More carefully specify when RNG info has to be added to inits (when no seed or RNG info is provided and jagsUI is running in parallel)

2 files changed, 22 insertions, 11 deletions

diff --git a/R/geninits.R b/R/geninits.R
index 5ddb7e4..da18cb8 100644
--- a/R/geninits.R
+++ b/R/geninits.R
@@ -1,5 +1,5 @@
 
-gen.inits <- function(inits,n.chains,seed){
+gen.inits <- function(inits,n.chains,seed,parallel){
   
   #Error check and run init function if necessary
   if(is.list(inits)){
@@ -54,18 +54,29 @@ gen.inits <- function(inits,n.chains,seed){
       
     } 
  
-  }
-  
-  if(is.null(init.values)&is.null(seed)){ #Have to do this to handle parallel chains correctly
     
-    init.rand <- floor(runif(n.chains,1,100000))
-    init.values <- vector("list",length=n.chains)
-    for(i in 1:n.chains){
-      init.values[[i]]$.RNG.name="base::Mersenne-Twister"
-      init.values[[i]]$.RNG.seed=init.rand[i]
-    }
+  #If seed is not set
+  } else {
     
+    other.RNG <- all(c(".RNG.name",".RNG.seed")%in%names(init.values[[1]]))
+    
+    needs.RNG <- is.null(init.values)|!other.RNG
+    
+    #If parallel and no custom RNG has been set, add one. Otherwise all chains will start with same seed.
+    if(needs.RNG&parallel){
+      
+      init.rand <- floor(runif(n.chains,1,100000))
+      
+      if(is.null(init.values)){init.values <- vector("list",length=n.chains)}
+
+      for(i in 1:n.chains){
+        init.values[[i]]$.RNG.name="base::Mersenne-Twister"
+        init.values[[i]]$.RNG.seed=init.rand[i]
+      }
+      
+    }
   }
 
+
   return(init.values) 
 }
diff --git a/R/processinput.R b/R/processinput.R
index e56cda2..748b23c 100644
--- a/R/processinput.R
+++ b/R/processinput.R
@@ -100,7 +100,7 @@ process.input = function(x,y,inits,n.chains,n.iter,n.burnin,n.thin,n.cores,DIC=F
   }
   
   #Get initial values
-  init.vals <- gen.inits(inits,n.chains,seed)
+  init.vals <- gen.inits(inits,n.chains,seed,parallel)
  
   if(verbose){cat('\nDone.','\n','\n')}
   return(list(data=x,params=params,inits=init.vals,n.cores=n.cores))