Merge pull request #2 from ldecicco-USGS/master

Updating naming convention + other minor changes.

DESCRIPTION

 Package: dataRetrieval
 Type: Package
 Title: Retrieval functions for hydrologic data
-Version: 1.3.1
-Date: 2014-07-01
+Version: 1.3.2
+Date: 2014-08-04
 Author: Robert M. Hirsch, Laura De Cicco
 Maintainer: Laura De Cicco <ldecicco@usgs.gov>
 Description: Collection of functions to help retrieve USGS data from either web

NAMESPACE

@@ -15,10 +15,8 @@ export(getDataFromFile)
 export(getGeneralWQPData)
 export(getMetaData)
 export(getParameterInfo)
-export(getQWData)
 export(getQWDataFromFile)
 export(getRDB1Data)
-export(getRawQWData)
 export(getSTORETSampleData)
 export(getSampleData)
 export(getSampleDataFromFile)
@@ -38,9 +36,10 @@ export(populateSiteINFO)
 export(processQWData)
 export(removeDuplicates)
 export(renameColumns)
-export(retrieveNWISData)
+export(retrieveNWISdvData)
 export(retrieveNWISqwData)
-export(retrieveUnitNWISData)
+export(retrieveNWISunitData)
+export(retrieveWQPqwData)
 import(RCurl)
 import(XML)
 import(reshape2)

NEWS

+dataRetrieval 1.3.2
+===========
+
+* Deprecated getQWData, updated getWQPData to take either parameter code or characteristic name.
+* Changed the name of raw data retrievals to: retrieveNWISqwData, retrieveNWISunitData, retrieveNWISdvData, and retrieveWQPqwData (from: retrieveNWISqwData, retrieveUnitNWISData, retrieveNWISData, getRawQWData)
+* Added NA warning to getDVData function
+
+
 dataRetrieval 1.2.2
 ===========
 

R/constructNWISURL.r

@@ -27,7 +27,7 @@
 #' url_unit <- constructNWISURL(siteNumber,pCode,"2012-06-28","2012-06-30",'iv')
 #' url_qw_single <- constructNWISURL(siteNumber,"01075",startDate,endDate,'qw')
 #' url_qw <- constructNWISURL(siteNumber,c('01075','00029','00453'),startDate,endDate,'qw')
-#' url_wqp <- constructNWISURL(siteNumber,c('01075','00029','00453'),startDate,endDate,'wqp')
+#' url_wqp <- constructNWISURL(paste("USGS",siteNumber,sep="-"),c('01075','00029','00453'),startDate,endDate,'wqp')
 #' url_daily_tsv <- constructNWISURL(siteNumber,pCode,startDate,endDate,'dv',statCd=c("00003","00001"),format="tsv")
 constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,statCd="00003", format="xml",expanded=FALSE,interactive=TRUE){
 
@@ -87,6 +87,14 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
          wqp = {
            siteNumber <- formatCheckSiteNumber(siteNumber, interactive=interactive)
            
+           #Check for pcode:
+           if(all(nchar(parameterCd) == 5)){
+             suppressWarnings(pCodeLogic <- all(!is.na(as.numeric(parameterCd))))
+           } else {
+             pCodeLogic <- FALSE
+             parameterCd <- URLencode(parameterCd)
+           }
+           
            if(length(parameterCd)>1){
              parameterCd <- paste(parameterCd, collapse=";")
            }
@@ -98,10 +106,10 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
              endDate <- format(as.Date(endDate), format="%m-%d-%Y")
            }
            
-           baseURL <- "http://www.waterqualitydata.us/Result/search?siteid=USGS-"
+           baseURL <- "http://www.waterqualitydata.us/Result/search?siteid="
            url <- paste(baseURL,
                         siteNumber,
-                        "&pCode=",
+                        ifelse(pCodeLogic,"&pCode=","&characteristicName="),
                         parameterCd,
                         "&startDateLo=",
                         startDate,

R/getDVData.r

@@ -18,14 +18,14 @@
 #' @keywords data import USGS WRTDS
 #' @export
 #' @return Daily dataframe
-#' @seealso \code{\link{retrieveNWISData}}, \code{\link{populateDaily}}
+#' @seealso \code{\link{retrieveNWISdvData}}, \code{\link{populateDaily}}
 #' @examples
 #' # These examples require an internet connection to run
 #' Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31')
 #' DailyCFS <- getDVData('01594440','00060', '1985-01-01', '1985-03-31',convert=FALSE)
 #' DailySuspSediment <- getDVData('01594440','80154', '1985-01-01', '1985-03-31')
 getDVData <- function (siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE,convert=TRUE,format="tsv"){
-  data <- retrieveNWISData(siteNumber,ParameterCd,StartDate,EndDate,interactive=interactive,format=format)
+  data <- retrieveNWISdvData(siteNumber,ParameterCd,StartDate,EndDate,interactive=interactive,format=format)
   
   #  need to setup conversion factor because the NWIS data are in cfs but we store in cms
   names(data) <- c('agency', 'site', 'dateTime', 'value', 'code')  # do a merge instead?

R/getQWData.r

-#' Data Import for USGS NWIS Water Quality Data
-#'
-#' Imports and processes data from NWIS web service. This function gets the data from here: \url{http://www.waterqualitydata.us}
-#' A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-#' A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
-#'
-#' @param siteNumber string USGS site number.  This is usually an 8 digit number
-#' @param ParameterCd string USGS parameter code.  This is usually an 5 digit number. Multiple parameter codes can be inputted with a ';' separator.  Leaving this blank will return all of the measured values during the specified time period.
-#' @param StartDate string starting date for data retrieval in the form YYYY-MM-DD.
-#' @param EndDate string ending date for data retrieval in the form YYYY-MM-DD.
-#' @param interactive logical Option for interactive mode.  If true, there is user interaction for error handling and data checks.
-#' @keywords data import USGS web service
-#' @return retval dataframe with first column dateTime, and at least one qualifier and value columns
-#' (subsequent qualifier/value columns could follow depending on requested parameter codes)
-#' @export
-#' @examples
-#' # These examples require an internet connection to run
-#' rawProcessedSample <- getQWData('01594440','01075', '1985-01-01', '1985-03-31')
-#' rawProcessedSampleAll <- getQWData('05114000','', '1985-01-01', '1985-03-31')
-#' rawProcessedSampleSelect <- getQWData('05114000','00915;00931', '1985-01-01', '1985-04-30')
-getQWData <- function(siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE){
-  rawSample <- getRawQWData(siteNumber,ParameterCd,StartDate,EndDate,interactive)
-  retval <- processQWData(rawSample)
-  return(retval)
-}

R/getRawQWData.r

@@ -16,20 +16,25 @@
 #' @import RCurl
 #' @examples
 #' # These examples require an internet connection to run
-#' rawSample <- getRawQWData('01594440','01075', '1985-01-01', '1985-03-31')
-#' rawSampleAll <- getRawQWData('05114000','', '1985-01-01', '1985-03-31')
-#' rawSampleSelect <- getRawQWData('05114000',c('00915','00931'), '1985-01-01', '1985-04-30')
-getRawQWData <- function(siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE){
+#' rawSample <- retrieveWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
+#' rawSampleAll <- retrieveWQPqwData('USGS-05114000','', '1985-01-01', '1985-03-31')
+#' rawSampleSelect <- retrieveWQPqwData('USGS-05114000',c('00915','00931'), '1985-01-01', '1985-04-30')
+#' rawStoret <- retrieveWQPqwData('WIDNR_WQX-10032762','Specific conductance', '', '')
+retrieveWQPqwData <- function(siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE){
 
   url <- constructNWISURL(siteNumber,ParameterCd,StartDate,EndDate,"wqp",interactive=interactive)
-#   require(RCurl)
+
   h <- basicHeaderGatherer()
   doc <- getURI(url, headerfunction = h$update)
   numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
-  suppressWarnings(retval <- read.delim(url, header = TRUE, quote="\"", dec=".", sep='\t', colClasses=c('character'), fill = TRUE))
-  actualNumReturned <- nrow(retval)
-  
-  if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
-  
-  return(retval)
+  if (!is.na(numToBeReturned) | numToBeReturned != 0){  
+    suppressWarnings(retval <- read.delim(url, header = TRUE, quote="\"", dec=".", sep='\t', colClasses=c('character'), fill = TRUE))
+    actualNumReturned <- nrow(retval)
+    
+    if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
+    
+    return(retval)
+  } else {
+    warning("No data to retrieve")
+  }
 }

R/getSTORETSampleData.R

 #' Import Sample Data for WRTDS
 #'
-#' Imports data from NWIS web service. This function gets the data from here: \url{http://qwwebservices.usgs.gov/}
-#' A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-#' A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
-#' For raw data, use getQWData.  This function will retrieve the raw data, and compress it (summing constituents). See
-#' chapter 7 of the EGRET user guide for more details.
+#' Imports data from the Water Quality Portal. 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.
 #'
 #' @param siteNumber string site number.  If USGS, it should be in the form :'USGS-XXXXXXXXX...'
 #' @param characteristicName string

R/getWQPData.r

 #' Data Import from Water Quality Portal
 #'
-#' Imports data from Water Quality Portal web service. This function gets the data from here: \url{http://www.waterqualitydata.us}. This function is more general than getQWData
+#' Imports data from Water Quality Portal web service. This function gets the data from: \url{http://www.waterqualitydata.us}. This function is more general than getQWData
 #' because it allows for other agencies rather than the USGS.  Therefore, the 5-digit parameter code cannot be used.
-#' Instead, this function uses characteristicName.  A complete list can be found here \url{http://www.waterqualitydata.us/Codes/Characteristicname}
+#' Instead, this function uses characteristicName.  A complete list can be found here 
 #'
 #' @param siteNumber string site number.  If USGS, it should be in the form :'USGS-XXXXXXXXX...'
 #' @param characteristicName string
@@ -16,77 +16,30 @@
 #' @import RCurl
 #' @examples
 #' # These examples require an internet connection to run
-#' getWQPData('USGS-01594440','Chloride', '', '')
-#' getWQPData('WIDNR_WQX-10032762','Specific conductance', '', '')
+#' Chloride <- getWQPData('USGS-01594440','Chloride', '', '')
+#' SC <- getWQPData('WIDNR_WQX-10032762','Specific conductance', '', '')
+#' NWIS_Cl <- getWQPData('USGS-04024000','30234', '', '')
+#' MultipleQW <- getWQPData('USGS-04024000',c('30234','90095'), '', '')
 getWQPData <- function(siteNumber,characteristicName,StartDate,EndDate,interactive=TRUE){
-
-#   require(RCurl)
-  
-  StartDate <- formatCheckDate(StartDate, "StartDate", interactive=interactive)
-  EndDate <- formatCheckDate(EndDate, "EndDate", interactive=interactive)
   
-  dateReturn <- checkStartEndDate(StartDate, EndDate, interactive=interactive)
-  StartDate <- dateReturn[1]
-  EndDate <- dateReturn[2]
-  
-  if (nzchar(StartDate)){
-    StartDate <- format(as.Date(StartDate), format="%m-%d-%Y")
-  }
-  if (nzchar(EndDate)){
-    EndDate <- format(as.Date(EndDate), format="%m-%d-%Y")
+  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
   }
-  
-  characteristicName <- URLencode(characteristicName)
-  
-  baseURL <- "http://www.waterqualitydata.us/Result/search?siteid="
-  url <- paste(baseURL,
-               siteNumber,
-               "&characteristicName=",
-               characteristicName,   # to get multi-parameters, use a semicolen 
-               "&startDateLo=",
-               StartDate,
-               "&startDateHi=",
-               EndDate,
-               "&countrycode=US&mimeType=tsv",sep = "")
-  h <- basicHeaderGatherer()
-  doc <- getURI(url, headerfunction = h$update)
-  numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
-  
-  suppressWarnings(retval <- read.delim(url, header = TRUE, quote="\"", dec=".", sep='\t', colClasses=c('character'), fill = TRUE))
-  
-  qualifier <- ifelse((retval$ResultDetectionConditionText == "Not Detected" | 
-                         retval$ResultDetectionConditionText == "Detected Not Quantified" |
-                         retval$ResultMeasureValue < retval$DetectionQuantitationLimitMeasure.MeasureValue),"<","")
-  
-  correctedData<-ifelse((nchar(qualifier)==0),retval$ResultMeasureValue,retval$DetectionQuantitationLimitMeasure.MeasureValue)
-  test <- data.frame(retval$CharacteristicName)
-  
-  #   test$dateTime <- as.POSIXct(strptime(paste(retval$ActivityStartDate,retval$ActivityStartTime.Time,sep=" "), "%Y-%m-%d %H:%M:%S"))
-  test$dateTime <- as.Date(retval$ActivityStartDate, "%Y-%m-%d")
-  
-  originalLength <- nrow(test)
-  
-  if (!is.na(numToBeReturned)){
-    if(originalLength != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", originalLength, " were returned")
-    
-    test$qualifier <- qualifier
-    test$value <- as.numeric(correctedData)
-    
-    test <- test[!is.na(test$dateTime),]
-    newLength <- nrow(test)
-    if (originalLength != newLength){
-      numberRemoved <- originalLength - newLength
-      warningMessage <- paste(numberRemoved, " rows removed because no date was specified", sep="")
-      warning(warningMessage)
-    }
-    
-    colnames(test)<- c("CharacteristicName","dateTime","qualifier","value")
-    data <- reshape(test, idvar="dateTime", timevar = "CharacteristicName", direction="wide")    
-    data$dateTime <- format(data$dateTime, "%Y-%m-%d")
-    data$dateTime <- as.Date(data$dateTime)
-    return(data)
+
+  if(nrow(retval) > 0){
+    data <- processQWData(retval,pCodeLogic)
   } else {
-    warning("No data retrieved")
+    data <- NULL
   }
   
+  return(data)
+  
 }

R/getWQPSites.R

-#' Site DAta Import from Water Quality Portal
+#' Site Data Import from Water Quality Portal
 #'
-#' Imports site data from Water Quality Portal web service. This function gets the data from here: \url{http://www.waterqualitydata.us}. This function is more general than getQWData
-#' because it allows for other agencies rather than the USGS.  Therefore, the 5-digit parameter code cannot be used.
-#' Instead, this function uses characteristicName.  A complete list can be found here \url{http://www.waterqualitydata.us/Codes/Characteristicname}
+#' Returns a list of sites from the Water Quality Portal web service. This function gets the data from: \url{http://www.waterqualitydata.us}.
+#' Arguments to the function should be based on \url{www.waterqualitydata.us/webservices_documentation.jsp}
 #'
 #' @param \dots see \url{www.waterqualitydata.us/webservices_documentation.jsp} for a complete list of options
 #' @keywords data import WQP web service

R/getWaterML1Data.r

@@ -17,6 +17,8 @@
 #' data <- getWaterML1Data(obs_url)
 #' urlMulti <- constructNWISURL("04085427",c("00060","00010"),startDate,endDate,'dv',statCd=c("00003","00001"))
 #' multiData <- getWaterML1Data(urlMulti)
+#' goundwaterExampleURL <- "http://waterservices.usgs.gov/nwis/gwlevels/?format=waterml&sites=431049071324301&startDT=2013-10-01&endDT=2014-06-30"
+#' groundWater <- getWaterML1Data(goundwaterExampleURL)
 getWaterML1Data <- function(obs_url){
 
   # This is more elegent, but requires yet another package dependency RCurl...which I now require for wqp
@@ -80,12 +82,20 @@ getWaterML1Data <- function(obs_url){
       assign(valueName,value)
       assign(qualName,qualifier)
       
-      df <- data.frame(dateTime,
-                       tzAbbriev,
-                       get(valueName),
-                       get(qualName)
-      )
-      names(df) <- c("dateTime","tz_cd",valueName,qualName)
+      if(length(get(qualName))!=0){
+        df <- data.frame(dateTime,
+                         tzAbbriev,
+                         get(valueName),
+                         get(qualName)
+        )
+        names(df) <- c("dateTime","tz_cd",valueName,qualName)
+      } else {
+        df <- data.frame(dateTime,
+                         tzAbbriev,
+                         get(valueName)
+        )
+        names(df) <- c("dateTime","tz_cd",valueName)       
+      }
  
       if (1 == i & valuesIndex[1] == j){
         mergedDF <- df

R/populateDaily.r

@@ -51,14 +51,9 @@ populateDaily <- function(rawData,qConvert,interactive=TRUE){  # rawData is a da
 
     qshift<- 0.001*mean(localDaily$Q, na.rm=TRUE) 
     if (interactive){
-      negNums <- length(which(localDaily$Q<0))
-      zeroNums <- length(which(localDaily$Q == 0))
-      
-      if (negNums > 0) {
-        cat("There were", as.character(negNums), "negative flow days \n")
-        cat("Negative values are not supported in the EGRET package\n")
-      }
       
+      zeroNums <- length(which(localDaily$Q == 0))
+
       if (zeroNums > 0){
         cat("There were", as.character(zeroNums), "zero flow days \n")
       }
@@ -70,6 +65,11 @@ populateDaily <- function(rawData,qConvert,interactive=TRUE){  # rawData is a da
     qshift<-0.0
   }
   
+  negNums <- length(which(localDaily$Q<0))
+  if (negNums > 0) {
+    cat("There were", as.character(negNums), "negative flow days \n")
+    cat("Negative values are not supported in the EGRET package\n")
+  }
   
   localDaily$Q<-localDaily$Q+qshift
   
@@ -94,7 +94,20 @@ populateDaily <- function(rawData,qConvert,interactive=TRUE){  # rawData is a da
 
     #these next two lines show the user where the gaps in the data are if there are any
     n<-nrow(localDaily)
-    for(i in 2:n) {if((localDaily$Julian[i]-localDaily$Julian[i-1])>1) cat("\n discharge data jumps from",as.character(localDaily$Date[i-1]),"to",as.character(localDaily$Date[i]))}
+    for(i in 2:n) {
+      if((localDaily$Julian[i]-localDaily$Julian[i-1])>1) cat("\n discharge data jumps from",as.character(localDaily$Date[i-1]),"to",as.character(localDaily$Date[i]))
+    }
+    
+    numNAs <- sum(is.na(localDaily$Q))
+    if(numNAs > 0){
+      cat(numNAs, "discharge measurements are not reported (NA's). \nMany of the EGRET functions will not work with missing discharge measurements.")
+      if (localDaily$Julian[max(which(is.na(localDaily$Q)),na.rm = TRUE)]-
+           localDaily$Julian[min(which(is.na(localDaily$Q)),na.rm = TRUE)]+1 ==  numNAs){
+        cat("\nNA gap is from",as.character(localDaily$Date[min(which(is.na(localDaily$Q)),na.rm = TRUE)]),"to",
+            as.character(localDaily$Date[max(which(is.na(localDaily$Q)),na.rm = TRUE)]))
+      } 
+    }
+    
   }
   
   return (localDaily)  

R/processQWData.r

@@ -4,16 +4,17 @@
 #' 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 
+#' @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 <- getRawQWData('01594440','01075', '1985-01-01', '1985-03-31')
+#' rawSample <- retrieveWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
 #' rawSampleSelect <- processQWData(rawSample)
-processQWData <- function(data){
+processQWData <- function(data,pCode=TRUE){
 
   qualifier <- ifelse((data$ResultDetectionConditionText == "Not Detected" | 
                     data$ResultDetectionConditionText == "Detected Not Quantified" |
@@ -37,8 +38,15 @@ processQWData <- function(data){
     warning(warningMessage)
   }
   
-  colnames(test)<- c("USGSPCode","dateTime","qualifier","value")
-  data <- suppressWarnings(reshape(test, idvar="dateTime", timevar = "USGSPCode", direction="wide"))  
+  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)

R/renameColumns.R

@@ -9,10 +9,10 @@
 #' @examples
 #' # This example requires an internet connection to run
 #' siteNumber <- '05114000' 
-#' rawData <- retrieveNWISData(siteNumber,c("00010","00060","00300"),"2001-01-01","2002-01-01",StatCd=c("00001","00003"))
+#' rawData <- retrieveNWISdvData(siteNumber,c("00010","00060","00300"),"2001-01-01","2002-01-01",StatCd=c("00001","00003"))
 #' rawData <- renameColumns(rawData)
 #' today <- as.character(Sys.Date())
-#' rawData2 <- retrieveUnitNWISData(siteNumber,c("00010","00060"),today,today)
+#' rawData2 <- retrieveNWISunitData(siteNumber,c("00010","00060"),today,today)
 #' rawData2 <- renameColumns(rawData2)
 renameColumns <- function(rawData){
   

R/retrieveNWISData.r

@@ -22,11 +22,11 @@
 #' startDate <- '2012-01-01'
 #' endDate <- '2012-06-30'
 #' pCode <- '00060'
-#' rawDailyQ <- retrieveNWISData(siteNumber,pCode, startDate, endDate)
-#' rawDailyTemperature <- retrieveNWISData(siteNumber,'00010', startDate, endDate, StatCd='00001')
-#' rawDailyTemperatureTSV <- retrieveNWISData(siteNumber,'00010', startDate, endDate, StatCd='00001',format='tsv')
-#' rawDailyQAndTempMeanMax <- retrieveNWISData(siteNumber,c('00010','00060'), startDate, endDate, StatCd=c('00001','00003'))
-retrieveNWISData <- function (siteNumber,ParameterCd,StartDate,EndDate,StatCd="00003",format="tsv",interactive=TRUE){  
+#' rawDailyQ <- retrieveNWISdvData(siteNumber,pCode, startDate, endDate)
+#' rawDailyTemperature <- retrieveNWISdvData(siteNumber,'00010', startDate, endDate, StatCd='00001')
+#' rawDailyTemperatureTSV <- retrieveNWISdvData(siteNumber,'00010', startDate, endDate, StatCd='00001',format='tsv')
+#' rawDailyQAndTempMeanMax <- retrieveNWISdvData(siteNumber,c('00010','00060'), startDate, endDate, StatCd=c('00001','00003'))
+retrieveNWISdvData <- function (siteNumber,ParameterCd,StartDate,EndDate,StatCd="00003",format="tsv",interactive=TRUE){  
   
   url <- constructNWISURL(siteNumber,ParameterCd,StartDate,EndDate,"dv",statCd=StatCd,format=format,interactive=interactive)
   

R/retrieveUnitNWISData.r

@@ -21,9 +21,9 @@
 #' StartDate <- as.character(Sys.Date())
 #' EndDate <- as.character(Sys.Date())
 #' # These examples require an internet connection to run
-#' rawData <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate)
-#' rawData2 <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate,"tsv")
-retrieveUnitNWISData <- function (siteNumber,ParameterCd,StartDate,EndDate,format="xml",interactive=TRUE){  
+#' rawData <- retrieveNWISunitData(siteNumber,ParameterCd,StartDate,EndDate)
+#' rawData2 <- retrieveNWISunitData(siteNumber,ParameterCd,StartDate,EndDate,"tsv")
+retrieveNWISunitData <- function (siteNumber,ParameterCd,StartDate,EndDate,format="xml",interactive=TRUE){  
   
   url <- constructNWISURL(siteNumber,ParameterCd,StartDate,EndDate,"uv",format=format,interactive=interactive)
   if (format == "xml") {

man/constructNWISURL.Rd

@@ -45,7 +45,7 @@ url_daily <- constructNWISURL(siteNumber,pCode,startDate,endDate,'dv',statCd=c("
 url_unit <- constructNWISURL(siteNumber,pCode,"2012-06-28","2012-06-30",'iv')
 url_qw_single <- constructNWISURL(siteNumber,"01075",startDate,endDate,'qw')
 url_qw <- constructNWISURL(siteNumber,c('01075','00029','00453'),startDate,endDate,'qw')
-url_wqp <- constructNWISURL(siteNumber,c('01075','00029','00453'),startDate,endDate,'wqp')
+url_wqp <- constructNWISURL(paste("USGS",siteNumber,sep="-"),c('01075','00029','00453'),startDate,endDate,'wqp')
 url_daily_tsv <- constructNWISURL(siteNumber,pCode,startDate,endDate,'dv',statCd=c("00003","00001"),format="tsv")
 }
 \keyword{USGS}

man/getDVData.Rd

@@ -40,7 +40,7 @@ DailyCFS <- getDVData('01594440','00060', '1985-01-01', '1985-03-31',convert=FAL
 DailySuspSediment <- getDVData('01594440','80154', '1985-01-01', '1985-03-31')
 }
 \seealso{
-\code{\link{retrieveNWISData}}, \code{\link{populateDaily}}
+\code{\link{retrieveNWISdvData}}, \code{\link{populateDaily}}
 }
 \keyword{USGS}
 \keyword{WRTDS}

man/getQWData.Rd

-% Generated by roxygen2 (4.0.1): do not edit by hand
-\name{getQWData}
-\alias{getQWData}
-\title{Data Import for USGS NWIS Water Quality Data}
-\usage{
-getQWData(siteNumber, ParameterCd, StartDate, EndDate, interactive = TRUE)
-}
-\arguments{
-\item{siteNumber}{string USGS site number.  This is usually an 8 digit number}
-
-\item{ParameterCd}{string USGS parameter code.  This is usually an 5 digit number. Multiple parameter codes can be inputted with a ';' separator.  Leaving this blank will return all of the measured values during the specified time period.}
-
-\item{StartDate}{string starting date for data retrieval in the form YYYY-MM-DD.}
-
-\item{EndDate}{string ending date for data retrieval in the form YYYY-MM-DD.}
-
-\item{interactive}{logical Option for interactive mode.  If true, there is user interaction for error handling and data checks.}
-}
-\value{
-retval dataframe with first column dateTime, and at least one qualifier and value columns
-(subsequent qualifier/value columns could follow depending on requested parameter codes)
-}
-\description{
-Imports and processes data from NWIS web service. This function gets the data from here: \url{http://www.waterqualitydata.us}
-A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
-}
-\examples{
-# These examples require an internet connection to run
-rawProcessedSample <- getQWData('01594440','01075', '1985-01-01', '1985-03-31')
-rawProcessedSampleAll <- getQWData('05114000','', '1985-01-01', '1985-03-31')
-rawProcessedSampleSelect <- getQWData('05114000','00915;00931', '1985-01-01', '1985-04-30')
-}
-\keyword{USGS}
-\keyword{data}
-\keyword{import}
-\keyword{service}
-\keyword{web}
-

man/getSTORETSampleData.Rd

@@ -21,11 +21,9 @@ getSTORETSampleData(siteNumber, characteristicName, StartDate, EndDate,
 Sample dataframe
 }
 \description{
-Imports data from NWIS web service. This function gets the data from here: \url{http://qwwebservices.usgs.gov/}
-A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
-For raw data, use getQWData.  This function will retrieve the raw data, and compress it (summing constituents). See
-chapter 7 of the EGRET user guide for more details.
+Imports data from the Water Quality Portal. 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.
 }
 \examples{
 # These examples require an internet connection to run