R/readWQPSample.R

In EGRET: Exploration and Graphics for RivEr Trends

#' Import Sample Data from the Water Quality Portal for WRTDS
#'
#' Imports data from the Water Quality Portal, so it could be STORET, USGS, or USDA data. 
#' This function gets the data from: \url{https://www.waterqualitydata.us}
#' For raw data, use readWQPdata.  This function will retrieve the raw data, 
#' compress it (summing constituents), then converts it to the Sample dataframe structure.
#' See chapter 7 of the EGRET user guide for more details.
#' @param siteNumber character site number.  If USGS, it should be in the form :'USGS-XXXXXXXXX...'
#' @param characteristicName character. Either a valid characteristic name, or a 5 digit 
#' USGS parameter code.
#' @param startDate character starting date for data retrieval in the form YYYY-MM-DD.
#' Default is empty quotes "" which will retrieve the full period of record.
#' @param endDate character ending date for data retrieval in the form YYYY-MM-DD.
#' Default is empty quotes "" which will retrieve the full period of record.
#' @param verbose logical specifying whether or not to display progress message
#' @keywords data import USGS WRTDS
#' @export
#' @return A data frame 'Sample' with the following columns:
#' \tabular{lll}{
#' Name \tab Type \tab Description \cr
#' Date \tab Date \tab Date \cr
#' ConcLow \tab numeric \tab Lower limit of concentration \cr
#' ConcHigh \tab numeric \tab Upper limit of concentration \cr
#' Uncen \tab integer \tab Uncensored data (1=TRUE, 0=FALSE) \cr
#' ConcAve \tab numeric \tab Average concentration \cr
#' Julian \tab integer \tab Number of days since Jan. 1, 1850\cr
#' Month \tab integer \tab Month of the year [1-12] \cr 
#' Day \tab integer \tab Day of the year [1-366] \cr
#' DecYear \tab numeric \tab Decimal year \cr
#' MonthSeq \tab integer \tab Number of months since January 1, 1850 \cr
#' SinDY \tab numeric \tab Sine of the DecYear \cr
#' CosDY \tab numeric \tab Cosine of the DecYear
#' }
#' @seealso \code{\link[dataRetrieval]{readWQPdata}}, \code{dataRetrieval::whatWQPsites}, 
#' \code{\link[dataRetrieval]{readWQPqw}}, \code{\link{compressData}}, \code{\link{populateSampleColumns}}
#' @examples
#' # These examples require an internet connection to run
#' \donttest{
#' # Sample_All <- readWQPSample('WIDNR_WQX-10032762','Specific conductance', '', '')
#' }
readWQPSample <- function(siteNumber,
                          characteristicName,
                          startDate = "",
                          endDate = "",
                          verbose = TRUE){
  
  url <- dataRetrieval::constructWQPURL(siteNumber,characteristicName,startDate,endDate)
  retval <- dataRetrieval::importWQP(url)
  if(nrow(retval) > 0){

    if(nrow(retval) > 0){
      data <- processQWData(retval)
    } else {
      data <- NULL
    }
    
    compressedData <- compressData(data[, c("dateTime",
                                            "qualifier",
                                            "value")],
                                   verbose=verbose)
    Sample <- populateSampleColumns(compressedData)
    Sample <- cbind(Sample, data[, names(data)[!names(data) %in% c("dateTime",
                                                                  "qualifier",
                                                                  "value")]])
  } else {
    Sample <- data.frame(Date=as.Date(character()),
                         ConcLow=numeric(), 
                         ConcHigh=numeric(), 
                         Uncen=numeric(),
                         ConcAve=numeric(),
                         Julian=numeric(),
                         Month=numeric(),
                         Day=numeric(),
                         DecYear=numeric(),
                         MonthSeq=numeric(),
                         SinDY=numeric(),
                         CosDY=numeric(),
                         stringsAsFactors=FALSE)
  }
  Sample <- Sample[order(Sample$Date), ]
  return(Sample)
}