Fixed issue that 4 element list and 1 element list approaches to spec…

…ifying random effects did not produce same result for the INLA model. As a side-effect of the fix, phylogenetic random effects no longer have sum-to-zero constraint. On reflection, this constraint should not have been there, but shouldn't make too much difference in most cases.

R/pglmm.R

@@ -1120,25 +1120,25 @@ communityPGLMM.bayes <- function(formula, data = list(), family = "gaussian",
   for(i in seq_along(random.effects)) {
     if(length(random.effects[[i]]) == 3) { # non-nested term
       if(length(random.effects[[i]][[1]]) == 1) { # 1 | sp, 1 | sp__, 1 | site, 1 | site__
-        f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], model = 'generic0', constr = TRUE, Cmatrix = inla_Cmat[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
+        f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], model = 'generic0', constr = FALSE, Cmatrix = inla_Cmat[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
       } else {  # x | sp, x | sp__, x | site, x | site__
-        f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], inla_weights[[", i, "]], model = 'generic0', constr = TRUE, Cmatrix = inla_Cmat[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
+        f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], inla_weights[[", i, "]], model = 'generic0', constr = FALSE, Cmatrix = inla_Cmat[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
       }
     } else { # nested term 1 | sp__@site, etc.
       if(length(random.effects[[i]]) == 4) { 
         if(length(random.effects[[i]][[1]]) == 1) {
-          f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], model = 'generic0', constr = TRUE, Cmatrix = inla_Cmat[[", i, "]], replicate = inla_reps[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
+          f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], model = 'generic0', constr = FALSE, Cmatrix = inla_Cmat[[", i, "]], replicate = inla_reps[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
         } else {
-          f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], model = 'generic0', constr = TRUE, Cmatrix = inla_Cmat[[", i, "]], replicate = inla_reps[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
+          f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], model = 'generic0', constr = FALSE, Cmatrix = inla_Cmat[[", i, "]], replicate = inla_reps[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
         }
       } else { # length of 1 or 2: specified as a matrix (1|sp__@site) or list of 2 (x|sp__@site)
         if(length(random.effects[[i]]) == 1) { # (1|sp__@site) etc.
-          f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], model = 'generic0', constr = TRUE, Cmatrix = inla_Cmat[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
+          f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], model = 'generic0', constr = FALSE, Cmatrix = inla_Cmat[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
         } else {
           if(length(random.effects[[i]]) == 2) { # (x|sp__@site) etc.
-            f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], inla_weights[[", i, "]], model = 'generic0', constr = TRUE, Cmatrix = inla_Cmat[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
+            f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], inla_weights[[", i, "]], model = 'generic0', constr = FALSE, Cmatrix = inla_Cmat[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
           } else { # other lengths? just in case ...
-            f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], model = 'generic0', constr = TRUE, Cmatrix = inla_Cmat[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
+            f_form[i] <- paste0("f(inla_effects[['", names(inla_effects)[i], "']], model = 'generic0', constr = FALSE, Cmatrix = inla_Cmat[[", i, "]], initial = s2.init[", i, "], diagonal = diagonal)")
           }
         }
       }