diff --git a/NAMESPACE b/NAMESPACE
index 74920c94e566ee84bbda77120cd7d706466c407b..880043c422561c2fd21f5388adcc61c5d5192598 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -12,7 +12,6 @@ export(getDVData)
 export(getDailyDataFromFile)
 export(getDataAvailability)
 export(getDataFromFile)
-export(getGeneralWQPData)
 export(getMetaData)
 export(getNWISData)
 export(getNWISSites)
diff --git a/NEWS b/NEWS
index 8308939a2fd7af4ca7829136379e7cb5fe5f4780..bd63ebe58994d4a09ee7e2920e4c8f5b9e18175a 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,12 @@
+dataRetrieval 1.3.3
+===========
+
+* Updated getSiteFileData to retrieve multiple site file datasets at once using a vector of siteNumbers as input argument.
+* Updated error-handling for Web service calls. More information is returned when errors happen
+* Added some basic processing to Water Quality Portal raw data retrievals. Date columns are returned as Date objects, value columns are numeric, and a column is created from the date/time/timezone columns that is POSIXct.
+* Added very generalized NWIS and WQP retrieval functions (getNWISData, getNWISSites, getGeneralWQPData, and getWQPSites) which allow the user to use any argument available on the Web service platform.
+
+
 dataRetrieval 1.3.2
 ===========
 
diff --git a/R/constructNWISURL.r b/R/constructNWISURL.r
index 7b3e72279dbd672e99487e5f3d207c67c9150b95..8e7c99bb6af82b2dc8e0e4fd9fc75f65800f6748 100644
--- a/R/constructNWISURL.r
+++ b/R/constructNWISURL.r
@@ -41,11 +41,14 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
   dateReturn <- checkStartEndDate(startDate, endDate, interactive=interactive)
   startDate <- dateReturn[1]
   endDate <- dateReturn[2]
+  multipleSites <- length(siteNumber) > 1
+  multiplePcodes <- length(parameterCd)>1
+  siteNumber <- paste(siteNumber, collapse=",")
   
   switch(service,
          qw = {
-             if(length(siteNumber) > 1){    
-               siteNumber <- paste(siteNumber, collapse=",")
+             if(multipleSites){    
+               
                siteNumber <- paste("multiple_site_no",siteNumber,sep="=")
                searchCriteria <- "multiple_site_no"
              } else {
@@ -54,7 +57,7 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
                searchCriteria <- "search_site_no"
              }
              
-             if(length(parameterCd)>1){
+             if(multiplePcodes){
                pCodes <- paste(parameterCd, collapse=",")
                pCodes <- paste('multiple_parameter_cds', pCodes, sep="=")
                pCodes <- paste(pCodes, "param_cd_operator=OR",sep="&")
@@ -95,10 +98,11 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
              suppressWarnings(pCodeLogic <- all(!is.na(as.numeric(parameterCd))))
            } else {
              pCodeLogic <- FALSE
+             parameterCd <- gsub(",","%2C",parameterCd)
              parameterCd <- URLencode(parameterCd)
            }
            
-           if(length(parameterCd)>1){
+           if(multiplePcodes){
              parameterCd <- paste(parameterCd, collapse=";")
            }
            
@@ -123,7 +127,7 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
         { # this will be either dv or uv
            
           # Check for 5 digit parameter code:
-          if(length(parameterCd)>1){
+          if(multiplePcodes){
             parameterCd <- paste(parameterCd, collapse=",")
           } else {
             parameterCd <- formatCheckParameterCd(parameterCd, interactive=interactive)
@@ -167,6 +171,6 @@ constructNWISURL <- function(siteNumber,parameterCd,startDate,endDate,service,st
         }
          
     )
-  
+
   return(url)
 }
diff --git a/R/getGeneralWQPData.R b/R/getGeneralWQPData.R
deleted file mode 100644
index 4faf41f2c250cf3e906b59b797fecb8d151b30a2..0000000000000000000000000000000000000000
--- a/R/getGeneralWQPData.R
+++ /dev/null
@@ -1,36 +0,0 @@
-#' General 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}.
-#' because it allows for other agencies rather than the USGS.  
-#'
-#' @param \dots see \url{www.waterqualitydata.us/webservices_documentation.jsp} for a complete list of options
-#' @keywords data import WQP 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
-#' nameToUse <- "pH"
-#' pHData <- getGeneralWQPData(siteid="USGS-04024315",characteristicName=nameToUse)
-getGeneralWQPData <- function(...){
-  
-  matchReturn <- match.call()
-  
-  options <- c("bBox","lat","long","within","countrycode","statecode","countycode","siteType","organization",
-               "siteid","huc","sampleMedia","characteristicType","characteristicName","pCode","activityId",
-               "startDateLo","startDateHi","mimeType","Zip","providers")
-  
-  if(!all(names(matchReturn[-1]) %in% options)) warning(matchReturn[!(names(matchReturn[-1]) %in% options)],"is not a valid query parameter to the Water Quality Portal")
-  
-  values <- sapply(matchReturn[-1], function(x) URLencode(as.character(paste(eval(x),collapse="",sep=""))))
-  
-  urlCall <- paste(paste(names(values),values,sep="="),collapse="&")
-  
-  
-  baseURL <- "http://www.waterqualitydata.us/Result/search?"
-  urlCall <- paste(baseURL,
-                   urlCall,
-                   "&mimeType=tsv",sep = "")
-  retVal <- basicWQPData(urlCall)
-  return(retVal)
-  
-}
\ No newline at end of file
diff --git a/R/getNWISData.r b/R/getNWISData.r
index bd1cf61f1f1e26f2a635b7787f39f64f9959e609..5905e359a5b376e55963afa3445c66d468b2e770 100644
--- a/R/getNWISData.r
+++ b/R/getNWISData.r
@@ -27,6 +27,5 @@ getNWISData <- function(service="dv", ...){
   }
   
   retval <- getRDB1Data(urlCall)
-  
   return(retval)
 }
diff --git a/R/getRDB1Data.r b/R/getRDB1Data.r
index c6e8ce718904895ef6a171db84ca333f23c565e5..ee553aadb0d38dd8bbaecc4c98fc35e9dca54d68 100644
--- a/R/getRDB1Data.r
+++ b/R/getRDB1Data.r
@@ -22,7 +22,6 @@
 #' unitDataURL <- constructNWISURL(siteNumber,property,
 #'          as.character(Sys.Date()),as.character(Sys.Date()),'uv',format='tsv')
 #' unitData <- getRDB1Data(unitDataURL, asDateTime=TRUE)
-#' mulitSites <- getRDB1Data("http://waterservices.usgs.gov/nwis/dv/?format=rdb&stateCd=OH&parameterCd=00010")
 getRDB1Data <- function(obs_url,asDateTime=FALSE){
   
   retval = tryCatch({
@@ -79,10 +78,10 @@ getRDB1Data <- function(obs_url,asDateTime=FALSE){
           
           mostCommonTZ <- names(sort(summary(as.factor(timeZone)),decreasing = TRUE)[1])
 
-          data[,regexpr('d$', dataType) > 0] <- as.POSIXct(data[,regexpr('d$', dataType) > 0], "%Y-%m-%d %H:%M", tz = mostCommonTZ)
+          data[,grep('d$', dataType)] <- as.POSIXct(data[,grep('d$', dataType)], "%Y-%m-%d %H:%M", tz = mostCommonTZ)
           additionalTZs <- names(sort(summary(as.factor(timeZone)),decreasing = TRUE)[-1])
           for(i in additionalTZs){
-            data[timeZone == i,regexpr('d$', dataType) > 0] <-  as.POSIXct(data[,regexpr('d$', dataType) > 0], "%Y-%m-%d %H:%M", tz = i)
+            data[timeZone == i,grep('d$', dataType)] <-  as.POSIXct(data[,grep('d$', dataType)], "%Y-%m-%d %H:%M", tz = i)
           }
         }
         
@@ -90,8 +89,6 @@ getRDB1Data <- function(obs_url,asDateTime=FALSE){
         for (i in grep('d$', dataType)){
           data[,i] <- as.Date(data[,i])
         }
-        
-        
       }
     }
     
diff --git a/R/getRawQWData.r b/R/getRawQWData.r
index a491059d3a909188ab2980205bb766376c2070f3..2a034385f3db9556b75b5fccdd2b6f3df3aa3efd 100644
--- a/R/getRawQWData.r
+++ b/R/getRawQWData.r
@@ -1,6 +1,11 @@
 #' Raw Data Import for Water Quality Portal
 #'
-#' Imports data from the Water Quality Portal. This function gets the data from here: \url{http://www.waterqualitydata.us}
+#' Imports data from the Water Quality Portal. 
+#' This function gets the data from here: \url{http://www.waterqualitydata.us}. There
+#' are four required input arguments: siteNumber, parameterCd, startDate, and endDate.
+#' parameterCd can either be a USGS 5-digit code, or a characteristic name. The sites can be 
+#' either USGS, or other Water Quality Portal offered sites. It is required to use the 'full'
+#' site name, such as 'USGS-01234567'. 
 #'
 #' @param siteNumber string site number. This needs to include the full agency code prefix.
 #' @param parameterCd vector of USGS 5-digit parameter code or string of characteristicNames. 
@@ -13,6 +18,8 @@
 #' start and end times.
 #' @export
 #' @import RCurl
+#' @seealso \code{\link{getWQPData}}, \code{\link{getWQPSites}}, 
+#' \code{\link{getSTORETSampleData}}, \code{\link{retrieveNWISqwData}}, and \code{\link{basicWQPData}}
 #' @examples
 #' # These examples require an internet connection to run
 #' rawSample <- retrieveWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
diff --git a/R/getSTORETSampleData.R b/R/getSTORETSampleData.R
index d100874b740385aa620d6d768ffd3ded185c3411..f1a3fbe37b6b47a10aceb66f30211735c1dac6b9 100644
--- a/R/getSTORETSampleData.R
+++ b/R/getSTORETSampleData.R
@@ -1,6 +1,6 @@
 #' 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)
diff --git a/R/getWQPData.r b/R/getWQPData.r
index 3fb3fdd89d62a037b64be5f8ab9d0cdbf948838f..2a6c567d02982df1e481e719c65333449cb2b2b4 100644
--- a/R/getWQPData.r
+++ b/R/getWQPData.r
@@ -1,45 +1,40 @@
-#' Data Import from Water Quality Portal
+#' General Data Import from Water Quality Portal
 #'
-#' 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 
+#' Imports data from Water Quality Portal web service. This function gets the data from here: \url{http://www.waterqualitydata.us}.
+#' because it allows for other agencies rather than the USGS.  
 #'
-#' @param siteNumber string site number.  If USGS, it should be in the form :'USGS-XXXXXXXXX...'
-#' @param characteristicName string
-#' @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.
+#' @param \dots see \url{www.waterqualitydata.us/webservices_documentation.jsp} for a complete list of options
 #' @keywords data import WQP 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
-#' @import RCurl
 #' @examples
-#' # These examples require an internet connection to run
-#' 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){
-  
-  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
-  }
+#' nameToUse <- "pH"
+#' pHData <- getWQPData(siteid="USGS-04024315",characteristicName=nameToUse)
+getWQPData <- function(...){
+  
+  matchReturn <- match.call()
+  
+  options <- c("bBox","lat","long","within","countrycode","statecode","countycode","siteType","organization",
+               "siteid","huc","sampleMedia","characteristicType","characteristicName","pCode","activityId",
+               "startDateLo","startDateHi","mimeType","Zip","providers")
+  
+  if(!all(names(matchReturn[-1]) %in% options)) warning(matchReturn[!(names(matchReturn[-1]) %in% options)],"is not a valid query parameter to the Water Quality Portal")
+  
+  values <- sapply(matchReturn[-1], function(x) URLencode(as.character(paste(eval(x),collapse="",sep=""))))
   
-  return(data)
+  values <- gsub(",","%2C",values)
+  values <- gsub("%20","+",values)
+  
+  urlCall <- paste(paste(names(values),values,sep="="),collapse="&")
+  
+  
+  baseURL <- "http://www.waterqualitydata.us/Result/search?"
+  urlCall <- paste(baseURL,
+                   urlCall,
+                   "&mimeType=tsv",sep = "")
+
+  retVal <- basicWQPData(urlCall)
+  return(retVal)
   
-}
+}
\ No newline at end of file
diff --git a/R/getWaterML1Data.r b/R/getWaterML1Data.r
index 5c7acac75634f695214be2b46771f446668ae2ae..4651109611b562ff6734483b55c89747c634f75e 100644
--- a/R/getWaterML1Data.r
+++ b/R/getWaterML1Data.r
@@ -52,11 +52,15 @@ getWaterML1Data <- function(obs_url){
   timeSeries <- xpathApply(doc, "//ns1:timeSeries", namespaces = ns)
   
   for (i in 1:length(timeSeries)){
-
+    
+    
     chunk <- xmlDoc(timeSeries[[i]])
     chunk <- xmlRoot(chunk)
     chunkNS <- xmlNamespaceDefinitions(chunk, simplify = TRUE)  
       
+#     site <- as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:siteProperty[@name='hucCd']", namespaces = chunkNS, xmlValue))
+    site <- as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:siteCode", namespaces = chunkNS, xmlValue))
+    agency <- as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:siteCode/@agencyCode", namespaces = chunkNS))
     pCode <-as.character(xpathApply(chunk, "ns1:variable/ns1:variableCode", namespaces = chunkNS, xmlValue))
     statCd <- as.character(xpathApply(chunk, "ns1:variable/ns1:options/ns1:option/@optionCode", namespaces = chunkNS))
 
@@ -76,14 +80,14 @@ getWaterML1Data <- function(obs_url){
       methodID <- padVariable(methodID,2)
       
       value <- as.numeric(xpathSApply(subChunk, "ns1:value",namespaces = chunkNS, xmlValue))  
-      dateTime <- as.POSIXct(strptime(xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS),"%Y-%m-%dT%H:%M:%S"))
+      datetime <- as.POSIXct(strptime(xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS),"%Y-%m-%dT%H:%M:%S"))
       tzHours <- substr(xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS),
                         24,
                         nchar(xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS)))
       if(mean(nchar(tzHours),rm.na=TRUE) == 6){
         tzAbbriev <- zoneAbbrievs[tzHours]
       } else {
-        tzAbbriev <- rep(as.character(zoneAbbrievs[1]),length(dateTime))
+        tzAbbriev <- rep(as.character(zoneAbbrievs[1]),length(datetime))
       }
       
       timeZoneLibrary <- setNames(c("America/New_York","America/New_York","America/Chicago","America/Chicago",
@@ -92,11 +96,11 @@ getWaterML1Data <- function(obs_url){
                                   c("EST","EDT","CST","CDT","MST","MDT","PST","PDT","AKST","AKDT","HAST","HST"))
       timeZone <- as.character(timeZoneLibrary[tzAbbriev])
       if(length(unique(timeZone)) == 1){
-       dateTime <- as.POSIXct(as.character(dateTime), tz = unique(timeZone))
+       datetime <- as.POSIXct(as.character(datetime), tz = unique(timeZone))
       } else {
         warning("Mixed time zone information")
-        for(i in seq_along(dateTime)){
-          dateTime[i] <- as.POSIXct(as.character(dateTime[i]), tz = timeZone[i])
+        for(i in seq_along(datetime)){
+          datetime[i] <- as.POSIXct(as.character(datetime[i]), tz = timeZone[i])
         }
       }
       
@@ -111,38 +115,34 @@ getWaterML1Data <- function(obs_url){
       assign(qualName,qualifier)
       
       if(length(get(qualName))!=0){
-        df <- data.frame(dateTime,
+        df <- data.frame(rep(agency,length(datetime)),
+                         rep(site,length(datetime)),
+                         datetime,
                          tzAbbriev,
                          get(valueName),
                          get(qualName),
                          stringsAsFactors=FALSE)
         
-        names(df) <- c("datetime","tz_cd",valueName,qualName)
+        names(df) <- c("agency_cd","site_no","datetime","tz_cd",valueName,qualName)
       } else {
-        df <- data.frame(dateTime,
+        df <- data.frame(rep(agency,length(datetime)),
+                         rep(site,length(datetime)),
+                         datetime,
                          tzAbbriev,
                          get(valueName),stringsAsFactors=FALSE)
         
-        names(df) <- c("datetime","tz_cd",valueName)       
+        names(df) <- c("agency_cd","site_no","datetime","tz_cd",valueName)       
       }
  
       if (1 == i & valuesIndex[1] == j){
         mergedDF <- df
       } else {
-        mergedDF <- merge(mergedDF, df,by=c("datetime","tz_cd"),all=TRUE)
+        similarNames <- intersect(names(mergedDF), names(df))
+        mergedDF <- merge(mergedDF, df,by=similarNames,all=TRUE)
+#         mergedDF <- merge(mergedDF, df,by=c("agency_cd","site_no","datetime","tz_cd"),all=TRUE)
       }
     }
   }
-
-  agencyCd <- as.character(xpathSApply(timeSeries[[1]], "ns1:sourceInfo/ns1:siteCode/@agencyCode",namespaces = chunkNS))
-  siteNo <- as.character(xpathSApply(timeSeries[[1]], "ns1:sourceInfo/ns1:siteCode",namespaces = chunkNS, xmlValue))
-  
-  mergedDF$agency_cd <- rep(agencyCd, nrow(mergedDF))
-  mergedDF$site_no <- rep(siteNo, nrow(mergedDF))
-  
-  reorder <- c(ncol(mergedDF)-1, ncol(mergedDF), 1:(ncol(mergedDF)-2))
-  
-  mergedDF <- mergedDF[,reorder]
   
   return (mergedDF)
 }
diff --git a/R/retrieveNWISData.r b/R/retrieveNWISData.r
index 1053808dfa521fc07224d1fcdef6d0776e34d685..fa90606f5e8fdfbe312ecf88cb26fa971c4988bf 100644
--- a/R/retrieveNWISData.r
+++ b/R/retrieveNWISData.r
@@ -4,7 +4,7 @@
 #' A list of parameter codes can be found here: \url{http://help.waterdata.usgs.gov/codes-and-parameters/parameters}
 #' A list of statistic codes can be found here: \url{http://help.waterdata.usgs.gov/code/stat_code_query?fmt=html}
 #'
-#' @param siteNumber string USGS site number.  This is usually an 8 digit number
+#' @param siteNumber string USGS site number.  This is usually an 8 digit number. Multiple sites can be requested with a string vector.
 #' @param parameterCd string or vector of USGS parameter code.  This is usually an 5 digit number..
 #' @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.
@@ -29,13 +29,15 @@
 #'        startDate, endDate, statCd='00001',format='tsv')
 #' rawDailyQAndTempMeanMax <- retrieveNWISdvData(siteNumber,c('00010','00060'),
 #'        startDate, endDate, statCd=c('00001','00003'))
+#' rawDailyMultiSites<- retrieveNWISdvData(c("01491000","01645000"),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)
   
   if (format == "xml") {
     data <- getWaterML1Data(url)
-    data$dateTime <- as.Date(data$dateTime)
+    data$datetime <- as.Date(data$datetime)
   } else {
     data <- getRDB1Data(url,asDateTime=FALSE)
   }
diff --git a/R/retrieveNWISqwData.r b/R/retrieveNWISqwData.r
index 4ce5ff5340152f7065febd14fae7975b812f457f..614e4849b6175dd77b6d78f8b93807c9470b3b90 100644
--- a/R/retrieveNWISqwData.r
+++ b/R/retrieveNWISqwData.r
@@ -4,7 +4,7 @@
 #' 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 or vector of strings USGS site number.  This is usually an 8 digit number
+#' @param siteNumber string or vector of of USGS site numbers.  This is usually an 8 digit number
 #' @param pCodes string or vector of USGS parameter code.  This is usually an 5 digit number.
 #' @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.
@@ -16,6 +16,8 @@
 #' @return data dataframe with agency, site, dateTime, value, and code columns
 #' @export
 #' @import reshape2
+#' @seealso \code{\link{getWQPData}}, \code{\link{getWQPSites}}, 
+#' \code{\link{retrieveWQPqwData}}, \code{\link{constructNWISURL}}
 #' @examples
 #' # These examples require an internet connection to run
 #' siteNumber <- c('04024430','04024000')
diff --git a/inst/doc/dataRetrieval.pdf b/inst/doc/dataRetrieval.pdf
index f62020ecfa6e09995d9db1351c3b6d48346e33b7..3c9343bb0e734cc31aa0513446f0cc9b147fe02f 100644
Binary files a/inst/doc/dataRetrieval.pdf and b/inst/doc/dataRetrieval.pdf differ
diff --git a/man/getGeneralWQPData.Rd b/man/getGeneralWQPData.Rd
deleted file mode 100644
index 2823493d861fc09b5dc67c66c32da15a20e87e24..0000000000000000000000000000000000000000
--- a/man/getGeneralWQPData.Rd
+++ /dev/null
@@ -1,28 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getGeneralWQPData}
-\alias{getGeneralWQPData}
-\title{General Data Import from Water Quality Portal}
-\usage{
-getGeneralWQPData(...)
-}
-\arguments{
-\item{\dots}{see \url{www.waterqualitydata.us/webservices_documentation.jsp} for a complete list of options}
-}
-\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 data from Water Quality Portal web service. This function gets the data from here: \url{http://www.waterqualitydata.us}.
-because it allows for other agencies rather than the USGS.
-}
-\examples{
-nameToUse <- "pH"
-pHData <- getGeneralWQPData(siteid="USGS-04024315",characteristicName=nameToUse)
-}
-\keyword{WQP}
-\keyword{data}
-\keyword{import}
-\keyword{service}
-\keyword{web}
-
diff --git a/man/getRDB1Data.Rd b/man/getRDB1Data.Rd
index 2a48835f8631b5dd4da2d2fd1231ec737925920d..f7249a09719cb5ec94e4f3a2366c690a966d15ea 100644
--- a/man/getRDB1Data.Rd
+++ b/man/getRDB1Data.Rd
@@ -32,6 +32,5 @@ multiData <- getRDB1Data(urlMulti)
 unitDataURL <- constructNWISURL(siteNumber,property,
          as.character(Sys.Date()),as.character(Sys.Date()),'uv',format='tsv')
 unitData <- getRDB1Data(unitDataURL, asDateTime=TRUE)
-mulitSites <- getRDB1Data("http://waterservices.usgs.gov/nwis/dv/?format=rdb&stateCd=OH&parameterCd=00010")
 }
 
diff --git a/man/getSTORETSampleData.Rd b/man/getSTORETSampleData.Rd
index 2323de842ae188bc362f9aa744820b678ac2e40c..ef391a0d3c971d7ffe27177ea698031020619cee 100644
--- a/man/getSTORETSampleData.Rd
+++ b/man/getSTORETSampleData.Rd
@@ -21,7 +21,7 @@ getSTORETSampleData(siteNumber, characteristicName, startDate, endDate,
 Sample dataframe
 }
 \description{
-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.
 }
@@ -31,6 +31,8 @@ Sample_01075 <- getSTORETSampleData('USGS-01594440','Chloride', '', '')
 Sample_All <- getSTORETSampleData('WIDNR_WQX-10032762','Specific conductance', '', '')
 }
 \seealso{
+\code{\link{getWQPData}}, \code{\link{getWQPSites}},
+\code{\link{retrieveWQPqwData}}, \code{\link{retrieveNWISqwData}}, and \code{\link{basicWQPData}},
 \code{\link{compressData}}, \code{\link{populateSampleColumns}}
 }
 \keyword{USGS}
diff --git a/man/getWQPData.Rd b/man/getWQPData.Rd
index e760d1ea4a9efde4491cf958f43c3467926226dc..c46578d06675cbb8442038e65d4048ec39c38f89 100644
--- a/man/getWQPData.Rd
+++ b/man/getWQPData.Rd
@@ -1,37 +1,24 @@
 % Generated by roxygen2 (4.0.2): do not edit by hand
 \name{getWQPData}
 \alias{getWQPData}
-\title{Data Import from Water Quality Portal}
+\title{General Data Import from Water Quality Portal}
 \usage{
-getWQPData(siteNumber, characteristicName, startDate, endDate,
-  interactive = TRUE)
+getWQPData(...)
 }
 \arguments{
-\item{siteNumber}{string site number.  If USGS, it should be in the form :'USGS-XXXXXXXXX...'}
-
-\item{characteristicName}{string}
-
-\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.}
+\item{\dots}{see \url{www.waterqualitydata.us/webservices_documentation.jsp} for a complete list of options}
 }
 \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 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
+Imports data from Water Quality Portal web service. This function gets the data from here: \url{http://www.waterqualitydata.us}.
+because it allows for other agencies rather than the USGS.
 }
 \examples{
-# These examples require an internet connection to run
-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'), '', '')
+nameToUse <- "pH"
+pHData <- getWQPData(siteid="USGS-04024315",characteristicName=nameToUse)
 }
 \keyword{WQP}
 \keyword{data}
diff --git a/man/retrieveNWISdvData.Rd b/man/retrieveNWISdvData.Rd
index 72badd54d2dcf4a56a9db5a2b73babb5f8e8c1e7..e7e0cc8d300622bb989df04e11f467d8b9727f22 100644
--- a/man/retrieveNWISdvData.Rd
+++ b/man/retrieveNWISdvData.Rd
@@ -7,7 +7,7 @@ retrieveNWISdvData(siteNumber, parameterCd, startDate, endDate,
   statCd = "00003", format = "tsv", interactive = TRUE)
 }
 \arguments{
-\item{siteNumber}{string USGS site number.  This is usually an 8 digit number}
+\item{siteNumber}{string USGS site number.  This is usually an 8 digit number. Multiple sites can be requested with a string vector.}
 
 \item{parameterCd}{string or vector of USGS parameter code.  This is usually an 5 digit number..}
 
@@ -44,6 +44,8 @@ rawDailyTemperatureTSV <- retrieveNWISdvData(siteNumber,'00010',
        startDate, endDate, statCd='00001',format='tsv')
 rawDailyQAndTempMeanMax <- retrieveNWISdvData(siteNumber,c('00010','00060'),
        startDate, endDate, statCd=c('00001','00003'))
+rawDailyMultiSites<- retrieveNWISdvData(c("01491000","01645000"),c('00010','00060'),
+       startDate, endDate, statCd=c('00001','00003'))
 }
 \keyword{USGS}
 \keyword{data}
diff --git a/man/retrieveNWISqwData.Rd b/man/retrieveNWISqwData.Rd
index 92b071a3b380954fa96bd885e55b443f388ba306..57b1784b72ce28a5781eeb7f46875d3226bbe88c 100644
--- a/man/retrieveNWISqwData.Rd
+++ b/man/retrieveNWISqwData.Rd
@@ -7,7 +7,7 @@ retrieveNWISqwData(siteNumber, pCodes, startDate, endDate, expanded = FALSE,
   interactive = TRUE)
 }
 \arguments{
-\item{siteNumber}{string or vector of strings USGS site number.  This is usually an 8 digit number}
+\item{siteNumber}{string or vector of of USGS site numbers.  This is usually an 8 digit number}
 
 \item{pCodes}{string or vector of USGS parameter code.  This is usually an 5 digit number.}
 
@@ -43,6 +43,10 @@ data$dateTime <- as.Date(data$dateTime)
 compressedData <- compressData(data)
 Sample <- populateSampleColumns(compressedData)
 }
+\seealso{
+\code{\link{getWQPData}}, \code{\link{getWQPSites}},
+\code{\link{retrieveWQPqwData}}, \code{\link{constructNWISURL}}
+}
 \keyword{USGS}
 \keyword{data}
 \keyword{import}
diff --git a/man/retrieveWQPqwData.Rd b/man/retrieveWQPqwData.Rd
index e79341e04b5daae51c77f0178278bec9fcf3ed9b..bf73f137496bd793ffb41d6cbe9255dff3083d63 100644
--- a/man/retrieveWQPqwData.Rd
+++ b/man/retrieveWQPqwData.Rd
@@ -23,7 +23,12 @@ retval dataframe raw data returned from the Water Quality Portal. Additionally,
 start and end times.
 }
 \description{
-Imports data from the Water Quality Portal. This function gets the data from here: \url{http://www.waterqualitydata.us}
+Imports data from the Water Quality Portal.
+This function gets the data from here: \url{http://www.waterqualitydata.us}. There
+are four required input arguments: siteNumber, parameterCd, startDate, and endDate.
+parameterCd can either be a USGS 5-digit code, or a characteristic name. The sites can be
+either USGS, or other Water Quality Portal offered sites. It is required to use the 'full'
+site name, such as 'USGS-01234567'.
 }
 \examples{
 # These examples require an internet connection to run
@@ -32,6 +37,10 @@ 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', '', '')
 }
+\seealso{
+\code{\link{getWQPData}}, \code{\link{getWQPSites}},
+\code{\link{getSTORETSampleData}}, \code{\link{retrieveNWISqwData}}, and \code{\link{basicWQPData}}
+}
 \keyword{USGS}
 \keyword{data}
 \keyword{import}
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index c30df2de1f939d12dfcc4addeed47cb367388f51..181c612dc70ef26bf5b9524e1b8f541b20fe6410 100644
--- a/vignettes/dataRetrieval-concordance.tex
+++ b/vignettes/dataRetrieval-concordance.tex
@@ -1,9 +1,9 @@
 \Sconcordance{concordance:dataRetrieval.tex:dataRetrieval.Rnw:%
-1 127 1 49 0 1 7 15 1 1 14 55 1 3 0 36 1 2 0 11 1 24 %
-0 24 1 3 0 23 1 3 0 6 1 7 0 18 1 3 0 25 1 1 0 17 1 9 %
-0 6 1 7 0 21 1 8 0 16 1 2 0 11 1 23 0 21 1 9 0 20 1 3 %
-0 6 1 17 0 27 1 6 0 11 1 9 0 15 1 12 0 19 1 4 0 21 1 %
-4 0 17 1 7 0 22 1 8 0 19 1 4 0 9 1 4 0 78 1 1 2 9 1 1 %
-4 4 1 20 0 44 1 4 0 30 1 4 0 22 1 4 0 21 1 37 0 13 1 %
-9 0 94 1 4 0 9 1 13 0 13 1 4 0 14 1 4 0 5 1 4 0 23 1 %
-18 0 8 1 4 0 55 1}
+1 127 1 49 0 1 7 15 1 1 14 55 1 3 0 36 1 2 0 8 1 9 0 %
+24 1 3 0 21 1 4 0 6 1 8 0 18 1 3 0 26 1 1 4 17 1 9 0 %
+6 1 7 0 22 1 8 0 16 1 2 0 11 1 23 0 22 1 9 0 20 1 3 0 %
+6 1 17 0 28 1 12 0 10 1 9 0 16 1 4 0 18 1 4 0 31 1 17 %
+0 39 1 14 0 18 1 2 0 14 1 2 0 23 1 4 0 17 1 7 0 22 1 %
+8 0 19 1 4 0 9 1 4 0 78 1 1 2 9 1 1 4 4 1 20 0 44 1 4 %
+0 30 1 4 0 22 1 4 0 21 1 37 0 13 1 9 0 94 1 4 0 9 1 %
+13 0 13 1 4 0 14 1 4 0 5 1 4 0 23 1 18 0 8 1 4 0 60 1}
diff --git a/vignettes/dataRetrieval.Rnw b/vignettes/dataRetrieval.Rnw
index e20955c89472a3539281a31606b2bb380775d505..0e36a3c5ee228ea23ad194192b159a9f2be35f0c 100644
--- a/vignettes/dataRetrieval.Rnw
+++ b/vignettes/dataRetrieval.Rnw
@@ -76,14 +76,14 @@
 \titlecontents{table}
 [0em]                 % adjust left margin
 {\sffamily}             % font formatting
-{\textbf{Table}\hspace*{2em} \contentslabel {2em}} % section label and offset
+{Table\hspace*{2em} \contentslabel {2em}} % section label and offset
 {\hspace*{4em}}
 {\titlerule*[0.25pc]{.}\contentspage}
 
 \titlecontents{figure}
 [0em]                 % adjust left margin
 {\sffamily}             % font formatting
-{\textbf{Figure}\hspace*{2em} \contentslabel {2em}} % section label and offset
+{Figure\hspace*{2em} \contentslabel {2em}} % section label and offset
 {\hspace*{4em}}
 {\titlerule*[0.25pc]{.}\contentspage}
 
@@ -184,7 +184,7 @@ addSpace <- function(x) ifelse(x != "1", "[5pt]","")
 The dataRetrieval package was created to simplify the process of loading hydrologic data into the R environment. It has been specifically designed to work seamlessly with the EGRET R package: Exploration and Graphics for RivEr Trends. See: \url{https://github.com/USGS-R/EGRET/wiki} for information on EGRET. EGRET is designed to provide analysis of water quality data sets using the Weighted Regressions on Time, Discharge and Season (WRTDS) method as well as analysis of discharge trends using robust time-series smoothing techniques.  Both of these capabilities provide both tabular and graphical analyses of long-term data sets.
 
 
-The dataRetrieval package is designed to retrieve many of the major data types of United States Geological Survey (USGS) hydrologic data that are available on the Web. Users may also load data from other sources (text files, spreadsheets) using dataRetrieval.  Section \ref{sec:genRetrievals} provides examples of how one can obtain raw data from USGS sources on the Web and load them into dataframes within the R environment.  The functionality described in section \ref{sec:genRetrievals} is for general use and is not tailored for the specific uses of the EGRET package.  The functionality described in section \ref{sec:EGRETdfs} is tailored specifically to obtaining input from the Web and structuring it for use in the EGRET package.  The functionality described in section \ref{sec:summary} is for converting hydrologic data from user-supplied files and structuring it specifically for use in the EGRET package.
+The dataRetrieval package is designed to retrieve many of the major data types of U.S. Geological Survey (USGS) hydrologic data that are available on the Web. Users may also load data from other sources (text files, spreadsheets) using dataRetrieval.  Section \ref{sec:genRetrievals} provides examples of how one can obtain raw data from USGS sources on the Web and load them into dataframes within the R environment.  The functionality described in section \ref{sec:genRetrievals} is for general use and is not tailored for the specific uses of the EGRET package.  The functionality described in section \ref{sec:EGRETdfs} is tailored specifically to obtaining input from the Web and structuring it for use in the EGRET package.  The functionality described in section \ref{sec:summary} is for converting hydrologic data from user-supplied files and structuring it specifically for use in the EGRET package.
 
 For information on getting started in R and installing the package, see (\ref{sec:appendix1}): Getting Started. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
 
@@ -222,14 +222,14 @@ Sample <- mergeReport()
 \section{General USGS Web Retrievals}
 \label{sec:genRetrievals}
 %------------------------------------------------------------ 
-In this section, five examples of Web retrievals document how to get raw data. This data includes site information (\ref{sec:usgsSite}), measured parameter information (\ref{sec:usgsParams}), historical daily values(\ref{sec:usgsDaily}), unit values (which include real-time data but can also include other sensor data stored at regular time intervals) (\ref{sec:usgsRT}), and water quality data (\ref{sec:usgsWQP}) or (\ref{sec:usgsSTORET}). We will use the Choptank River near Greensboro, MD as an example.  The site-ID for this streamgage is 01491000. Daily discharge measurements are available as far back as 1948.  Additionally, nitrate has been measured since 1964. 
+In this section, five examples of Web retrievals document how to get raw data. This data includes site information (\ref{sec:usgsSite}), measured parameter information (\ref{sec:usgsParams}), historical daily values(\ref{sec:usgsDaily}), unit values (which include real-time data but can also include other sensor data stored at regular time intervals) (\ref{sec:usgsRT}), and water quality data (\ref{sec:usgsWQP}) or (\ref{sec:usgsSTORET}). We will use the Choptank River near Greensboro, MD as an example.  The siteNumber for this streamgage is 01491000. Daily discharge measurements are available as far back as 1948.  Additionally, nitrate has been measured since 1964. 
 
 % %------------------------------------------------------------
 % \subsection{Introduction}
 % %------------------------------------------------------------
-The USGS organizes hydrologic data in a standard structure.  Streamgages are located throughout the United States, and each streamgage has a unique ID.  Often (but not always), these ID's are 8 digits.  The first step to finding data is discovering this 8-digit ID. There are many ways to do this, one is the National Water Information System: Mapper \url{http://maps.waterdata.usgs.gov/mapper/index.html}.
+The USGS organizes hydrologic data in a standard structure.  Streamgages are located throughout the United States, and each streamgage has a unique ID (referred in this document and throughout the dataRetrieval package as \enquote{siteNumber}).  Often (but not always), these ID's are 8 digits.  The first step to finding data is discovering this siteNumber. There are many ways to do this, one is the National Water Information System: Mapper \url{http://maps.waterdata.usgs.gov/mapper/index.html}.
 
-Once the site-ID (siteNumber) is known, the next required input for USGS data retrievals is the \enquote{parameter code}.  This is a 5-digit code that specifies the measured parameter being requested.  For example, parameter code 00631 represents \enquote{Nitrate plus nitrite, water, filtered, milligrams per liter as nitrogen}, with units of \enquote{mg/l as N}. A complete list of possible USGS parameter codes can be found at \url{http://nwis.waterdata.usgs.gov/usa/nwis/pmcodes?help}.
+Once the siteNumber is known, the next required input for USGS data retrievals is the \enquote{parameter code}.  This is a 5-digit code that specifies the measured parameter being requested.  For example, parameter code 00631 represents \enquote{Nitrate plus nitrite, water, filtered, milligrams per liter as nitrogen}, with units of \enquote{mg/l as N}. A complete list of possible USGS parameter codes can be found at \url{http://nwis.waterdata.usgs.gov/usa/nwis/pmcodes?help}.
 
 Not every station will measure all parameters. A short list of commonly measured parameters is shown in Table \ref{tab:params}.
 
@@ -259,9 +259,6 @@ A complete list (as of September 25, 2013) is available as data attached to the
 library(dataRetrieval)
 parameterCdFile <-  parameterCdFile
 names(parameterCdFile)
-
-# Sorting out some common values:
-subset(parameterCdFile,parameter_cd %in% c("00060","00010","00400"))
 @
 
 
@@ -301,20 +298,18 @@ Examples for using these siteNumber's, parameter codes, and stat codes will be p
 \subsubsection{getSiteFileData}
 \label{sec:usgsSiteFileData}
 %------------------------------------------------------------
-Use the \texttt{getSiteFileData} function to obtain all of the information available for a particular USGS site such as full station name, drainage area, latitude, and longitude:
+Use the \texttt{getSiteFileData} function to obtain all of the information available for a particular USGS site such as full station name, drainage area, latitude, and longitude. \texttt{getSiteFileData} can also access information about multiple sites with a vector input.
 
 
 <<getSite, echo=TRUE>>=
-
-# Choptank River near Greensboro, MD
-siteNumber <- "01491000" 
-ChoptankInfo <- getSiteFileData(siteNumber)
+siteNumbers <- c("01491000","01645000") 
+siteINFO <- getSiteFileData(siteNumbers)
 @
 
 A specific example piece of information can be retrieved, in this case a station name, as follows:
 
 <<siteNames2, echo=TRUE>>=
-ChoptankInfo$station.nm
+siteINFO$station.nm
 @
 Site information is obtained from \url{http://waterservices.usgs.gov/rest/Site-Test-Tool.html}
 \FloatBarrier
@@ -330,23 +325,28 @@ To discover what data is available for a particular USGS site, including measure
 # Continuing from the previous example:
 # This pulls out just the daily data:
 
-ChoptankDailyData <- getDataAvailability(siteNumber,
+dailyDataAvailable <- getDataAvailability(siteNumbers,
                     type="dv")
 
 @
 
 
 <<tablegda, echo=FALSE,results='asis'>>=
-tableData <- with(ChoptankDailyData, 
-      data.frame( srsname=srsname, 
+tableData <- with(dailyDataAvailable, 
+      data.frame( 
+      siteNumber= site_no,
+      srsname=srsname, 
       startDate=as.character(startDate), 
       endDate=as.character(endDate), 
       count=as.character(count),
       units=parameter_units,
+      statCd = statCd,
       stringsAsFactors=FALSE)
       )
 
 tableData$units[which(tableData$units == "ft3/s")] <- "ft$^3$/s"
+tableData$units[which(tableData$units == "uS/cm @25C")] <- "$\\mu$S/cm @25C"
+
 
 print(xtable(tableData,label="tab:gda",
     caption="Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]"),
@@ -368,7 +368,7 @@ See Section \ref{app:createWordTable} for instructions on converting an R datafr
 \subsection{Parameter Information}
 \label{sec:usgsParams}
 %------------------------------------------------------------
-To obtain all of the available information concerning a measured parameter, use the \texttt{getParameterInfo} function:
+To obtain all of the available information concerning a measured parameter (or multiple parameters), use the \texttt{getParameterInfo} function:
 
 <<label=getPCodeInfo, echo=TRUE>>=
 # Using defaults:
@@ -395,7 +395,8 @@ The dates (start and end) must be in the format \texttt{"}YYYY-MM-DD\texttt{"} (
 <<label=getNWISDaily, echo=TRUE, eval=TRUE>>=
 
 # Continuing with our Choptank River example
-parameterCd <- "00060"  # Discharge (ft3/s)
+siteNumber <- "01491000"
+parameterCd <- "00060"  # Discharge
 startDate <- ""  # Will request earliest date
 endDate <- "" # Will request latest date
 
@@ -446,8 +447,9 @@ with(temperatureAndFlow, plot(
   col="red",type="l",xaxt="n",yaxt="n",xlab="",ylab="",axes=FALSE
   ))
 axis(4,col="red",col.axis="red")
-mtext("Mean Discharge [ft3/s]",side=4,line=3,col="red")
-title(paste(ChoptankInfo$station.nm,"2012",sep=" "))
+mtext(expression(paste("Mean Discharge [ft"^"3","/s]",
+                       sep="")),side=4,line=3,col="red")
+title(paste(siteINFO$station.nm[1],"2012",sep=" "))
 legend("topleft", c("Max Temperature", "Mean Discharge"), 
        col=c("black","red"),lty=c(NA,1),pch=c(1,NA))
 @
@@ -465,7 +467,7 @@ Any data collected at regular time intervals (such as 15-minute or hourly) are k
 
 <<label=getNWISUnit, echo=TRUE>>=
 
-parameterCd <- "00060"  # Discharge (ft3/s)
+parameterCd <- "00060"  # Discharge
 startDate <- "2012-05-12" 
 endDate <- "2012-05-13" 
 dischargeToday <- retrieveNWISunitData(siteNumber, parameterCd, 
@@ -489,7 +491,7 @@ Note that time now becomes important, so the variable datetime is a POSIXct, and
 \subsection{Water Quality Values}
 \label{sec:usgsWQP}
 %------------------------------------------------------------
-To get USGS water quality data from water samples collected at the streamgage or other monitoring site (as distinct from unit values collected through some type of automatic monitor) we can use the function \texttt{retrieveNWISqwData}, with the input arguments: siteNumber, parameterCd, startDate, endDate, and interactive (similar to \texttt{retrieveNWISunitData} and \texttt{retrieveNWISdvData}).
+To get USGS water quality data from water samples collected at the streamgage or other monitoring site (as distinct from unit values collected through some type of automatic monitor) we can use the function \texttt{retrieveNWISqwData}, with the input arguments: siteNumber, parameterCd, startDate, endDate, and interactive (similar to \texttt{retrieveNWISunitData} and \texttt{retrieveNWISdvData}). Additionally, the argument \texttt{"}expanded\texttt{"} is a logical input that allows the user to choose between a simple return of datetimes/qualifier/values (expanded=FALSE), or a more complete and verbose output (expanded=TRUE). Expaned = TRUE includes such columns as remark codes, value qualifying text, and detection level.
 
 
 <<label=getQW, echo=TRUE>>=
@@ -500,38 +502,38 @@ startDate <- "1985-10-01"
 endDate <- "2012-09-30"
 
 dissolvedNitrate <- retrieveNWISqwData(siteNumber, parameterCd, 
-      startDate, endDate)
+      startDate, endDate, expanded=TRUE)
 names(dissolvedNitrate)
 
+
 @
 
-% Note that in this \enquote{simple} dataframe, datetime is imported as Dates (no times are included), and the qualifier is either blank or \verb@"<"@ signifying a censored value. A plotting example is shown in Figure \ref{fig:getQWtemperaturePlot}.
 
-<<getQWtemperaturePlot, echo=TRUE, fig.cap="Nitrate plot of Choptank River.">>=
+<<getQWtemperaturePlot, echo=TRUE, fig.cap=paste(parameterINFO$parameter_nm, "at", siteINFO$station.nm[1])>>=
 with(dissolvedNitrate, plot(
-  dateTime, value_00618,
+  dateTime, result_va_00618,
   xlab="Date",ylab = paste(parameterINFO$srsname,
       "[",parameterINFO$parameter_units,"]")
   ))
-title(ChoptankInfo$station.nm)
+title(siteINFO$station.nm[1])
 @
 
 \FloatBarrier
 
+
+
 %------------------------------------------------------------
 \subsection{STORET Water Quality Retrievals}
 \label{sec:usgsSTORET}
 %------------------------------------------------------------
-There are additional water quality data sets available from the Water Quality Data Portal (\url{http://www.waterqualitydata.us/}).  These data sets can be housed in either the STORET (data from EPA) or NWIS database.  Because STORET does not use USGS parameter codes, a \texttt{"}characteristic name\texttt{"} must be supplied.  The \texttt{getWQPData} function can retrieve either STORET or NWIS, but requires a characteristic name rather than parameter code. The Water Quality Data Portal includes data discovery tools and information on characteristic names. The following example retrieves specific conductance from a DNR site in Wisconsin. 
+There are additional water quality data sets available from the Water Quality Data Portal (\url{http://www.waterqualitydata.us/}).  These data sets can be housed in either the STORET (data from EPA), NWIS database (data from USGS), and additional databases are slated to be included.  Because only USGS uses parameter codes, a \texttt{"}characteristic name\texttt{"} must be supplied.  The \texttt{retrieveWQPqwData} function can take either a USGS parameter code, or a more general cahracteristic name in the parameterCd input argument. The Water Quality Data Portal includes data discovery tools and information on characteristic names. The following example retrieves specific conductance from a DNR site in Wisconsin. 
 
 
-<<label=getQWData, echo=TRUE>>=
-specificCond <- getWQPData('WIDNR_WQX-10032762',
+<<label=getQWData, echo=TRUE, eval=FALSE>>=
+specificCond <- retrieveWQPqwData('WIDNR_WQX-10032762',
                 'Specific conductance','2011-05-01','2011-09-30')
-head(specificCond)
 @
 
-\FloatBarrier
 %------------------------------------------------------------
 \subsection{URL Construction}
 \label{sec:usgsURL}
@@ -550,6 +552,110 @@ url_dv <- constructNWISURL(siteNumber,"00060",startDate,endDate,
 url_uv <- constructNWISURL(siteNumber,"00060",startDate,endDate,'uv')
 @
 
+\FloatBarrier
+
+%------------------------------------------------------------
+\subsection{Generalized Retrievals}
+\label{sec:general}
+%------------------------------------------------------------
+The previous examples all took specific input arguments: siteNumber, parameterCd (or characteristic name), startDate, endDate, etc. However, the Web services that supply the data can accept a wide variety of additional arguments. 
+
+%------------------------------------------------------------
+\subsubsection{Generalized NWIS site retrievals}
+\label{sec:NWISGenSite}
+%------------------------------------------------------------
+The function \texttt{getNWISSites} can be used to discover NWIS sites based on any query that the NWIS Site Service offers. This is done by using the \texttt{"..."} argument, which allows the user to use any arbitrary input argument. We can then use the service here:
+
+\url{http://waterservices.usgs.gov/rest/Site-Test-Tool.html}
+
+to discover many options for searching for NWIS sites. For example, you may want to search for sites in a lat/lon bounding box, or only sites tidal streams, or sites with water quality samples, sites above a certain altitude, etc. The results of this site query generate a URL. For example, the tool provided a search within a specified bounding box, for sites that have daily discharge (parameter code = 00060) and temperature (parameter code = 00010). The generated URL is:
+
+\url{http://waterservices.usgs.gov/nwis/site/?format=rdb&bBox=-83.0,36.5,-81.0,38.5&parameterCd=00010,00060&hasDataTypeCd=dv}
+
+The following dataRetrieval code can be used to get those sites:
+
+<<siteSearch>>=
+sites <- getNWISSites(bBox="-83.0,36.5,-81.0,38.5", 
+                      parameterCd="00010,00060",
+                      hasDataTypeCd="dv")
+
+names(sites)
+nrow(sites)
+@
+
+
+%------------------------------------------------------------
+\subsubsection{Generalized NWIS data retrievals}
+\label{sec:NWISGenData}
+%------------------------------------------------------------
+For NWIS data, the function \texttt{getNWISData} can be used. The argument listed in the R help file is \texttt{"..."} and \texttt{"}service\texttt{"} (only for data requests). Table \ref{tab:NWISGeneral} describes the services are available.
+
+\begin{table}[!ht]
+\begin{minipage}{\linewidth}
+{\footnotesize
+\caption{NWIS general data calls} 
+\label{tab:NWISGeneral}
+\begin{tabular}{lll}
+  \hline
+\multicolumn{1}{c}{\textbf{\textsf{Service}}} &
+\multicolumn{1}{c}{\textbf{\textsf{Description}}}  &
+\multicolumn{1}{c}{\textbf{\textsf{Reference URL}}} \\  [0pt]
+  \hline
+  daily values &  dv & \url{http://waterservices.usgs.gov/rest/DV-Test-Tool.html}\\
+  [5pt]instantaneous & iv & \url{http://waterservices.usgs.gov/rest/IV-Test-Tool.html}\\
+  [5pt]groundwater levels & gwlevels & \url{http://waterservices.usgs.gov/rest/GW-Levels-Test-Tool.html}\\
+  [5pt]water quality & qwdata & \url{http://nwis.waterdata.usgs.gov/nwis/qwdata}\\
+   \hline
+\end{tabular}
+}
+\end{minipage}
+\end{table}
+
+The \texttt{"..."} argument allows the user to create their own queries based on the instructions found in the web links above. The links provide instructions on how to create a URL to request data. Perhaps you want sites only in Wisconsin, with a drainage area less than 50 mi$^2$, and the most recent daily dischage data. That request would be done as follows:
+
+<<dataExample>>=
+dischargeWI <- getNWISData(stateCd="WI",
+                           parameterCd="00060",
+                           drainAreaMin="50",
+                           statCd="00003")
+names(dischargeWI)
+nrow(dischargeWI)
+@
+
+%------------------------------------------------------------
+\subsubsection{Generalized Water Quality Portal site retrievals}
+\label{sec:WQPGenSite}
+%------------------------------------------------------------
+
+Just as with NWIS, the Water Quality Portal (WQP) offers a variety of ways to search for sites and request data. The possible Web service arguments for WQP site searches is found here:
+
+\url{http://www.waterqualitydata.us/webservices_documentation.jsp}
+
+To discover available sites in the WQP in New Jersey that have measured Chloride, use the function \texttt{getWQPSites}.
+
+<<NJChloride, eval=FALSE>>=
+
+sitesNJ <- getWQPSites(statecode="US:34",
+                       characteristicName="Chloride")
+
+@
+
+
+%------------------------------------------------------------
+\subsubsection{Generalized Water Quality Portal data retrievals}
+\label{sec:WQPGenData}
+%------------------------------------------------------------
+Finally, to get data from the WQP using generalized Web service calls, use the function \texttt{getWQPData}. For example, to get all the pH data in Wisconsin:
+
+<<phData, eval=FALSE>>=
+
+dataPH <- getWQPData(statecode="US:55", 
+                 characteristicName="pH")
+
+@
+
+
+
 \FloatBarrier
 
 %------------------------------------------------------------
@@ -859,7 +965,7 @@ head(Sample)
 %------------------------------------------------------------
 The Daily, Sample, and INFO dataframes (described in Secs. \ref{INFOsubsection} - \ref{Samplesubsection}) are specifically formatted to be used with the EGRET package. The EGRET package has powerful modeling capabilities that use WRTDS, but EGRET also has graphing and tabular tools for exploring the data without using the WRTDS algorithm. See the EGRET vignette, user guide, and/or wiki (\url{https://github.com/USGS-R/EGRET/wiki}) for detailed information. Figure \ref{fig:egretEx} shows one of the plotting functions that can be used directly from the dataRetrieval dataframes.
 
-<<egretEx, echo=TRUE, eval=TRUE, fig.cap="Default multiPlotDataOverview">>=
+<<egretEx, echo=TRUE, eval=TRUE, fig.cap="Default \\texttt{multiPlotDataOverview}">>=
 # Continuing Choptank example from the previous sections
 library(EGRET)
 multiPlotDataOverview()
@@ -1066,6 +1172,11 @@ From Excel, it is simple to copy and paste the tables in other Microsoft\textreg
 
 \clearpage
 
+%-------------------------------------
+\section{Disclaimer}
+%------------------------------------
+This information is preliminary and is subject to revision. It is being provided to meet the need for timely best science. The information is provided on the condition that neither the U.S. Geological Survey nor the U.S. Government may be held liable for any damages resulting from the authorized or unauthorized use of the information.
+
 % %------------------------------------------------------------
 % % BIBLIO
 % %------------------------------------------------------------
diff --git a/vignettes/dataRetrieval.lof b/vignettes/dataRetrieval.lof
deleted file mode 100644
index 603352223e668078ae445cfb60e567cf294ec38b..0000000000000000000000000000000000000000
--- a/vignettes/dataRetrieval.lof
+++ /dev/null
@@ -1,7 +0,0 @@
-\select@language {american}
-\contentsline {figure}{\numberline {1}{\ignorespaces Temperature and discharge plot of Choptank River in 2012}}{10}{figure.caption.4}
-\contentsline {figure}{\numberline {2}{\ignorespaces Nitrate plot of Choptank River}}{13}{figure.caption.5}
-\contentsline {figure}{\numberline {3}{\ignorespaces Default multiPlotDataOverview}}{23}{figure.caption.10}
-\contentsline {figure}{\numberline {4}{\ignorespaces A simple R help file\relax }}{27}{figure.caption.14}
-\contentsline {figure}{\numberline {5}{\ignorespaces A simple table produced in Microsoft\textregistered \ Excel. Additional formatting will be requried, for example converting u to $\mu $ \relax }}{30}{figure.caption.15}
-\contentsfinish 
diff --git a/vignettes/dataRetrieval.log b/vignettes/dataRetrieval.log
deleted file mode 100644
index 34e622c2d5d5fa501f5705896d6824243d1752b1..0000000000000000000000000000000000000000
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+++ /dev/null
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diff --git a/vignettes/dataRetrieval.lot b/vignettes/dataRetrieval.lot
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index 47ede036fecb200f86521bf8ffe04ef7bc918967..0000000000000000000000000000000000000000
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@@ -1,10 +0,0 @@
-\select@language {american}
-\contentsline {table}{\numberline {1}{\ignorespaces Common USGS Parameter Codes\relax }}{4}{table.caption.1}
-\contentsline {table}{\numberline {2}{\ignorespaces Commonly used USGS Stat Codes\relax }}{5}{table.caption.2}
-\contentsline {table}{\numberline {3}{\ignorespaces Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]\relax }}{7}{table.caption.3}
-\contentsline {table}{\numberline {4}{\ignorespaces Daily dataframe\relax }}{16}{table.caption.6}
-\contentsline {table}{\numberline {5}{\ignorespaces Sample dataframe\relax }}{17}{table.caption.8}
-\contentsline {table}{\numberline {6}{\ignorespaces Example data\relax }}{18}{table.caption.9}
-\contentsline {table}{\numberline {7}{\ignorespaces dataRetrieval functions\relax }}{25}{table.caption.12}
-\contentsline {table}{\numberline {8}{\ignorespaces dataRetrieval miscellaneous functions\relax }}{25}{table.caption.13}
-\contentsfinish 
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-%\VignetteIndexEntry{Introduction to the dataRetrieval package}
-%\VignetteEngine{knitr::knitr}
-%\VignetteDepends{}
-%\VignetteSuggests{xtable,EGRET}
-%\VignetteImports{zoo, XML, RCurl}
-%\VignettePackage{dataRetrieval}
-
-\documentclass[a4paper,11pt]{article}\usepackage[]{graphicx}\usepackage[]{color}
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-%------------------------------------------------------------
-\title{The dataRetrieval R package}
-%------------------------------------------------------------
-\author[1]{Laura De Cicco}
-\author[1]{Robert Hirsch}
-\affil[1]{United States Geological Survey}
-
-
-
-
-\noindent{\huge\textsf{\textbf{The dataRetrieval R package}}}
-
-\noindent\textsf{By Laura De Cicco and Robert Hirsch}
-
-\noindent\textsf{\today}
-
-% \maketitle
-% 
-% \newpage 
-
-\tableofcontents
-\listoffigures
-\listoftables
-
-\newpage
-
-%------------------------------------------------------------
-\section{Introduction to dataRetrieval}
-%------------------------------------------------------------ 
-The dataRetrieval package was created to simplify the process of loading hydrologic data into the R environment. It has been specifically designed to work seamlessly with the EGRET R package: Exploration and Graphics for RivEr Trends. See: \url{https://github.com/USGS-R/EGRET/wiki} for information on EGRET. EGRET is designed to provide analysis of water quality data sets using the Weighted Regressions on Time, Discharge and Season (WRTDS) method as well as analysis of discharge trends using robust time-series smoothing techniques.  Both of these capabilities provide both tabular and graphical analyses of long-term data sets.
-
-
-The dataRetrieval package is designed to retrieve many of the major data types of United States Geological Survey (USGS) hydrologic data that are available on the Web. Users may also load data from other sources (text files, spreadsheets) using dataRetrieval.  Section \ref{sec:genRetrievals} provides examples of how one can obtain raw data from USGS sources on the Web and load them into dataframes within the R environment.  The functionality described in section \ref{sec:genRetrievals} is for general use and is not tailored for the specific uses of the EGRET package.  The functionality described in section \ref{sec:EGRETdfs} is tailored specifically to obtaining input from the Web and structuring it for use in the EGRET package.  The functionality described in section \ref{sec:summary} is for converting hydrologic data from user-supplied files and structuring it specifically for use in the EGRET package.
-
-For information on getting started in R and installing the package, see (\ref{sec:appendix1}): Getting Started. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
-
-A quick workflow for major dataRetrieval functions:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{library}\hlstd{(dataRetrieval)}
-\hlcom{# Choptank River near Greensboro, MD}
-\hlstd{siteNumber} \hlkwb{<-} \hlstr{"01491000"}
-\hlstd{ChoptankInfo} \hlkwb{<-} \hlkwd{getSiteFileData}\hlstd{(siteNumber)}
-\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"}
-
-\hlcom{#Raw daily data:}
-\hlstd{rawDailyData} \hlkwb{<-} \hlkwd{retrieveNWISdvData}\hlstd{(siteNumber,parameterCd,}
-                      \hlstr{"1980-01-01"}\hlstd{,}\hlstr{"2010-01-01"}\hlstd{)}
-\hlcom{# Data compiled for EGRET analysis}
-\hlstd{Daily} \hlkwb{<-} \hlkwd{getDVData}\hlstd{(siteNumber,parameterCd,}
-                      \hlstr{"1980-01-01"}\hlstd{,}\hlstr{"2010-01-01"}\hlstd{)}
-
-\hlcom{# Sample data Nitrate:}
-\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00618"}
-\hlstd{Sample} \hlkwb{<-} \hlkwd{getSampleData}\hlstd{(siteNumber,parameterCd,}
-                      \hlstr{"1980-01-01"}\hlstd{,}\hlstr{"2010-01-01"}\hlstd{)}
-
-\hlcom{# Metadata on site and nitrate:}
-\hlstd{INFO} \hlkwb{<-} \hlkwd{getMetaData}\hlstd{(siteNumber,parameterCd)}
-
-\hlcom{# Merge discharge and nitrate data to one dataframe:}
-\hlstd{Sample} \hlkwb{<-} \hlkwd{mergeReport}\hlstd{()}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-
-%------------------------------------------------------------
-\section{General USGS Web Retrievals}
-\label{sec:genRetrievals}
-%------------------------------------------------------------ 
-In this section, five examples of Web retrievals document how to get raw data. This data includes site information (\ref{sec:usgsSite}), measured parameter information (\ref{sec:usgsParams}), historical daily values(\ref{sec:usgsDaily}), unit values (which include real-time data but can also include other sensor data stored at regular time intervals) (\ref{sec:usgsRT}), and water quality data (\ref{sec:usgsWQP}) or (\ref{sec:usgsSTORET}). We will use the Choptank River near Greensboro, MD as an example.  The site-ID for this streamgage is 01491000. Daily discharge measurements are available as far back as 1948.  Additionally, nitrate has been measured since 1964. 
-
-% %------------------------------------------------------------
-% \subsection{Introduction}
-% %------------------------------------------------------------
-The USGS organizes hydrologic data in a standard structure.  Streamgages are located throughout the United States, and each streamgage has a unique ID.  Often (but not always), these ID's are 8 digits.  The first step to finding data is discovering this 8-digit ID. There are many ways to do this, one is the National Water Information System: Mapper \url{http://maps.waterdata.usgs.gov/mapper/index.html}.
-
-Once the site-ID (siteNumber) is known, the next required input for USGS data retrievals is the \enquote{parameter code}.  This is a 5-digit code that specifies the measured parameter being requested.  For example, parameter code 00631 represents \enquote{Nitrate plus nitrite, water, filtered, milligrams per liter as nitrogen}, with units of \enquote{mg/l as N}. A complete list of possible USGS parameter codes can be found at \url{http://nwis.waterdata.usgs.gov/usa/nwis/pmcodes?help}.
-
-Not every station will measure all parameters. A short list of commonly measured parameters is shown in Table \ref{tab:params}.
-
-
-% latex table generated in R 3.1.1 by xtable 1.7-4 package
-% Wed Sep 17 13:24:06 2014
-\begin{table}[ht]
-\caption{Common USGS Parameter Codes} 
-\label{tab:params}
-{\footnotesize
-\begin{tabular}{rll}
-  \hline
- & \multicolumn{1}{c}{\textbf{\textsf{pCode}}} & \multicolumn{1}{c}{\textbf{\textsf{shortName}}} \\ 
-  \hline
- & 00060 & Discharge [ft$^3$/s] \\ 
-  [5pt] & 00065 & Gage height [ft] \\ 
-  [5pt] & 00010 & Temperature [C] \\ 
-  [5pt] & 00045 & Precipitation [in] \\ 
-  [5pt] & 00400 & pH \\ 
-   \hline
-\end{tabular}
-}
-\end{table}
-
-
-A complete list (as of September 25, 2013) is available as data attached to the package. It is accessed by the following:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{library}\hlstd{(dataRetrieval)}
-\hlstd{parameterCdFile} \hlkwb{<-}  \hlstd{parameterCdFile}
-\hlkwd{names}\hlstd{(parameterCdFile)}
-\end{alltt}
-\begin{verbatim}
-[1] "parameter_cd"       "parameter_group_nm"
-[3] "parameter_nm"       "casrn"             
-[5] "srsname"            "parameter_units"   
-\end{verbatim}
-\begin{alltt}
-\hlcom{# Sorting out some common values:}
-\hlkwd{subset}\hlstd{(parameterCdFile,parameter_cd} \hlopt{%in%} \hlkwd{c}\hlstd{(}\hlstr{"00060"}\hlstd{,}\hlstr{"00010"}\hlstd{,}\hlstr{"00400"}\hlstd{))}
-\end{alltt}
-\begin{verbatim}
-     parameter_cd parameter_group_nm
-1179        00010           Physical
-1206        00060           Physical
-1266        00400           Physical
-                                     parameter_nm casrn
-1179          Temperature, water, degrees Celsius      
-1206             Discharge, cubic feet per second      
-1266 pH, water, unfiltered, field, standard units      
-                      srsname parameter_units
-1179       Temperature, water           deg C
-1206 Stream flow, mean. daily           ft3/s
-1266                       pH       std units
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-
-For unit values data (sensor data measured at regular time intervals such as 15 minutes or hourly), knowing the parameter code and siteNumber is enough to make a request for data.  For most variables that are measured on a continuous basis, the USGS also stores the historical data as daily values.  These daily values are statistical summaries of the continuous data, e.g. maximum, minimum, mean, or median. The different statistics are specified by a 5-digit statistics code.  A complete list of statistic codes can be found here:
-
-\url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
-
-Some common codes are shown in Table \ref{tab:stat}.
-
-% latex table generated in R 3.1.1 by xtable 1.7-4 package
-% Wed Sep 17 13:24:07 2014
-\begin{table}[ht]
-\caption{Commonly used USGS Stat Codes} 
-\label{tab:stat}
-{\footnotesize
-\begin{tabular}{rll}
-  \hline
- & \multicolumn{1}{c}{\textbf{\textsf{StatCode}}} & \multicolumn{1}{c}{\textbf{\textsf{shortName}}} \\ 
-  \hline
- & 00001 & Maximum \\ 
-  [5pt] & 00002 & Minimum \\ 
-  [5pt] & 00003 & Mean \\ 
-  [5pt] & 00008 & Median \\ 
-   \hline
-\end{tabular}
-}
-\end{table}
-
-
-Examples for using these siteNumber's, parameter codes, and stat codes will be presented in subsequent sections.
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsection{Site Information}
-\label{sec:usgsSite}
-%------------------------------------------------------------
-
-%------------------------------------------------------------
-\subsubsection{getSiteFileData}
-\label{sec:usgsSiteFileData}
-%------------------------------------------------------------
-Use the \texttt{getSiteFileData} function to obtain all of the information available for a particular USGS site such as full station name, drainage area, latitude, and longitude:
-
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlcom{# Choptank River near Greensboro, MD}
-\hlstd{siteNumber} \hlkwb{<-} \hlstr{"01491000"}
-\hlstd{ChoptankInfo} \hlkwb{<-} \hlkwd{getSiteFileData}\hlstd{(siteNumber)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-A specific example piece of information can be retrieved, in this case a station name, as follows:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{ChoptankInfo}\hlopt{$}\hlstd{station.nm}
-\end{alltt}
-\begin{verbatim}
-[1] "CHOPTANK RIVER NEAR GREENSBORO, MD"
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-Site information is obtained from \url{http://waterservices.usgs.gov/rest/Site-Test-Tool.html}
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsubsection{getDataAvailability}
-\label{sec:usgsDataAvailability}
-%------------------------------------------------------------
-To discover what data is available for a particular USGS site, including measured parameters, period of record, and number of samples (count), use the \texttt{getDataAvailability} function. It is possible to limit the retrieval information to a subset of types (\texttt{"}dv\texttt{"}, \texttt{"}uv\texttt{"}, or \texttt{"}qw\texttt{"}). In the following example, we limit the retrieved Choptank data to only daily data. Leaving the \texttt{"}type\texttt{"} argument blank returns all of the available data for that site.
-
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlcom{# Continuing from the previous example:}
-\hlcom{# This pulls out just the daily data:}
-
-\hlstd{ChoptankDailyData} \hlkwb{<-} \hlkwd{getDataAvailability}\hlstd{(siteNumber,}
-                    \hlkwc{type}\hlstd{=}\hlstr{"dv"}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-
-% latex table generated in R 3.1.1 by xtable 1.7-4 package
-% Wed Sep 17 13:24:07 2014
-\begin{table}[ht]
-\caption{Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]} 
-\label{tab:gda}
-{\footnotesize
-\begin{tabular}{rlllll}
-  \hline
- & \multicolumn{1}{c}{\textbf{\textsf{srsname}}} & \multicolumn{1}{c}{\textbf{\textsf{startDate}}} & \multicolumn{1}{c}{\textbf{\textsf{endDate}}} & \multicolumn{1}{c}{\textbf{\textsf{count}}} & \multicolumn{1}{c}{\textbf{\textsf{units}}} \\ 
-  \hline
- & Temperature, water & 1988-10-01 & 2012-05-09 & 894 & deg C \\ 
-  [5pt] & Temperature, water & 2010-10-01 & 2012-05-09 & 529 & deg C \\ 
-  [5pt] & Temperature, water & 2010-10-01 & 2012-05-09 & 529 & deg C \\ 
-  [5pt] & Stream flow, mean. daily & 1948-01-01 & 2014-09-16 & 24366 & ft$^3$/s \\ 
-  [5pt] & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & uS/cm @25C \\ 
-  [5pt] & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & uS/cm @25C \\ 
-  [5pt] & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & uS/cm @25C \\ 
-  [5pt] & Suspended sediment concentration (SSC) & 1980-10-01 & 1991-09-30 & 3651 & mg/l \\ 
-  [5pt] & Suspended sediment discharge & 1980-10-01 & 1991-09-30 & 3652 & tons/day \\ 
-   \hline
-\end{tabular}
-}
-\end{table}
-
-
-See Section \ref{app:createWordTable} for instructions on converting an R dataframe to a table in Microsoft\textregistered\ software Excel or Word to display a data availability table similar to Table \ref{tab:gda}. Excel, Microsoft, PowerPoint, Windows, and Word are registered trademarks of Microsoft Corporation in the United States and other countries.
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsection{Parameter Information}
-\label{sec:usgsParams}
-%------------------------------------------------------------
-To obtain all of the available information concerning a measured parameter, use the \texttt{getParameterInfo} function:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlcom{# Using defaults:}
-\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00618"}
-\hlstd{parameterINFO} \hlkwb{<-} \hlkwd{getParameterInfo}\hlstd{(parameterCd)}
-\hlkwd{colnames}\hlstd{(parameterINFO)}
-\end{alltt}
-\begin{verbatim}
-[1] "parameter_cd"       "parameter_group_nm"
-[3] "parameter_nm"       "casrn"             
-[5] "srsname"            "parameter_units"   
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-A specific example piece of information, in this case parameter name, can be obtained as follows:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{parameterINFO}\hlopt{$}\hlstd{parameter_nm}
-\end{alltt}
-\begin{verbatim}
-[1] "Nitrate, water, filtered, milligrams per liter as nitrogen"
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-Parameter information can obtained from \url{http://nwis.waterdata.usgs.gov/usa/nwis/pmcodes}
-\FloatBarrier
-%------------------------------------------------------------
-\subsection{Daily Values}
-\label{sec:usgsDaily}
-%------------------------------------------------------------
-To obtain daily records of USGS data, use the \texttt{retrieveNWISdvData} function. The arguments for this function are siteNumber, parameterCd, startDate, endDate, statCd, and a logical (TRUE/FALSE) interactive. There are 2 default arguments: statCd (defaults to \texttt{"}00003\texttt{"}), and interactive (defaults to TRUE).  If you want to use the default values, you do not need to list them in the function call. By setting the \texttt{"}interactive\texttt{"} option to FALSE, the operation of the function will advance automatically. It might make more sense to run large batch collections with the interactive option set to FALSE. 
-
-The dates (start and end) must be in the format \texttt{"}YYYY-MM-DD\texttt{"} (note: the user must include the quotes).  Setting the start date to \texttt{"}\texttt{"} (no space) will prompt the program to ask for the earliest date, and setting the end date to \texttt{"}\texttt{"} (no space) will prompt for the latest available date.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlcom{# Continuing with our Choptank River example}
-\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"}  \hlcom{# Discharge (ft3/s)}
-\hlstd{startDate} \hlkwb{<-} \hlstr{""}  \hlcom{# Will request earliest date}
-\hlstd{endDate} \hlkwb{<-} \hlstr{""} \hlcom{# Will request latest date}
-
-\hlstd{discharge} \hlkwb{<-} \hlkwd{retrieveNWISdvData}\hlstd{(siteNumber,}
-                    \hlstd{parameterCd, startDate, endDate)}
-\hlkwd{names}\hlstd{(discharge)}
-\end{alltt}
-\begin{verbatim}
-[1] "agency_cd"          "site_no"           
-[3] "datetime"           "X02_00060_00003"   
-[5] "X02_00060_00003_cd"
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-The column \texttt{"}datetime\texttt{"} in the returned dataframe is automatically imported as a variable of class \texttt{"}Date\texttt{"} in R. Each requested parameter has a value and remark code column.  The names of these columns depend on the requested parameter and stat code combinations. USGS remark codes are often \texttt{"}A\texttt{"} (approved for publication) or \texttt{"}P\texttt{"} (provisional data subject to revision). A more complete list of remark codes can be found here:
-\url{http://nwis.waterdata.usgs.gov/usa/nwis/pmcodes}
-
-Another example that doesn't use the defaults would be a request for mean and maximum daily temperature and discharge in early 2012:
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{parameterCd} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00010"}\hlstd{,}\hlstr{"00060"}\hlstd{)}  \hlcom{# Temperature and discharge}
-\hlstd{statCd} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00001"}\hlstd{,}\hlstr{"00003"}\hlstd{)}  \hlcom{# Mean and maximum}
-\hlstd{startDate} \hlkwb{<-} \hlstr{"2012-01-01"}
-\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-05-01"}
-
-\hlstd{temperatureAndFlow} \hlkwb{<-} \hlkwd{retrieveNWISdvData}\hlstd{(siteNumber, parameterCd,}
-        \hlstd{startDate, endDate,} \hlkwc{statCd}\hlstd{=statCd)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-Daily data is pulled from \url{http://waterservices.usgs.gov/rest/DV-Test-Tool.html}.
-
-The column names can be automatically adjusted based on the parameter and statistic codes using the \texttt{renameColumns} function. This is not necessary, but may be useful when analyzing the data. 
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{names}\hlstd{(temperatureAndFlow)}
-\end{alltt}
-\begin{verbatim}
-[1] "agency_cd"          "site_no"           
-[3] "datetime"           "X01_00010_00001"   
-[5] "X01_00010_00001_cd" "X01_00010_00003"   
-[7] "X01_00010_00003_cd" "X02_00060_00003"   
-[9] "X02_00060_00003_cd"
-\end{verbatim}
-\begin{alltt}
-\hlstd{temperatureAndFlow} \hlkwb{<-} \hlkwd{renameColumns}\hlstd{(temperatureAndFlow)}
-\hlkwd{names}\hlstd{(temperatureAndFlow)}
-\end{alltt}
-\begin{verbatim}
-[1] "agency_cd"                                  
-[2] "site_no"                                    
-[3] "datetime"                                   
-[4] "Temperature_water_degrees_Celsius_Max_01"   
-[5] "Temperature_water_degrees_Celsius_Max_01_cd"
-[6] "Temperature_water_degrees_Celsius_01"       
-[7] "Temperature_water_degrees_Celsius_01_cd"    
-[8] "Discharge_cubic_feet_per_second"            
-[9] "Discharge_cubic_feet_per_second_cd"         
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-An example of plotting the above data (Figure \ref{fig:getNWIStemperaturePlot}):
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{par}\hlstd{(}\hlkwc{mar}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{5}\hlstd{,}\hlnum{5}\hlstd{,}\hlnum{5}\hlstd{,}\hlnum{5}\hlstd{))} \hlcom{#sets the size of the plot window}
-
-\hlkwd{with}\hlstd{(temperatureAndFlow,} \hlkwd{plot}\hlstd{(}
-  \hlstd{datetime, Temperature_water_degrees_Celsius_Max_01,}
-  \hlkwc{xlab}\hlstd{=}\hlstr{"Date"}\hlstd{,}\hlkwc{ylab}\hlstd{=}\hlstr{"Max Temperature [C]"}
-  \hlstd{))}
-\hlkwd{par}\hlstd{(}\hlkwc{new}\hlstd{=}\hlnum{TRUE}\hlstd{)}
-\hlkwd{with}\hlstd{(temperatureAndFlow,} \hlkwd{plot}\hlstd{(}
-  \hlstd{datetime, Discharge_cubic_feet_per_second,}
-  \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,}\hlkwc{type}\hlstd{=}\hlstr{"l"}\hlstd{,}\hlkwc{xaxt}\hlstd{=}\hlstr{"n"}\hlstd{,}\hlkwc{yaxt}\hlstd{=}\hlstr{"n"}\hlstd{,}\hlkwc{xlab}\hlstd{=}\hlstr{""}\hlstd{,}\hlkwc{ylab}\hlstd{=}\hlstr{""}\hlstd{,}\hlkwc{axes}\hlstd{=}\hlnum{FALSE}
-  \hlstd{))}
-\hlkwd{axis}\hlstd{(}\hlnum{4}\hlstd{,}\hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,}\hlkwc{col.axis}\hlstd{=}\hlstr{"red"}\hlstd{)}
-\hlkwd{mtext}\hlstd{(}\hlstr{"Mean Discharge [ft3/s]"}\hlstd{,}\hlkwc{side}\hlstd{=}\hlnum{4}\hlstd{,}\hlkwc{line}\hlstd{=}\hlnum{3}\hlstd{,}\hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}
-\hlkwd{title}\hlstd{(}\hlkwd{paste}\hlstd{(ChoptankInfo}\hlopt{$}\hlstd{station.nm,}\hlstr{"2012"}\hlstd{,}\hlkwc{sep}\hlstd{=}\hlstr{" "}\hlstd{))}
-\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"Max Temperature"}\hlstd{,} \hlstr{"Mean Discharge"}\hlstd{),}
-       \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"black"}\hlstd{,}\hlstr{"red"}\hlstd{),}\hlkwc{lty}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{NA}\hlstd{,}\hlnum{1}\hlstd{),}\hlkwc{pch}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{NA}\hlstd{))}
-\end{alltt}
-\end{kframe}\begin{figure}[]
-
-\includegraphics[width=1\linewidth,height=1\linewidth]{figure/getNWIStemperaturePlot} \caption[Temperature and discharge plot of Choptank River in 2012]{Temperature and discharge plot of Choptank River in 2012.\label{fig:getNWIStemperaturePlot}}
-\end{figure}
-
-
-\end{knitrout}
-
-
-There are occasions where NWIS values are not reported as numbers, instead there might be text describing a certain event such as \enquote{Ice.}  Any value that cannot be converted to a number will be reported as NA in this package (not including remark code columns).
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsection{Unit Values}
-\label{sec:usgsRT}
-%------------------------------------------------------------
-Any data collected at regular time intervals (such as 15-minute or hourly) are known as \enquote{unit values.} Many of these are delivered on a real time basis and very recent data (even less than an hour old in many cases) are available through the function \texttt{retrieveNWISunitData}.  Some of these unit values are available for many years, and some are only available for a recent time period such as 120 days.  Here is an example of a retrieval of such data.  
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"}  \hlcom{# Discharge (ft3/s)}
-\hlstd{startDate} \hlkwb{<-} \hlstr{"2012-05-12"}
-\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-05-13"}
-\hlstd{dischargeToday} \hlkwb{<-} \hlkwd{retrieveNWISunitData}\hlstd{(siteNumber, parameterCd,}
-        \hlstd{startDate, endDate)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-The retrieval produces the following dataframe:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{verbatim}
-  agency_cd  site_no            datetime tz_cd
-1      USGS 01491000 2012-05-12 00:00:00   EST
-2      USGS 01491000 2012-05-12 00:15:00   EST
-3      USGS 01491000 2012-05-12 00:30:00   EST
-4      USGS 01491000 2012-05-12 00:45:00   EST
-5      USGS 01491000 2012-05-12 01:00:00   EST
-6      USGS 01491000 2012-05-12 01:15:00   EST
-  X02_00060_00011 X02_00060_00011_cd
-1              83                  A
-2              83                  A
-3              83                  A
-4              83                  A
-5              85                  A
-6              83                  A
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-Note that time now becomes important, so the variable datetime is a POSIXct, and the time zone is included in a separate column. Data are retrieved from \url{http://waterservices.usgs.gov/rest/IV-Test-Tool.html}. There are occasions where NWIS values are not reported as numbers, instead a common example is \enquote{Ice.}  Any value that cannot be converted to a number will be reported as NA in this package.
-
-\newpage
-
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsection{Water Quality Values}
-\label{sec:usgsWQP}
-%------------------------------------------------------------
-To get USGS water quality data from water samples collected at the streamgage or other monitoring site (as distinct from unit values collected through some type of automatic monitor) we can use the function \texttt{retrieveNWISqwData}, with the input arguments: siteNumber, parameterCd, startDate, endDate, and interactive (similar to \texttt{retrieveNWISunitData} and \texttt{retrieveNWISdvData}).
-
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlcom{# Dissolved Nitrate parameter codes:}
-\hlstd{parameterCd} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00618"}\hlstd{,}\hlstr{"71851"}\hlstd{)}
-\hlstd{startDate} \hlkwb{<-} \hlstr{"1985-10-01"}
-\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-09-30"}
-
-\hlstd{dissolvedNitrate} \hlkwb{<-} \hlkwd{retrieveNWISqwData}\hlstd{(siteNumber, parameterCd,}
-      \hlstd{startDate, endDate)}
-\hlkwd{names}\hlstd{(dissolvedNitrate)}
-\end{alltt}
-\begin{verbatim}
-[1] "dateTime"        "site"            "qualifier_00618"
-[4] "value_00618"     "qualifier_71851" "value_71851"    
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-% Note that in this \enquote{simple} dataframe, datetime is imported as Dates (no times are included), and the qualifier is either blank or \verb@"<"@ signifying a censored value. A plotting example is shown in Figure \ref{fig:getQWtemperaturePlot}.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{with}\hlstd{(dissolvedNitrate,} \hlkwd{plot}\hlstd{(}
-  \hlstd{dateTime, value_00618,}
-  \hlkwc{xlab}\hlstd{=}\hlstr{"Date"}\hlstd{,}\hlkwc{ylab} \hlstd{=} \hlkwd{paste}\hlstd{(parameterINFO}\hlopt{$}\hlstd{srsname,}
-      \hlstr{"["}\hlstd{,parameterINFO}\hlopt{$}\hlstd{parameter_units,}\hlstr{"]"}\hlstd{)}
-  \hlstd{))}
-\hlkwd{title}\hlstd{(ChoptankInfo}\hlopt{$}\hlstd{station.nm)}
-\end{alltt}
-\end{kframe}\begin{figure}[]
-
-\includegraphics[width=\maxwidth]{figure/getQWtemperaturePlot} \caption[Nitrate plot of Choptank River]{Nitrate plot of Choptank River.\label{fig:getQWtemperaturePlot}}
-\end{figure}
-
-
-\end{knitrout}
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsection{STORET Water Quality Retrievals}
-\label{sec:usgsSTORET}
-%------------------------------------------------------------
-There are additional water quality data sets available from the Water Quality Data Portal (\url{http://www.waterqualitydata.us/}).  These data sets can be housed in either the STORET (data from EPA) or NWIS database.  Because STORET does not use USGS parameter codes, a \texttt{"}characteristic name\texttt{"} must be supplied.  The \texttt{getWQPData} function can retrieve either STORET or NWIS, but requires a characteristic name rather than parameter code. The Water Quality Data Portal includes data discovery tools and information on characteristic names. The following example retrieves specific conductance from a DNR site in Wisconsin. 
-
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{specificCond} \hlkwb{<-} \hlkwd{getWQPData}\hlstd{(}\hlstr{'WIDNR_WQX-10032762'}\hlstd{,}
-                \hlstr{'Specific conductance'}\hlstd{,}\hlstr{'2011-05-01'}\hlstd{,}\hlstr{'2011-09-30'}\hlstd{)}
-\hlkwd{head}\hlstd{(specificCond)}
-\end{alltt}
-\begin{verbatim}
-    dateTime qualifier. value.
-1 2011-05-09              1000
-2 2011-06-05               800
-3 2011-07-06               860
-4 2011-08-08               471
-5 2011-09-11               750
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-\FloatBarrier
-%------------------------------------------------------------
-\subsection{URL Construction}
-\label{sec:usgsURL}
-%------------------------------------------------------------
-There may be times when you might be interested in seeing the URL (Web address) that was used to obtain the raw data. The \texttt{constructNWISURL} function returns the URL.  In addition to input variables that have been described, there is a new argument \texttt{"}service\texttt{"}. The service argument can be \texttt{"}dv\texttt{"} (daily values), \texttt{"}uv\texttt{"} (unit values), \texttt{"}qw\texttt{"} (NWIS water quality values), or \texttt{"}wqp\texttt{"} (general Water Quality Portal values).
- 
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlcom{# Dissolved Nitrate parameter codes:}
-\hlstd{pCode} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00618"}\hlstd{,}\hlstr{"71851"}\hlstd{)}
-\hlstd{startDate} \hlkwb{<-} \hlstr{"1964-06-11"}
-\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-12-18"}
-\hlstd{url_qw} \hlkwb{<-} \hlkwd{constructNWISURL}\hlstd{(siteNumber,pCode,startDate,endDate,}\hlstr{'qw'}\hlstd{)}
-\hlstd{url_dv} \hlkwb{<-} \hlkwd{constructNWISURL}\hlstd{(siteNumber,}\hlstr{"00060"}\hlstd{,startDate,endDate,}
-                           \hlstr{'dv'}\hlstd{,}\hlkwc{statCd}\hlstd{=}\hlstr{"00003"}\hlstd{)}
-\hlstd{url_uv} \hlkwb{<-} \hlkwd{constructNWISURL}\hlstd{(siteNumber,}\hlstr{"00060"}\hlstd{,startDate,endDate,}\hlstr{'uv'}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\section{Data Retrievals Structured For Use In The EGRET Package}
-\label{sec:EGRETdfs}
-%------------------------------------------------------------ 
-Rather than using the raw data as retrieved by the Web, the dataRetrieval package also includes functions that return the data in a structure that has been designed to work with the EGRET R package (\url{https://github.com/USGS-R/EGRET/wiki}). In general, these dataframes may be much more 'R-friendly' than the raw data, and will contain additional date information that allows for efficient data analysis.
-
-In this section, we use 3 dataRetrieval functions to get sufficient data to perform an EGRET analysis.  We will continue analyzing the Choptank River. We retrieve essentially the same data that were retrieved in section \ref{sec:genRetrievals}, but in this case the data are structured into three EGRET-specific dataframes.  The daily discharge data are placed in a dataframe called Daily.  The nitrate sample data are placed in a dataframe called Sample.  The data about the site and the parameter are placed in a dataframe called INFO.  Although these dataframes were designed to work with the EGRET R package, they can be very useful for a wide range of hydrology studies that don't use EGRET.
-
-%------------------------------------------------------------
-\subsection{INFO Data}
-\label{INFOsubsection}
-%------------------------------------------------------------
-The \texttt{getMetaData} function obtains metadata, or data about the streamgage and measured parameters. This function combines \texttt{getSiteFileData} and \texttt{getParameterInfo}, producing one dataframe called INFO.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00618"}
-\hlstd{INFO} \hlkwb{<-}\hlkwd{getMetaData}\hlstd{(siteNumber,parameterCd,} \hlkwc{interactive}\hlstd{=}\hlnum{FALSE}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsection{Daily Data}
-\label{Dailysubsection}
-%------------------------------------------------------------
-The \texttt{getDVData} function retrieves the daily values (discharge in this case).  It requires the inputs siteNumber, parameterCd, startDate, endDate, interactive, and convert. Most of these arguments are described in section \ref{sec:genRetrievals}, however \texttt{"}convert\texttt{"} is a new argument (that defaults to TRUE). The convert argument tells the program to convert the values from cubic feet per second (ft\textsuperscript{3}/s) to cubic meters per second (m\textsuperscript{3}/s) as shown in the example Daily data frame in Table \ref{tab:DailyDF1}. For EGRET applications with NWIS Web retrieval, do not use this argument (the default is TRUE), EGRET assumes that discharge is always stored in units of cubic meters per second. If you don't want this conversion and are not using EGRET, set convert=FALSE in the function call. 
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{siteNumber} \hlkwb{<-} \hlstr{"01491000"}
-\hlstd{startDate} \hlkwb{<-} \hlstr{"2000-01-01"}
-\hlstd{endDate} \hlkwb{<-} \hlstr{"2013-01-01"}
-\hlcom{# This call will get NWIS (ft3/s) data , and convert it to m3/s:}
-\hlstd{Daily} \hlkwb{<-} \hlkwd{getDVData}\hlstd{(siteNumber,} \hlstr{"00060"}\hlstd{, startDate, endDate)}
-\end{alltt}
-\begin{verbatim}
-There are 4750 data points, and 4750 days.
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-
-
-% latex table generated in R 3.1.1 by xtable 1.7-4 package
-% Wed Sep 17 13:24:23 2014
-\begin{table}[ht]
-\caption{Daily dataframe} 
-\label{tab:DailyDF1}
-{\footnotesize
-\begin{tabular}{rllll}
-  \hline
- & \multicolumn{1}{c}{\textbf{\textsf{ColumnName}}} & \multicolumn{1}{c}{\textbf{\textsf{Type}}} & \multicolumn{1}{c}{\textbf{\textsf{Description}}} & \multicolumn{1}{c}{\textbf{\textsf{Units}}} \\ 
-  \hline
- & Date & Date & Date & date \\ 
-  [5pt] & Q & number & Discharge in m$^3$/s & m$^3$/s \\ 
-  [5pt] & Julian & number & Number of days since January 1, 1850 & days \\ 
-  [5pt] & Month & integer & Month of the year [1-12] & months \\ 
-  [5pt] & Day & integer & Day of the year [1-366] & days \\ 
-  [5pt] & DecYear & number & Decimal year & years \\ 
-  [5pt] & MonthSeq & integer & Number of months since January 1, 1850 & months \\ 
-  [5pt] & Qualifier & string & Qualifying code & character \\ 
-  [5pt] & i & integer & Index of days, starting with 1 & days \\ 
-  [5pt] & LogQ & number & Natural logarithm of Q & numeric \\ 
-  [5pt] & Q7 & number & 7 day running average of Q & m$^3$/s \\ 
-  [5pt] & Q30 & number & 30 day running average of Q & m$^3$/s \\ 
-   \hline
-\end{tabular}
-}
-\end{table}
-
-
-
-If discharge values are negative or zero, the code will set all of these values to zero and then add a small constant to all of the daily discharge values.  This constant is 0.001 times the mean discharge.  The code will also report on the number of zero and negative values and the size of the constant.  Use EGRET analysis only if the number of zero values is a very small fraction of the total days in the record (say less than 0.1\% of the days), and there are no negative discharge values.  Columns Q7 and Q30 are the 7 and 30 day running averages for the 7 or 30 days ending on this specific date. Table \ref{tab:DailyDF1} lists details of the Daily data frame.
-
-Notice that the \enquote{Day of the year} column can span from 1 to 366. The 366 accounts for leap years. Every day has a consistent day of the year. This means, February 28\textsuperscript{th} is always the 59\textsuperscript{th} day of the year, Feb. 29\textsuperscript{th} is always the 60\textsuperscript{th} day of the year, and March 1\textsuperscript{st} is always the 61\textsuperscript{st} day of the year whether or not it is a leap year.
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsection{Sample Data}
-\label{Samplesubsection}
-%------------------------------------------------------------
-The \texttt{getSampleData} function retrieves USGS sample data from NWIS. The arguments for this function are also siteNumber, parameterCd, startDate, endDate, interactive. These are the same inputs as \texttt{retrieveWQPqwData} or \texttt{getWQPData} as described in the previous section.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00618"}
-\hlstd{Sample} \hlkwb{<-}\hlkwd{getSampleData}\hlstd{(siteNumber,parameterCd,}
-      \hlstd{startDate, endDate)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-The \texttt{getSTORETSampleData} function retrieves STORET sample data (or other non-NWIS data) from the water quality portal. The arguments for this function are siteNumber, characteristicName, startDate, endDate, interactive. Table \ref{tab:SampleDataframe} lists details of the Sample data frame. 
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{site} \hlkwb{<-} \hlstr{'WIDNR_WQX-10032762'}
-\hlstd{characteristicName} \hlkwb{<-} \hlstr{'Specific conductance'}
-\hlstd{Sample} \hlkwb{<-}\hlkwd{getSTORETSampleData}\hlstd{(site,characteristicName,}
-      \hlstd{startDate, endDate)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-
-\pagebreak
-
-
-\begin{table}
-{\footnotesize
-  \begin{threeparttable}[b]
-  \caption{Sample dataframe}
-  \label{tab:SampleDataframe}
-  \begin{tabular}{llll}
-  \hline
-\multicolumn{1}{c}{\textbf{\textsf{ColumnName}}} & 
-\multicolumn{1}{c}{\textbf{\textsf{Type}}} & 
-\multicolumn{1}{c}{\textbf{\textsf{Description}}} & 
-\multicolumn{1}{c}{\textbf{\textsf{Units}}} \\ 
-  \hline
-  Date & Date & Date & date \\ 
-  [5pt]ConcLow & number & Lower limit of concentration & mg/L \\ 
-  [5pt]ConcHigh & number & Upper limit of concentration & mg/L \\ 
-  [5pt]Uncen & integer & Uncensored data (1=true, 0=false) & integer \\ 
-  [5pt]ConcAve & number & Average of ConcLow and ConcHigh & mg/L \\ 
-  [5pt]Julian & number & Number of days since January 1, 1850 & days \\ 
-  [5pt]Month & integer & Month of the year [1-12] & months \\ 
-  [5pt]Day & integer & Day of the year [1-366] & days \\ 
-  [5pt]DecYear & number & Decimal year & years \\ 
-  [5pt]MonthSeq & integer & Number of months since January 1, 1850 & months \\ 
-  [5pt]SinDY & number & Sine of DecYear & numeric \\ 
-  [5pt]CosDY & number & Cosine of DecYear & numeric \\ 
-  [5pt]Q \tnote{1} & number & Discharge & m\textsuperscript{3}/s \\ 
-  [5pt]LogQ \tnote{1} & number & Natural logarithm of discharge & numeric \\ 
-   \hline
-\end{tabular}
-
-  \begin{tablenotes}
-    \item[1] Discharge columns are populated from data in the Daily dataframe after calling the \texttt{mergeReport} function.
-  \end{tablenotes}
- \end{threeparttable}
-}
-\end{table}
-
-Notice that the \enquote{Day of the year} column can span from 1 to 366. The 366 accounts for leap years. Every day has a consistent day of the year. This means, February 28\textsuperscript{th} is always the 59\textsuperscript{th} day of the year, Feb. 29\textsuperscript{th} is always the 60\textsuperscript{th} day of the year, and March 1\textsuperscript{st} is always the 61\textsuperscript{st} day of the year whether or not it is a leap year.
-
-Section \ref{sec:cenValues} is about summing multiple constituents, including how interval censoring is used. Since the Sample data frame is structured to only contain one constituent, when more than one parameter codes are requested, the \texttt{getSampleData} function will sum the values of each constituent as described below.
-
-\FloatBarrier
-
-
-%------------------------------------------------------------
-\subsection{Censored Values: Summation Explanation}
-\label{sec:cenValues}
-%------------------------------------------------------------
-In the typical case where none of the data are censored (that is, no values are reported as \enquote{less-than} values), the ConcLow = ConcHigh = ConcAve and Uncen = 1 are equal to the reported value.  For the most common type of censoring, where a value is reported as less than the reporting limit, then ConcLow = NA, ConcHigh = reporting limit, ConcAve = 0.5 * reporting limit, and Uncen = 0.
-
-To illustrate how the dataRetrieval package handles a more complex censoring problem, let us say that in 2004 and earlier, we computed total phosphorus (tp) as the sum of dissolved phosphorus (dp) and particulate phosphorus (pp). From 2005 and onward, we have direct measurements of total phosphorus (tp). A small subset of this fictional data looks like Table \ref{tab:exampleComplexQW}.
-
-
-
-% latex table generated in R 3.1.1 by xtable 1.7-4 package
-% Wed Sep 17 13:24:25 2014
-\begin{table}[ht]
-\caption{Example data} 
-\label{tab:exampleComplexQW}
-{\footnotesize
-\begin{tabular}{rllrlrlr}
-  \hline
- & \multicolumn{1}{c}{\textbf{\textsf{cdate}}} & \multicolumn{1}{c}{\textbf{\textsf{rdp}}} & \multicolumn{1}{c}{\textbf{\textsf{dp}}} & \multicolumn{1}{c}{\textbf{\textsf{rpp}}} & \multicolumn{1}{c}{\textbf{\textsf{pp}}} & \multicolumn{1}{c}{\textbf{\textsf{rtp}}} & \multicolumn{1}{c}{\textbf{\textsf{tp}}} \\ 
-  \hline
- & 2003-02-15 &  & 0.020 &  & 0.500 &  &  \\ 
-  [5pt] & 2003-06-30 & $<$ & 0.010 &  & 0.300 &  &  \\ 
-  [5pt] & 2004-09-15 & $<$ & 0.005 & $<$ & 0.200 &  &  \\ 
-  [5pt] & 2005-01-30 &  &  &  &  &  & 0.430 \\ 
-  [5pt] & 2005-05-30 &  &  &  &  & $<$ & 0.050 \\ 
-  [5pt] & 2005-10-30 &  &  &  &  & $<$ & 0.020 \\ 
-   \hline
-\end{tabular}
-}
-\end{table}
-
-
-The dataRetrieval package will \enquote{add up} all the values in a given row to form the total for that sample when using the Sample dataframe. Thus, you only want to enter data that should be added together. If you want a dataframe with multiple constituents that are not summed, do not use getSampleData, getSTORETSampleData, or getSampleDataFromFile. The raw data functions: \texttt{getWQPData}, \texttt{retrieveNWISqwData}, \texttt{retrieveWQPqwData}, \texttt{getWQPData} will not sum constituents, but leave them in their individual columns. 
-
-For example, we might know the value for dp on 5/30/2005, but we don't want to put it in the table because under the rules of this data set, we are not supposed to add it in to the values in 2005.
-
-For every sample, the EGRET package requires a pair of numbers to define an interval in which the true value lies (ConcLow and ConcHigh). In a simple uncensored case (the reported value is above the detection limit), ConcLow equals ConcHigh and the interval collapses down to a single point. In a simple censored case, the value might be reported as \verb@<@0.2, then ConcLow=NA and ConcHigh=0.2. We use NA instead of 0 as a way to elegantly handle future logarithm calculations.
-
-For the more complex example case, let us say dp is reported as \verb@<@0.01 and pp is reported as 0.3. We know that the total must be at least 0.3 and could be as much as 0.31. Therefore, ConcLow=0.3 and ConcHigh=0.31. Another case would be if dp is reported as \verb@<@0.005 and pp is reported \verb@<@0.2. We know in this case that the true value could be as low as zero, but could be as high as 0.205. Therefore, in this case, ConcLow=NA and ConcHigh=0.205. The Sample dataframe for the example data would be:
-
-
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-  \hlstd{Sample}
-\end{alltt}
-\begin{verbatim}
-        Date ConcLow ConcHigh Uncen ConcAve Julian Month
-1 2003-02-15    0.52    0.520     1  0.5200  55927     2
-2 2003-06-30    0.30    0.310     0  0.3050  56062     6
-3 2004-09-15      NA    0.205     0  0.1025  56505     9
-4 2005-01-30    0.43    0.430     1  0.4300  56642     1
-5 2005-05-30      NA    0.050     0  0.0250  56762     5
-6 2005-10-30      NA    0.020     0  0.0100  56915    10
-  Day DecYear MonthSeq    SinDY   CosDY
-1  46    2003     1838  0.70253  0.7117
-2 182    2003     1842  0.03872 -0.9993
-3 259    2005     1857 -0.96134 -0.2754
-4  30    2005     1861  0.48251  0.8759
-5 151    2005     1865  0.54163 -0.8406
-6 304    2006     1870 -0.88205  0.4712
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-Section \ref{sec:userFiles} discusses inputting user-generated files. The functions \texttt{getSampleDataFromFile} and \texttt{getSampleData} assume summation with interval censoring inputs, and are discussed in sections \ref{sec:DailyFile} and \ref{sec:SampleFile}.
-
-\FloatBarrier
-
-%------------------------------------------------------------ 
-\subsection{User-Generated Data Files}
-\label{sec:userFiles}
-%------------------------------------------------------------ 
-In addition to retrieving data from the USGS Web services, the dataRetrieval package also includes functions to generate the Daily and Sample data frame from local files.
-
-%------------------------------------------------------------ 
-\subsubsection{getDailyDataFromFile}
-\label{sec:DailyFile}
-%------------------------------------------------------------ 
-The \texttt{getDailyDataFromFile} function will load a user-supplied text file and convert it to the Daily dataframe. The file should have two columns, the first dates, the second values.  The dates are formatted either mm/dd/yyyy or yyyy-mm-dd. Using a 4-digit year is required. This function has the following inputs: filePath, fileName,hasHeader (TRUE/FALSE), separator, qUnit, and interactive (TRUE/FALSE). filePath is a string that defines the path to your file, and the string can either be a full path, or path relative to your R working directory. The input fileName is a string that defines the file name (including the extension).
-
-Text files that contain this sort of data require some sort of a separator, for example, a \enquote{csv} file (comma-separated value) file uses a comma to separate the date and value column. A tab delimited file would use a tab (\verb@"\t"@) rather than the comma (\texttt{"},\texttt{"}). Define the type of separator you choose to use in the function call in the \texttt{"}separator\texttt{"} argument, the default is \texttt{"},\texttt{"}. Another function input is a logical variable: hasHeader.  The default is TRUE. If your data does not have column names, set this variable to FALSE.
-
-Finally, qUnit is a numeric argument that defines the discharge units used in the input file.  The default is qUnit = 1 which assumes discharge is in cubic feet per second.  If the discharge in the file is already in cubic meters per second then set qUnit = 2.  If it is in some other units (like liters per second or acre-feet per day), the user must pre-process the data with a unit conversion that changes it to either cubic feet per second or cubic meters per second.
-
-So, if you have a file called \enquote{ChoptankRiverFlow.txt} located in a folder called \enquote{RData} on the C drive (this example is for the Windows\textregistered\ operating systems), and the file is structured as follows (tab-separated):
-
-
-% \singlespacing
-\begin{verbatim}
-date  Qdaily
-10/1/1999  107
-10/2/1999  85
-10/3/1999	76
-10/4/1999	76
-10/5/1999	113
-10/6/1999	98
-...
-\end{verbatim}
-% \doublespacing
-
-The call to open this file, convert the discharge to cubic meters per second, and populate the Daily data frame would be:
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{fileName} \hlkwb{<-} \hlstr{"ChoptankRiverFlow.txt"}
-\hlstd{filePath} \hlkwb{<-}  \hlstr{"C:/RData/"}
-\hlstd{Daily} \hlkwb{<-} \hlkwd{getDailyDataFromFile}\hlstd{(filePath,fileName,}
-                    \hlkwc{separator}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-Microsoft\textregistered\ Excel files can be a bit tricky to import into R directly. The simplest way to get Excel data into R is to open the Excel file in Excel, then save it as a .csv file (comma-separated values). 
-
-\FloatBarrier
-
-%------------------------------------------------------------ 
-\subsubsection{getSampleDataFromFile}
-\label{sec:SampleFile}
-%------------------------------------------------------------ 
-
-The \texttt{getSampleDataFromFile} function will import a user-generated file and populate the Sample dataframe. The difference between sample data and discharge data is that the code requires a third column that contains a remark code, either blank or \verb@"<"@, which will tell the program that the data were \enquote{left-censored} (or, below the detection limit of the sensor). Therefore, the data must be in the form: date, remark, value.   An example of a comma-delimited file is:
-
-\singlespacing
-\begin{verbatim}
-cdate;remarkCode;Nitrate
-10/7/1999,,1.4
-11/4/1999,<,0.99
-12/3/1999,,1.42
-1/4/2000,,1.59
-2/3/2000,,1.54
-...
-\end{verbatim}
-
-The call to open this file, and populate the Sample dataframe is:
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{fileName} \hlkwb{<-} \hlstr{"ChoptankRiverNitrate.csv"}
-\hlstd{filePath} \hlkwb{<-}  \hlstr{"C:/RData/"}
-\hlstd{Sample} \hlkwb{<-} \hlkwd{getSampleDataFromFile}\hlstd{(filePath,fileName,}
-                                \hlkwc{separator}\hlstd{=}\hlstr{","}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-When multiple constituents are to be summed, the format can be date, remark\_A, value\_A, remark\_b, value\_b, etc... A tab-separated example might look like the file below, where the columns are date, remark dissolved phosphate (rdp), dissolved phosphate (dp), remark particulate phosphorus (rpp), particulate phosphorus (pp), remark total phosphate (rtp), and total phosphate (tp):
-
-\singlespacing
-\begin{verbatim}
-date  rdp	dp	rpp	pp	rtp	tp
-2003-02-15		0.020		0.500		
-2003-06-30	<	0.010		0.300		
-2004-09-15	<	0.005	<	0.200		
-2005-01-30						0.430
-2005-05-30					<	0.050
-2005-10-30					<	0.020
-...
-\end{verbatim}
-
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{fileName} \hlkwb{<-} \hlstr{"ChoptankPhosphorus.txt"}
-\hlstd{filePath} \hlkwb{<-}  \hlstr{"C:/RData/"}
-\hlstd{Sample} \hlkwb{<-} \hlkwd{getSampleDataFromFile}\hlstd{(filePath,fileName,}
-                                \hlkwc{separator}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsection{Merge Report}
-%------------------------------------------------------------
-Finally, there is a function called \texttt{mergeReport} that will look at both the Daily and Sample dataframe, and populate Q and LogQ columns into the Sample dataframe. The default arguments are Daily and Sample, however if you want to use other similarly structured dataframes, you can specify localDaily or localSample. Once \texttt{mergeReport} has been run, the Sample dataframe will be augmented with the daily discharges for all the days with samples.  None of the water quality functions in EGRET will work without first having run the \texttt{mergeReport} function.
-
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{siteNumber} \hlkwb{<-} \hlstr{"01491000"}
-\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00631"}  \hlcom{# Nitrate}
-\hlstd{startDate} \hlkwb{<-} \hlstr{"2000-01-01"}
-\hlstd{endDate} \hlkwb{<-} \hlstr{"2013-01-01"}
-
-\hlstd{Daily} \hlkwb{<-} \hlkwd{getDVData}\hlstd{(siteNumber,} \hlstr{"00060"}\hlstd{, startDate, endDate)}
-\end{alltt}
-\begin{verbatim}
-There are 4750 data points, and 4750 days.
-\end{verbatim}
-\begin{alltt}
-\hlstd{Sample} \hlkwb{<-} \hlkwd{getSampleData}\hlstd{(siteNumber,parameterCd, startDate, endDate)}
-\hlstd{Sample} \hlkwb{<-} \hlkwd{mergeReport}\hlstd{()}
-\end{alltt}
-\begin{verbatim}
-
- Discharge Record is 4750 days long, which is 13 years
- First day of the discharge record is 2000-01-01 and last day is 2013-01-01
- The water quality record has 222 samples
- The first sample is from 2000-01-04 and the last sample is from 2012-12-18
- Discharge: Minimum, mean and maximum 0.00991 4.55 246
- Concentration: Minimum, mean and maximum 0.2 1.2 2.4
- Percentage of the sample values that are censored is 0 %
-\end{verbatim}
-\begin{alltt}
-\hlkwd{head}\hlstd{(Sample)}
-\end{alltt}
-\begin{verbatim}
-        Date      Q   LogQ ConcLow ConcHigh Uncen ConcAve
-1 2000-01-04  2.747 1.0104    1.59     1.59     1    1.59
-2 2000-02-03  3.936 1.3702    1.54     1.54     1    1.54
-3 2000-02-15 10.845 2.3837    1.37     1.37     1    1.37
-4 2000-02-19 15.518 2.7420    1.24     1.24     1    1.24
-5 2000-03-23 56.917 4.0416    0.52     0.52     1    0.52
-6 2000-06-05  1.812 0.5946    1.11     1.11     1    1.11
-  Julian Month Day DecYear MonthSeq   SinDY   CosDY
-1  54789     1   4    2000     1801 0.05576  0.9984
-2  54819     2  34    2000     1802 0.54031  0.8415
-3  54831     2  46    2000     1802 0.70101  0.7132
-4  54835     2  50    2000     1802 0.74829  0.6634
-5  54868     3  83    2000     1803 0.98742  0.1581
-6  54942     6 157    2000     1806 0.44325 -0.8964
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsection{EGRET Plots}
-%------------------------------------------------------------
-The Daily, Sample, and INFO dataframes (described in Secs. \ref{INFOsubsection} - \ref{Samplesubsection}) are specifically formatted to be used with the EGRET package. The EGRET package has powerful modeling capabilities that use WRTDS, but EGRET also has graphing and tabular tools for exploring the data without using the WRTDS algorithm. See the EGRET vignette, user guide, and/or wiki (\url{https://github.com/USGS-R/EGRET/wiki}) for detailed information. Figure \ref{fig:egretEx} shows one of the plotting functions that can be used directly from the dataRetrieval dataframes.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlcom{# Continuing Choptank example from the previous sections}
-\hlkwd{library}\hlstd{(EGRET)}
-\hlkwd{multiPlotDataOverview}\hlstd{()}
-\end{alltt}
-\end{kframe}\begin{figure}[]
-
-\includegraphics[width=\maxwidth]{figure/egretEx} \caption[Default multiPlotDataOverview]{Default multiPlotDataOverview\label{fig:egretEx}}
-\end{figure}
-
-
-\end{knitrout}
-
-\FloatBarrier
-\clearpage
-
-
-%------------------------------------------------------------
-\section{Summary}
-\label{sec:summary}
-%------------------------------------------------------------
-
-Tables \ref{tab:dataRetrievalFunctions1} and \ref{tab:dataRetrievalMisc} summarize the data retrieval functions:
-
-\begin{table}
-{\footnotesize
-  \begin{threeparttable}[b]
-  \caption{dataRetrieval functions}
-  \label{tab:dataRetrievalFunctions1}
-%   \doublespacing
-\begin{tabular}{lll}
-  \hline
-\multicolumn{1}{c}{\textbf{\textsf{Data Type}}} &
-\multicolumn{1}{c}{\textbf{\textsf{Function Name}}} &
-\multicolumn{1}{c}{\textbf{\textsf{Description}}} \\ [0pt]
-  \hline
-  Daily & \texttt{retrieveNWISdvData} & Raw USGS daily data \\ 
-  [5pt]Daily\tnote{1} & \texttt{getDVData} & USGS daily values \\ 
-  [5pt]Daily\tnote{1} & \texttt{getDailyDataFromFile} & User generated daily data \\ 
-  [5pt]Sample & \texttt{retrieveNWISqwData} & Raw USGS water quality data \\
-  [5pt]Sample & \texttt{retrieveWQPqwData} & Raw Water Quality Data Portal data \\ 
-  [5pt]Sample & \texttt{getQWDataFromFile} & Raw user generated water quality data \\ 
-  [5pt]Sample & \texttt{getWQPData} & General Water Quality Portal\\
-  [5pt]Sample\tnote{1} & \texttt{getSampleData} & USGS water quality data\\
-  [5pt]Sample\tnote{1} & \texttt{getSTORETSampleData} & STORET Water Quality Data Portal data \\
-  [5pt]Sample\tnote{1} & \texttt{getSampleDataFromFile} & User generated sample data \\ 
-  [5pt]Unit & \texttt{retrieveNWISunitData} & Raw USGS instantaneous data \\
-  [5pt]Information\tnote{1} & \texttt{getMetaData} & USGS station and parameter code information \\ 
-  [5pt]Information & \texttt{getParameterInfo} & USGS parameter code information \\ 
-  [5pt]Information & \texttt{getSiteFileData} & USGS station information \\ 
-  [5pt]Information & \texttt{getDataAvailability} & Data available at USGS stations \\ 
-   \hline
-\end{tabular}
-
-  \begin{tablenotes}
-    \item[1] Indicates that the function creates a data frame suitable for use in EGRET software
-  \end{tablenotes}
- \end{threeparttable}
-}
-\end{table}
-
-
-\begin{table}[!ht]
-\begin{minipage}{\linewidth}
-{\footnotesize
-\caption{dataRetrieval miscellaneous functions} 
-\label{tab:dataRetrievalMisc}
-\begin{tabular}{ll}
-  \hline
-\multicolumn{1}{c}{\textbf{\textsf{Function Name}}} &
-\multicolumn{1}{c}{\textbf{\textsf{Description}}} \\  [0pt]
-  \hline
-  \texttt{compressData} &  Converts value/qualifier into ConcLow, ConcHigh, Uncen\\
-  [5pt]\texttt{getRDB1Data} & Retrieves and converts RDB data to dataframe\\
-  [5pt]\texttt{getWaterML1Data} & Retrieves and converts WaterML1 data to dataframe\\
-  [5pt]\texttt{getWaterML2Data} & Retrieves and converts WaterML2 data to dataframe\\
-  [5pt]\texttt{mergeReport} & Merges flow data from the daily record into the sample record\\
-  [5pt]\texttt{populateDateColumns} & Generates Julian, Month, Day, DecYear, and MonthSeq columns\\
-  [5pt]\texttt{removeDuplicates} & Removes duplicated rows\\
-  [5pt]\texttt{renameColumns} & Renames columns from raw data retrievals\\
-   \hline
-\end{tabular}
-}
-\end{minipage}
-\end{table}
-
-\FloatBarrier
-\clearpage
-
-
-%------------------------------------------------------------ 
-\section{Getting Started in R}
-\label{sec:appendix1}
-%------------------------------------------------------------ 
-This section describes the options for downloading and installing the dataRetrieval package.
-
-%------------------------------------------------------------
-\subsection{New to R?}
-%------------------------------------------------------------ 
-If you are new to R, you will need to first install the latest version of R, which can be found here: \url{http://www.r-project.org/}.
-
-At any time, you can get information about any function in R by typing a question mark before the functions name.  This will open a file (in RStudio, in the Help window) that describes the function, the required arguments, and provides working examples.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlopt{?}\hlstd{removeDuplicates}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-This will open a help file similar to Figure \ref{fig:help}.
-
-\FloatBarrier
-
-To see the raw code for a particular code, type the name of the function, without parentheses.:
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{removeDuplicates}
-\end{alltt}
-\begin{verbatim}
-function (localSample = Sample) 
-{
-    Sample1 <- localSample[!duplicated(localSample[c("DecYear", 
-        "ConcHigh")]), ]
-    return(Sample1)
-}
-<environment: namespace:dataRetrieval>
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-
-\begin{figure}[ht!]
-\centering
- \resizebox{0.95\textwidth}{!}{\includegraphics{Rhelp.png}} 
-\caption{A simple R help file}
-\label{fig:help}
-\end{figure}
-
-Additionally, many R packages have vignette files attached (such as this paper). To view the vignette:
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{vignette}\hlstd{(dataRetrieval)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-\FloatBarrier
-\clearpage
-%------------------------------------------------------------
-\subsection{R User: Installing dataRetrieval}
-%------------------------------------------------------------ 
-The following command installs dataRetrieval and subsequent required packages:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{install.packages}\hlstd{(}\hlstr{"dataRetrieval"}\hlstd{,}
-\hlkwc{repos}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"http://usgs-r.github.com"}\hlstd{,}\hlstr{"http://cran.us.r-project.org"}\hlstd{),}
-\hlkwc{dependencies}\hlstd{=}\hlnum{TRUE}\hlstd{,}
-\hlkwc{type}\hlstd{=}\hlstr{"both"}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-After installing the package, you need to open the library each time you re-start R.  This is done with the simple command:
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{library}\hlstd{(dataRetrieval)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-
-%------------------------------------------------------------ 
-\section{Creating tables in Microsoft\textregistered\ software from R}
-\label{app:createWordTable}
-%------------------------------------------------------------
-There are a few steps that are required in order to create a table in Microsoft\textregistered\ software (Excel, Word, PowerPoint, etc.) from an R dataframe. There are certainly a variety of good methods, one of which is detailed here. The example we will step through here will be to create a table in Microsoft Excel based on the dataframe tableData:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{availableData} \hlkwb{<-} \hlkwd{getDataAvailability}\hlstd{(siteNumber)}
-\hlstd{dailyData} \hlkwb{<-} \hlstd{availableData[}\hlstr{"dv"} \hlopt{==} \hlstd{availableData}\hlopt{$}\hlstd{service,]}
-\hlstd{dailyData} \hlkwb{<-} \hlstd{dailyData[}\hlstr{"00003"} \hlopt{==} \hlstd{dailyData}\hlopt{$}\hlstd{statCd,]}
-
-\hlstd{tableData} \hlkwb{<-} \hlkwd{with}\hlstd{(dailyData,}
-      \hlkwd{data.frame}\hlstd{(}
-        \hlkwc{shortName}\hlstd{=srsname,}
-        \hlkwc{Start}\hlstd{=startDate,}
-        \hlkwc{End}\hlstd{=endDate,}
-        \hlkwc{Count}\hlstd{=count,}
-        \hlkwc{Units}\hlstd{=parameter_units)}
-      \hlstd{)}
-\hlstd{tableData}
-\end{alltt}
-\begin{verbatim}
-                               shortName      Start
-1                     Temperature, water 2010-10-01
-2               Stream flow, mean. daily 1948-01-01
-3                   Specific conductance 2010-10-01
-4 Suspended sediment concentration (SSC) 1980-10-01
-5           Suspended sediment discharge 1980-10-01
-         End Count      Units
-1 2012-05-09   529      deg C
-2 2014-09-16 24366      ft3/s
-3 2012-05-09   527 uS/cm @25C
-4 1991-09-30  3651       mg/l
-5 1991-09-30  3652   tons/day
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-First, save the dataframe as a tab delimited file (you don't want to use comma delimited because there are commas in some of the data elements):
-
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{write.table}\hlstd{(tableData,} \hlkwc{file}\hlstd{=}\hlstr{"tableData.tsv"}\hlstd{,}\hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{,}
-            \hlkwc{row.names} \hlstd{=} \hlnum{FALSE}\hlstd{,}\hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-This will save a file in your working directory called tableData.tsv.  You can see your working directory by typing getwd() in the R console. Opening the file in a general-purpose text editor, you should see the following:
-
-\begin{verbatim}
-shortName  Start  End	Count	Units
-Temperature, water	2010-10-01	2012-06-24	575	deg C
-Stream flow, mean. daily	1948-01-01	2013-03-13	23814	ft3/s
-Specific conductance	2010-10-01	2012-06-24	551	uS/cm @25C
-Suspended sediment concentration (SSC)	1980-10-01	1991-09-30	3651	mg/l
-Suspended sediment discharge	1980-10-01	1991-09-30	3652	tons/day
-\end{verbatim}
-
-Next, follow the steps below to open this file in Excel:
-\begin{enumerate}
-\item Open Excel
-\item Click on the File tab
-\item Click on the Open option
-\item Navigate to the working directory (as shown in the results of \texttt{getwd()})
-\item Next to the File name text box, change the dropdown type to All Files (*.*)
-\item Double click tableData.tsv
-\item A text import wizard will open up, in the first window, choose the Delimited radio button if it is not automatically picked, then click on Next.
-\item In the second window, click on the Tab delimiter if it is not automatically checked, then click Finished.
-\item Use the many formatting tools within Excel to customize the table
-\end{enumerate}
-
-From Excel, it is simple to copy and paste the tables in other Microsoft\textregistered\ software. An example using one of the default Excel table formats is here.
-
-\begin{figure}[ht!]
-\centering
- \resizebox{0.9\textwidth}{!}{\includegraphics{table1.png}} 
-\caption{A simple table produced in Microsoft\textregistered\ Excel. Additional formatting will be requried, for example converting u to  $\mu$ }
-\label{overflow}
-\end{figure}
-
-\clearpage
-
-% %------------------------------------------------------------
-% % BIBLIO
-% %------------------------------------------------------------
-% \begin{thebibliography}{10}
-% 
-% \bibitem{HirschI}
-% Helsel, D.R. and R. M. Hirsch, 2002. Statistical Methods in Water Resources Techniques of Water Resources Investigations, Book 4, chapter A3. U.S. Geological Survey. 522 pages. \url{http://pubs.usgs.gov/twri/twri4a3/}
-% 
-% \bibitem{HirschII}
-% Hirsch, R. M., Moyer, D. L. and Archfield, S. A. (2010), Weighted Regressions on Time, Discharge, and Season (WRTDS), with an Application to Chesapeake Bay River Inputs. JAWRA Journal of the American Water Resources Association, 46: 857-880. doi: 10.1111/j.1752-1688.2010.00482.x \url{http://onlinelibrary.wiley.com/doi/10.1111/j.1752-1688.2010.00482.x/full}
-% 
-% \bibitem{HirschIII}
-% Sprague, L. A., Hirsch, R. M., and Aulenbach, B. T. (2011), Nitrate in the Mississippi River and Its Tributaries, 1980 to 2008: Are We Making Progress? Environmental Science \& Technology, 45 (17): 7209-7216. doi: 10.1021/es201221s \url{http://pubs.acs.org/doi/abs/10.1021/es201221s}
-% 
-% \end{thebibliography}
-
-% \end{document}
-
-\end{document}
diff --git a/vignettes/dataRetrieval.toc b/vignettes/dataRetrieval.toc
deleted file mode 100644
index ba00912a81727dfab78c593237beb430f2856331..0000000000000000000000000000000000000000
--- a/vignettes/dataRetrieval.toc
+++ /dev/null
@@ -1,28 +0,0 @@
-\select@language {american}
-\contentsline {section}{\numberline {1}Introduction to dataRetrieval}{3}{section.1}
-\contentsline {section}{\numberline {2}General USGS Web Retrievals}{4}{section.2}
-\contentsline {subsection}{\numberline {2.1}Site Information}{6}{subsection.2.1}
-\contentsline {subsubsection}{\numberline {2.1.1}getSiteFileData}{6}{subsubsection.2.1.1}
-\contentsline {subsubsection}{\numberline {2.1.2}getDataAvailability}{6}{subsubsection.2.1.2}
-\contentsline {subsection}{\numberline {2.2}Parameter Information}{7}{subsection.2.2}
-\contentsline {subsection}{\numberline {2.3}Daily Values}{7}{subsection.2.3}
-\contentsline {subsection}{\numberline {2.4}Unit Values}{11}{subsection.2.4}
-\contentsline {subsection}{\numberline {2.5}Water Quality Values}{12}{subsection.2.5}
-\contentsline {subsection}{\numberline {2.6}STORET Water Quality Retrievals}{14}{subsection.2.6}
-\contentsline {subsection}{\numberline {2.7}URL Construction}{14}{subsection.2.7}
-\contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{14}{section.3}
-\contentsline {subsection}{\numberline {3.1}INFO Data}{15}{subsection.3.1}
-\contentsline {subsection}{\numberline {3.2}Daily Data}{15}{subsection.3.2}
-\contentsline {subsection}{\numberline {3.3}Sample Data}{16}{subsection.3.3}
-\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{17}{subsection.3.4}
-\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{19}{subsection.3.5}
-\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{19}{subsubsection.3.5.1}
-\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{20}{subsubsection.3.5.2}
-\contentsline {subsection}{\numberline {3.6}Merge Report}{21}{subsection.3.6}
-\contentsline {subsection}{\numberline {3.7}EGRET Plots}{22}{subsection.3.7}
-\contentsline {section}{\numberline {4}Summary}{24}{section.4}
-\contentsline {section}{\numberline {5}Getting Started in R}{26}{section.5}
-\contentsline {subsection}{\numberline {5.1}New to R?}{26}{subsection.5.1}
-\contentsline {subsection}{\numberline {5.2}R User: Installing dataRetrieval}{28}{subsection.5.2}
-\contentsline {section}{\numberline {6}Creating tables in Microsoft\textregistered \ software from R}{28}{section.6}
-\contentsfinish 
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