Minor bug fix in average.spec.se() function

Author: Shawn P. Serbin

R/average.spec.se.R

@@ -216,11 +216,16 @@ average.spec.se <- function(file.dir=NULL,out.dir=NULL,spec.type=NULL,spec.file.
   #good.spec <- droplevels(in.spec3[which(in.spec3$Wave_450<=bias),])
   if (length(good.spec.temp2)>0){
     good.spec <- droplevels(in.spec3[good.spec.temp2,])  
+    dims <- dim(good.spec)
+    check <- length(wht.ref)+dim(good.spec)[1]+dim(bad.spec)[1]==dim(in.spec3)[1]
   } else {
-    good.spec <- droplevels(in.spec3[good.spec.temp,])       
+    #good.spec <- droplevels(in.spec3[good.spec.temp,])
+    good.spec <- wht.ref.spec
+    dims <- dim(good.spec)
+    check <- length(wht.ref)+dim(bad.spec)[1]==dim(in.spec3)[1]
   }              
-  dims <- dim(good.spec)
-  check <- length(wht.ref)+dim(good.spec)[1]+dim(bad.spec)[1]==dim(in.spec3)[1]
+  #dims <- dim(good.spec)
+  #check <- length(wht.ref)+dim(good.spec)[1]+dim(bad.spec)[1]==dim(in.spec3)[1]
 
   # temporary debugging flag
   if (check==FALSE) {