigma2.Q);
-   sigma.Q <- sqrt(sigma2.Q);
+   sigma.Q ~ dunif(0,1);
+   sigma2.Q <- sigma.Q*sigma.Q;
    invQ <- 1/sigma2.Q;
    # process error model
    for(j in 1:numClones) {
@@ -50,11 +48,9 @@
    }
 
    # R is observation error
-   logsigma2.R ~ dunif(-13.81551,2);
-   sigma2.R <- exp(logsigma2.R);
-   sigma.R <- sqrt(sigma2.R);
+   sigma.R ~ dunif(0,1);
+   sigma2.R <- sigma.R*sigma.R;
    invR <- 1/sigma2.R;
-
    for(j in 1:numClones) {
       for(i in 1:N) {
          Y[i,j] ~ dnorm(states[i,j], invR)