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#' Import USGS Sample Data for EGRET analysis
#'
#' Imports data from USGS web service.
#' For raw data, use \code{\link[dataRetrieval]{read_USGS_samples}} from the dataRetrieval package.
#' This function will retrieve the raw data, and compress it (summing constituents) if
#' more than 1 parameter code is supplied. See
#' section 3.2.4 of the vignette for more details.
#'
#' @param siteNumber character USGS site number. This is usually an 8 digit number
#' @param parameterCd character USGS parameter code. This is usually an 5 digit number.
#' @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{compressData}}, \code{\link{populateSampleColumns}},
#' \code{\link[dataRetrieval]{readWQPqw}}
#' @examplesIf interactive()
#' \donttest{
#' # These examples require an internet connection to run
#'
#' Sample_01075 <- readNWISSample('01594440','01075', '1985-01-01', '1985-03-31')
#' }
readNWISSample <- function(siteNumber,
parameterCd,
startDate = "",
endDate = "",
verbose = TRUE){
siteNumber <- paste0("USGS-", siteNumber)
data <- suppressMessages( dataRetrieval::read_USGS_samples(monitoringLocationIdentifier = siteNumber,
usgsPCode = parameterCd,
activityStartDateLower = startDate,
activityStartDateUpper = endDate))
extra_cols <- c("ActivityStartDateTime",
"USGSPCode",
"ActivityMediaSubdivisionName",
"ActivityMediaName",
"ResultSampleFractionText",
"ResultStatusIdentifier",
"ResultValueTypeName",
"ActivityTypeCode")
conversion_names <- data.frame(legacy_names = c("ResultDetectionConditionText",
"ResultMeasureValue",
"DetectionQuantitationLimitMeasure.MeasureValue",
"CharacteristicName",
"ActivityStartDate",
extra_cols),
new_names = c("Result_ResultDetectionCondition",
"Result_Measure",
"DetectionLimit_MeasureA",
"Result_Characteristic",
"Activity_StartDate",
"Activity_StartDateTime",
"USGSpcode",
"Activity_MediaSubdivisionName",
"Activity_Media",
"Result_SampleFraction",
"Result_MeasureStatusIdentifier",
"Result_MeasureType",
"Activity_TypeCode"))
for(i in seq_len(nrow(conversion_names))){
names(data)[which(names(data) == conversion_names$new_names[i])] <- conversion_names$legacy_names[i]
}
if(nrow(data) == 0){
warning("No data returned")
}
if(nrow(data) > 0){
data <- processQWData(data)
first_three <- c("dateTime",
"qualifier",
"value")
compressedData <- compressData(data[, first_three],
verbose = verbose)
combined_data <- cbind(compressedData, data[, names(data)[!names(data) %in% first_three]])
combined_data <- remove_zeros(combined_data, verbose = verbose)
Sample <- populateSampleColumns(combined_data)
orig_Sample <- c("Date", "ConcLow", "ConcHigh", "Uncen", "ConcAve",
"Julian", "Month", "Day", "DecYear", "waterYear", "MonthSeq",
"SinDY", "CosDY")
Sample <- Sample[, c(orig_Sample, names(Sample)[!names(Sample) %in% orig_Sample])]
Sample <- Sample[order(Sample$Date), ]
} 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)
}
return(Sample)
}
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