Test fix to issue where parameter names are not sorted correctly in summary when saving only a slice

2 files changed, 26 insertions, 6 deletions

diff --git a/R/processoutput.R b/R/processoutput.R
index bcf1d19..834f0f3 100644
--- a/R/processoutput.R
+++ b/R/processoutput.R
@@ -73,7 +73,7 @@ calc.stats <- function(i){
   if(!is.na(dim[i][1])){
     
     #Get all samples
-    sims.list[[i]] <<- mat[,expand==i]
+    sims.list[[i]] <<- mat[,expand==i,drop=FALSE]
 
 	#if every iteration is NA, don't do anything else
 	if(all(is.na(sims.list[[i]]))){return(NA)}
@@ -81,8 +81,9 @@ calc.stats <- function(i){
     #If more than 1 chain, calculate rhat 
     #Done separately for each element of non-scalar parameter to avoid errors
     if(m > 1 && (!i%in%params.omit)){
-      hold <- x[,expand==i]
-      rhat.vals <- sapply(1:dim(hold[[1]])[2],gd,hold=hold)
+      hold <- x[,expand==i,drop=FALSE]
+      nelements <- sum(expand==i)
+      rhat.vals <- sapply(1:nelements,gd,hold=hold)
       names(rhat.vals) <- colnames(hold[[1]])
       rhat[[i]] <<- populate(rhat.vals,dim[[i]])
     } else if (m == 1){
diff --git a/R/summarymatrix.R b/R/summarymatrix.R
index 09b9a8c..8949d44 100644
--- a/R/summarymatrix.R
+++ b/R/summarymatrix.R
@@ -3,9 +3,28 @@ summary.matrix <- function(output,samples,n.chains,codaOnly){
   
   hold <- unlist(output$mean[!names(output$mean)%in%codaOnly])
   toremove <- which(!is.na(hold))
+
+  #Get rownames
+  rnames = c()
+  for (i in 1:length(output$sd)){
+    if(length(output$sd[[i]])>1){
+      raw.ind <- which(!is.na(output$sd[[i]]),arr.ind=T)
+      if(is.matrix(raw.ind)){
+        ind <- apply(raw.ind,1,paste,collapse=',')
+      } else {
+        ind <- raw.ind
+      }
+
+      newnames <- paste(names(output$sd)[i],'[',ind,']',sep='')
+      rnames <- c(rnames,newnames)
+
+    } else {
+      rnames <- c(rnames,names(output$sd[i]))
+    }
+  }
   
   cleanup <- function(input,codaOnly){
-    
+
     out.raw <- unlist(input[!names(input)%in%codaOnly])
     
     out <- out.raw[toremove]
@@ -19,7 +38,7 @@ summary.matrix <- function(output,samples,n.chains,codaOnly){
                  cleanup(output$Rhat,codaOnly),cleanup(output$n.eff,codaOnly),
                  cleanup(output$overlap0,codaOnly),cleanup(output$f,codaOnly))
  
-  p <- colnames(samples[[1]])
+  p <- rnames
   expand <- sapply(strsplit(p, "\\["), "[", 1)  
   row.names(y) = p[!expand%in%codaOnly]
   names(y) = c('mean','sd','2.5%','25%','50%','75%','97.5%','Rhat','n.eff','overlap0','f')
@@ -28,4 +47,4 @@ summary.matrix <- function(output,samples,n.chains,codaOnly){
   }
   
   return(as.matrix(y))
-}
\ No newline at end of file
+}