Added some help. Deprecated old getWQPData (this was the only place it was used).

R/getSTORETSampleData.R

 #' Import Sample Data for WRTDS
 #'
-#' Imports data from the Water Quality Portal. This function gets the data from: \url{http://www.waterqualitydata.us}
+#' Imports data from the Water Quality Portal, so it could be STORET, NWIS, or . This function gets the data from: \url{http://www.waterqualitydata.us}
 #' For raw data, use getWQPData.  This function will retrieve the raw data, and compress it (summing constituents). See
 #' chapter 7 of the EGRET user guide for more details, then converts it to the Sample dataframe structure.
 #'
@@ -12,13 +12,33 @@
 #' @keywords data import USGS WRTDS
 #' @export
 #' @return Sample dataframe
-#' @seealso \code{\link{compressData}}, \code{\link{populateSampleColumns}}
+#' @seealso \code{\link{getWQPData}}, \code{\link{getWQPSites}}, 
+#' \code{\link{retrieveWQPqwData}}, \code{\link{retrieveNWISqwData}}, and \code{\link{basicWQPData}}, 
+#' \code{\link{compressData}}, \code{\link{populateSampleColumns}}
 #' @examples
 #' # These examples require an internet connection to run
 #' Sample_01075 <- getSTORETSampleData('USGS-01594440','Chloride', '', '')
 #' Sample_All <- getSTORETSampleData('WIDNR_WQX-10032762','Specific conductance', '', '')
 getSTORETSampleData <- function(siteNumber,characteristicName,startDate,endDate,interactive=TRUE){
-  data <- getWQPData(siteNumber,characteristicName,startDate,endDate,interactive=interactive)
+  
+  retval <- retrieveWQPqwData(siteNumber=siteNumber,
+                              parameterCd=characteristicName,
+                              startDate=startDate,
+                              endDate=endDate,
+                              interactive=interactive)
+  #Check for pcode:
+  if(all(nchar(characteristicName) == 5)){
+    suppressWarnings(pCodeLogic <- all(!is.na(as.numeric(characteristicName))))
+  } else {
+    pCodeLogic <- FALSE
+  }
+  
+  if(nrow(retval) > 0){
+    data <- processQWData(retval,pCodeLogic)
+  } else {
+    data <- NULL
+  }
+  
   compressedData <- compressData(data, interactive=interactive)
   Sample <- populateSampleColumns(compressedData)
   return(Sample)