processQWData.r

#' Processing of USGS NWIS Water Quality Data
#'
#' Processes water quality portal data. This function looks at detection limit and detection 
#' conditions to determine if a value is left censored or not. Censored values are given the qualifier
#' "<".  The dataframe is also converted from a long to wide format.
#' 
#' @param data dataframe from Water Quality Portal
#' @param pCode logical if TRUE, assume data came from a pCode search, if FALSE, characteristic name.
#' @keywords data import USGS web service
#' @return data dataframe with first column dateTime, and at least one qualifier and value columns
#' (subsequent qualifier/value columns could follow depending on the number of parameter codes)
#' @export
#' @examples
#' # These examples require an internet connection to run
#' rawSample <- retrieveWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
#' rawSampleSelect <- processQWData(rawSample)
processQWData <- function(data,pCode=TRUE){

  qualifier <- ifelse((data$ResultDetectionConditionText == "Not Detected" | 
                    data$ResultDetectionConditionText == "Detected Not Quantified" |
                    data$ResultMeasureValue < data$DetectionQuantitationLimitMeasure.MeasureValue),"<","")
  
  correctedData<-ifelse((nchar(qualifier)==0),data$ResultMeasureValue,data$DetectionQuantitationLimitMeasure.MeasureValue)
  test <- data.frame(data$USGSPCode)
  
  #   test$dateTime <- as.POSIXct(strptime(paste(data$ActivityStartDate,data$ActivityStartTime.Time,sep=" "), "%Y-%m-%d %H:%M:%S"))
  test$dateTime <- as.Date(data$ActivityStartDate, "%Y-%m-%d")
  
  originalLength <- nrow(test)
  test$qualifier <- qualifier
  test$value <- as.numeric(correctedData)
  
  test <- test[!is.na(test$dateTime),]
  newLength <- nrow(test)
  if (originalLength != newLength){
    numberRemoved <- originalLength - newLength
    warningMessage <- paste(numberRemoved, " rows removed because no date was specified", sep="")
    warning(warningMessage)
  }
  
  if (pCode){
    colnames(test)<- c("USGSPCode","dateTime","qualifier","value")
    newTimeVar <- "USGSPCode"
  } else {
    colnames(test)<- c("CharacteristicName","dateTime","qualifier","value")
    newTimeVar <- "CharacteristicName"
  }
  
  data <- suppressWarnings(reshape(test, idvar="dateTime", timevar = newTimeVar, direction="wide"))  
  data$dateTime <- format(data$dateTime, "%Y-%m-%d")
  data$dateTime <- as.Date(data$dateTime)
  return(data)
}