Patch the bug on aggregate when aggregating by samples

R/aggregate.R

@@ -12,6 +12,7 @@ aggregate.metabarcoding.data=function(x, by, FUN,...,
 									  default.layer=NULL,
 									  layers=NULL) {	
   
+
 	uniq.value = function(z) {
 		
 		if (is.null(z) | 
@@ -56,19 +57,22 @@ aggregate.metabarcoding.data=function(x, by, FUN,...,
 		MARGIN=2
 	
 	reads = x@reads
-	  
+	
+	
 	if (MARGIN==1) {
 		# prepare the aggrevation arguments for the read table
 		# from the function arguments
 	  dotted = list(...)
-	  if (length(dotted) > 0)
+	  
+
+		if (length(dotted) > 0)
 	    aggr.args = list(reads,by=by,FUN=FUN,...=dotted,simplify=FALSE)
 	  else
 	    aggr.args = list(reads,by=by,FUN=FUN,simplify=FALSE)
 	  		
 		# Aggregate the read table
 		ragr = do.call(aggregate,aggr.args)
-		
+
 		# extrat new ids from the aggregated table
 		ncat = length(by)
 		ids  = as.character(interaction(ragr[,1:ncat,drop=FALSE]))
@@ -118,27 +122,28 @@ aggregate.metabarcoding.data=function(x, by, FUN,...,
       rownames(lagr)=ids
 			la[[n]]=lagr
 		}
-		
+
 		# aggragate the sample table according to the same criteria
 		#
 		# TODO: We have to take special care of factors in the samples
 		#       data.frame
 		
 		sagr = aggregate(samples(x),by,uniq.value,simplify=FALSE)
-		
+
 		# move the first columns of the resulting data frame (the aggregations
 		# modalities to the last columns of the data.frame
 		sagr = sagr[,c((ncat+1):(dim(sagr)[2]),1:ncat),drop=FALSE]
 		larg = c(lapply(sagr,unlist),list(stringsAsFactors=FALSE))	
-		sagr = do.call(data.frame,larg)
+		sagr = data.frame(do.call(data.frame,larg))
 		
 		# set samples ids to the ids computed from modalities
-		sagr$id=ids
+
 		rownames(sagr)=ids
+		sagr$id=ids
 		
 		# build the new metabarcoding data instance
-		newdata = copy.metabarcoding.data(x,reads=ragr,samples=sagr)
-		
+		newdata = copy.metabarcoding.data(x,reads=ragr,samples=sagr,layers=la)
+
 	}
 	else {
 		# prepare the aggregation arguments for the read table