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) | 
@@ -57,11 +58,14 @@ aggregate.metabarcoding.data=function(x, by, FUN,...,
 	
 	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)
@@ -130,14 +134,15 @@ aggregate.metabarcoding.data=function(x, by, FUN,...,
 		# 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 {