From 223ada5e530f9c87433cc533f41e9582374fa762 Mon Sep 17 00:00:00 2001
From: unknown <ldecicco@usgs.gov>
Date: Mon, 22 Sep 2014 14:06:33 -0500
Subject: [PATCH] Updated naming convention.

---
 NAMESPACE                 | 10 ++++-
 NEWS                      |  4 +-
 R/basicWQPData.R          |  4 +-
 R/getDVData.r             | 48 +++++++++++++++++++++--
 R/getDailyDataFromFile.r  | 38 ++++++++++++++++++-
 R/getDataAvailability.r   | 80 +++++++++++++++++++++++++++++++++++++--
 R/getMetaData.r           |  4 +-
 R/getParameterInfo.r      | 42 +++++++++++---------
 R/getQWDataFromFile.r     | 46 ----------------------
 R/getRawQWData.r          |  4 +-
 R/getSTORETSampleData.R   | 52 +++++++++++++++++++++++--
 R/getSampleData.r         | 45 +++++++++++++++++++---
 R/getSampleDataFromFile.r | 35 +++++++++++++++--
 R/getSiteFileData.r       | 67 ++++++++++++++++++++++++++++++--
 R/getWQPData.r            |  2 +-
 R/populateParameterINFO.r |  4 +-
 R/populateSiteINFO.r      |  2 +-
 R/renameColumns.R         |  2 +-
 18 files changed, 387 insertions(+), 102 deletions(-)
 delete mode 100644 R/getQWDataFromFile.r

diff --git a/NAMESPACE b/NAMESPACE
index 880043c4..1a36ddfa 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,5 @@
 # Generated by roxygen2 (4.0.2): do not edit by hand
 
-export(basicWQPData)
 export(checkStartEndDate)
 export(compressData)
 export(constructNWISURL)
@@ -13,7 +12,12 @@ export(getDailyDataFromFile)
 export(getDataAvailability)
 export(getDataFromFile)
 export(getMetaData)
+export(getNWISDaily)
 export(getNWISData)
+export(getNWISDataAvailability)
+export(getNWISPcodeInfo)
+export(getNWISSample)
+export(getNWISSiteInfo)
 export(getNWISSites)
 export(getParameterInfo)
 export(getQWDataFromFile)
@@ -22,7 +26,10 @@ export(getSTORETSampleData)
 export(getSampleData)
 export(getSampleDataFromFile)
 export(getSiteFileData)
+export(getUserDaily)
+export(getUserSample)
 export(getWQPData)
+export(getWQPSample)
 export(getWQPSites)
 export(getWaterML1Data)
 export(getWaterML2Data)
@@ -35,6 +42,7 @@ export(populateParameterINFO)
 export(populateSampleColumns)
 export(populateSiteINFO)
 export(processQWData)
+export(readWQPData)
 export(removeDuplicates)
 export(renameColumns)
 export(retrieveNWISdvData)
diff --git a/NEWS b/NEWS
index bd63ebe5..fc0f774a 100644
--- a/NEWS
+++ b/NEWS
@@ -1,7 +1,7 @@
 dataRetrieval 1.3.3
 ===========
 
-* Updated getSiteFileData to retrieve multiple site file datasets at once using a vector of siteNumbers as input argument.
+* Updated getNWISSiteInfo 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.
@@ -19,7 +19,7 @@ dataRetrieval 1.3.2
 dataRetrieval 1.2.2
 ===========
 
-* Added getDataAvailability function to find measured parameters and period of record information for a requested station.
+* Added getNWISDataAvailability function to find measured parameters and period of record information for a requested station.
 
 * Added constructNWISURL function to get the URL that is used to retrieve the data.
 
diff --git a/R/basicWQPData.R b/R/basicWQPData.R
index b80e94cb..470b5403 100644
--- a/R/basicWQPData.R
+++ b/R/basicWQPData.R
@@ -10,8 +10,8 @@
 #' @examples
 #' # These examples require an internet connection to run
 #' rawSampleURL <- constructNWISURL('USGS-01594440','01075', '1985-01-01', '1985-03-31',"wqp")
-#' rawSample <- basicWQPData(rawSampleURL)
-basicWQPData <- function(url){
+#' rawSample <- readWQPData(rawSampleURL)
+readWQPData <- function(url){
   
   h <- basicHeaderGatherer()
   
diff --git a/R/getDVData.r b/R/getDVData.r
index f627846b..209f69a6 100644
--- a/R/getDVData.r
+++ b/R/getDVData.r
@@ -1,5 +1,44 @@
 #' Import Daily Data for WRTDS
 #'
+#' This function is being deprecated for \code{\link{getNWISDaily}}.
+#' 
+#' @param siteNumber string USGS site number.  This is usually an 8 digit number
+#' @param parameterCd string USGS parameter code.  This is usually an 5 digit number.
+#' @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 convert logical Option to include a conversion from cfs to cms (35.314667). The default is TRUE, 
+#' which is appropriate for using NWIS data in the EGRET package.  Set this to FALSE to not include the conversion. If the parameter code is not 00060 (NWIS discharge),
+#' there is no conversion applied.
+#' @param format string, can be "tsv" or "xml", and is only applicable for daily and unit value requests.  "tsv" returns results faster, but there is a possiblitiy that an incomplete file is returned without warning. XML is slower, 
+#' but will offer a warning if the file was incomplete (for example, if there was a momentary problem with the internet connection). It is possible to safely use the "tsv" option, 
+#' but the user must carefully check the results to see if the data returns matches what is expected. The default is "tsv".
+#' @keywords data import USGS WRTDS
+#' @export
+#' @return Daily dataframe
+#' @seealso \code{\link{retrieveNWISdvData}}, \code{\link{populateDaily}}, \code{\link{getNWISData}}
+#' @examples
+#' # These examples require an internet connection to run
+#' \dontrun{Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31')}
+#' \dontrun{DailyCFS <- getDVData('01594440','00060', '1985-01-01', '1985-03-31',convert=FALSE)}
+#' \dontrun{DailySuspSediment <- getDVData('01594440','80154', '1985-01-01', '1985-03-31')}
+getDVData <- function (siteNumber,parameterCd,startDate,endDate,interactive=TRUE,convert=TRUE,format="tsv"){
+  warning("This function is being deprecated, please use getNWISData")
+  data <- retrieveNWISdvData(siteNumber,parameterCd,startDate,endDate,interactive=interactive,format=format)
+  
+  #  need to setup conversion factor because the NWIS data are in cfs but we store in cms
+  names(data) <- c('agency', 'site', 'dateTime', 'value', 'code')  # do a merge instead?
+  
+  qConvert <- ifelse("00060" == parameterCd, 35.314667, 1)
+  qConvert<- ifelse(convert,qConvert,1)
+  
+  localDaily <- populateDaily(data,qConvert,interactive=interactive)
+  return (localDaily)
+}
+
+
+#' Import NWIS Daily Data for EGRET analysis
+#'
 #' Imports data from NWIS web service. This function gets the data from here: \url{http://waterservices.usgs.gov/}
 #' A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
 #' A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
@@ -21,10 +60,11 @@
 #' @seealso \code{\link{retrieveNWISdvData}}, \code{\link{populateDaily}}
 #' @examples
 #' # These examples require an internet connection to run
-#' Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31')
-#' DailyCFS <- getDVData('01594440','00060', '1985-01-01', '1985-03-31',convert=FALSE)
-#' DailySuspSediment <- getDVData('01594440','80154', '1985-01-01', '1985-03-31')
-getDVData <- function (siteNumber,parameterCd,startDate,endDate,interactive=TRUE,convert=TRUE,format="tsv"){
+#' Daily <- getNWISDaily('01594440','00060', '1985-01-01', '1985-03-31')
+#' DailyCFS <- getNWISDaily('01594440','00060', '1985-01-01', '1985-03-31',convert=FALSE)
+#' DailySuspSediment <- getNWISDaily('01594440','80154', '1985-01-01', '1985-03-31')
+getNWISDaily <- function (siteNumber,parameterCd,startDate,endDate,interactive=TRUE,convert=TRUE,format="tsv"){
+
   data <- retrieveNWISdvData(siteNumber,parameterCd,startDate,endDate,interactive=interactive,format=format)
   
   #  need to setup conversion factor because the NWIS data are in cfs but we store in cms
diff --git a/R/getDailyDataFromFile.r b/R/getDailyDataFromFile.r
index 714af5f3..94e0fd76 100644
--- a/R/getDailyDataFromFile.r
+++ b/R/getDailyDataFromFile.r
@@ -1,6 +1,6 @@
 #' Import Daily Data for WRTDS
 #'
-#' Imports data from a user-supplied file, and converts it to a Daily data frame, appropriate for WRTDS calculations.
+#' This function is being deprecated for \code{\link{getUserDaily}}.
 #'
 #' @param filePath string specifying the path to the file
 #' @param fileName string name of file to open
@@ -16,8 +16,42 @@
 #' filePath <- system.file("extdata", package="dataRetrieval")
 #' filePath <- paste(filePath,"/",sep="")
 #' fileName <- "ChoptankRiverFlow.txt"
-#' Daily <- getDailyDataFromFile(filePath,fileName,separator="\t")
+#' \dontrun{Daily <- getDailyDataFromFile(filePath,fileName,separator="\t")}
 getDailyDataFromFile <- function (filePath,fileName,hasHeader=TRUE,separator=",",qUnit=1,interactive=TRUE){
+  
+  warning("This function is being deprecated, please use getUserDaily")
+  
+  data <- getDataFromFile(filePath,fileName,hasHeader=hasHeader,separator=separator)
+  convertQ<-c(35.314667,1,0.035314667,0.001)
+  qConvert<-convertQ[qUnit]
+  if (interactive){
+    if(qUnit==1) cat("\n the input discharge are assumed to be in cubic feet per second\nif they are in cubic meters per second, then the call to getDailyDataFromFile should specify qUnit=2\n")
+  }
+  localDaily <- populateDaily(data,qConvert, interactive=interactive)
+  localDaily <- localDaily[!is.na(localDaily$Q),]
+  return(localDaily)
+}
+
+#' Import user daily data for EGRET analysis
+#'
+#' Imports data from a user-supplied file, and converts it to a Daily data frame, appropriate for WRTDS calculations.
+#'
+#' @param filePath string specifying the path to the file
+#' @param fileName string name of file to open
+#' @param hasHeader logical true if the first row of data is the column headers
+#' @param separator string character that separates data cells
+#' @param qUnit number 1 is cubic feet per second, 2 is cubic meters per second, 3 is 10^3 cubic feet per second, and 4 is 10^3 cubic meters per second
+#' @param interactive logical Option for interactive mode.  If true, there is user interaction for error handling and data checks.
+#' @keywords data import file
+#' @keywords data import USGS WRTDS
+#' @export
+#' @return Daily dataframe
+#' @examples
+#' filePath <- system.file("extdata", package="dataRetrieval")
+#' filePath <- paste(filePath,"/",sep="")
+#' fileName <- "ChoptankRiverFlow.txt"
+#' Daily <- getUserDaily(filePath,fileName,separator="\t")
+getUserDaily <- function (filePath,fileName,hasHeader=TRUE,separator=",",qUnit=1,interactive=TRUE){
   data <- getDataFromFile(filePath,fileName,hasHeader=hasHeader,separator=separator)
   convertQ<-c(35.314667,1,0.035314667,0.001)
   qConvert<-convertQ[qUnit]
diff --git a/R/getDataAvailability.r b/R/getDataAvailability.r
index 1da65952..bf1ff0dc 100644
--- a/R/getDataAvailability.r
+++ b/R/getDataAvailability.r
@@ -10,11 +10,11 @@
 #' @import RCurl
 #' @examples
 #' # These examples require an internet connection to run
-#' availableData <- getDataAvailability('05114000')
+#' availableData <- getNWISDataAvailability('05114000')
 #' # To find just unit value ('instantaneous') data:
-#' uvData <- getDataAvailability('05114000',type="uv")
-#' uvDataMulti <- getDataAvailability(c('05114000','09423350'),type="uv")
-getDataAvailability <- function(siteNumber,type=c("uv","dv","qw")){
+#' uvData <- getNWISDataAvailability('05114000',type="uv")
+#' uvDataMulti <- getNWISDataAvailability(c('05114000','09423350'),type="uv")
+getNWISDataAvailability <- function(siteNumber,type=c("uv","dv","qw")){
   
   siteNumber <- paste(siteNumber,collapse=",")
   
@@ -33,6 +33,78 @@ getDataAvailability <- function(siteNumber,type=c("uv","dv","qw")){
     return(NA)
   }) 
   
+  if(h$value()["Content-Type"] == "text/plain;charset=UTF-8"){
+    SiteFile <- read.delim(
+      textConnection(doc),
+      header = TRUE,
+      quote="\"",
+      dec=".",
+      sep='\t',
+      colClasses=c('character'),
+      fill = TRUE,
+      comment.char="#")
+    
+    SiteFile <- SiteFile[-1,]
+    
+    SiteFile <- with(SiteFile, data.frame(site_no=site_no, parameter_cd=parm_cd, statCd=stat_cd, startDate=begin_date,endDate=end_date, count=count_nu,service=data_type_cd,stringsAsFactors = FALSE))
+    
+    SiteFile <- SiteFile[!is.na(SiteFile$parameter_cd),]
+    SiteFile <- SiteFile["" != SiteFile$parameter_cd,]
+    SiteFile$startDate <- as.Date(SiteFile$startDate)
+    SiteFile$endDate <- as.Date(SiteFile$endDate)
+    SiteFile$count <- as.numeric(SiteFile$count)
+    
+    pCodes <- unique(SiteFile$parameter_cd)
+    
+    pcodeINFO <- parameterCdFile[parameterCdFile$parameter_cd %in% pCodes,]
+    SiteFile <- merge(SiteFile,pcodeINFO,by="parameter_cd")
+    SiteFile <- SiteFile[SiteFile$service %in% type,]
+    return(SiteFile)
+  } else {
+    message(paste("URL caused an error:", urlSitefile))
+    message("Content-Type=",h$value()["Content-Type"])
+    return(NA)
+  }
+}
+
+
+#' USGS data availability
+#'
+#' This function is being deprecated for \code{\link{getNWISDataAvailability}}.
+#'
+#' @param siteNumber string USGS site number.
+#' @param type vector string. Options are "uv", "dv", "qw"
+#' @keywords data import USGS web service
+#' @return retval dataframe with all information found in the expanded site file
+#' @export
+#' @import RCurl
+#' @examples
+#' # These examples require an internet connection to run
+#' \dontrun{availableData <- getDataAvailability('05114000')}
+#' # To find just unit value ('instantaneous') data:
+#' \dontrun{uvData <- getDataAvailability('05114000',type="uv")}
+#' \dontrun{uvDataMulti <- getDataAvailability(c('05114000','09423350'),type="uv")}
+getDataAvailability <- function(siteNumber,type=c("uv","dv","qw")){
+  
+  warning("This function is being deprecated, please use getNWISDataAvailability")
+  
+  siteNumber <- paste(siteNumber,collapse=",")
+  
+  urlSitefile <- paste("http://waterservices.usgs.gov/nwis/site/?format=rdb&seriesCatalogOutput=true&sites=",siteNumber,sep = "")
+  
+  doc = tryCatch({
+    h <- basicHeaderGatherer()
+    doc <- getURL(urlSitefile, headerfunction = h$update)
+    
+  }, warning = function(w) {
+    message(paste("URL caused a warning:", urlSitefile))
+    message(w)
+  }, error = function(e) {
+    message(paste("URL does not seem to exist:", urlSitefile))
+    message(e)
+    return(NA)
+  }) 
+  
   if(h$value()["Content-Type"] == "text/plain;charset=UTF-8"){
     SiteFile <- read.delim(
       textConnection(doc),
diff --git a/R/getMetaData.r b/R/getMetaData.r
index 9793e2e3..cf64794f 100644
--- a/R/getMetaData.r
+++ b/R/getMetaData.r
@@ -20,7 +20,7 @@
 #' INFO <- getMetaData('05114000','00010')
 getMetaData <- function(siteNumber="", parameterCd="",interactive=TRUE){
   if (nzchar(siteNumber)){
-    INFO <- getSiteFileData(siteNumber)
+    INFO <- getNWISSiteInfo(siteNumber)
   } else {
     INFO <- as.data.frame(matrix(ncol = 2, nrow = 1))
     names(INFO) <- c('site.no', 'shortName')    
@@ -28,7 +28,7 @@ getMetaData <- function(siteNumber="", parameterCd="",interactive=TRUE){
   INFO <- populateSiteINFO(INFO, siteNumber, interactive=interactive)
   
   if (nzchar(parameterCd)){
-    parameterData <- getParameterInfo(parameterCd,interactive=interactive)
+    parameterData <- getNWISPcodeInfo(parameterCd,interactive=interactive)
     INFO$param.nm <- parameterData$parameter_nm
     INFO$param.units <- parameterData$parameter_units
     INFO$paramShortName <- parameterData$srsname
diff --git a/R/getParameterInfo.r b/R/getParameterInfo.r
index 6cbf51e7..05a5480c 100644
--- a/R/getParameterInfo.r
+++ b/R/getParameterInfo.r
@@ -10,26 +10,34 @@
 #' @export
 #' @examples
 #' # These examples require an internet connection to run
-#' paramINFO <- getParameterInfo(c('01075','00060','00931'))
-getParameterInfo <- function(parameterCd,interactive=TRUE){
+#' paramINFO <- getNWISPcodeInfo(c('01075','00060','00931'))
+getNWISPcodeInfo <- function(parameterCd,interactive=TRUE){
   parameterCd <- formatCheckParameterCd(parameterCd, interactive=interactive)
-
-#   urlparameterCd <- "http://nwis.waterdata.usgs.gov/nwis/pmcodes/pmcodes?radio_pm_search=param_group&pm_group=All+--+include+all+parameter+groups&pm_search=&casrn_search=&srsname_search=&format=rdb&show=parameter_group_nm&show=parameter_nm&show=casrn&show=srsname&show=parameter_units"
-# #   urlparameterCd <- "http://help.waterdata.usgs.gov/code/parameter_cd_query?fmt=rdb&group_cd=%"
-#   parameterCdFile <- read.delim(  
-#     urlparameterCd, 
-#     header = TRUE, 
-#     quote="\"", 
-#     dec=".", 
-#     sep='\t',
-#     colClasses=c('character'),
-#     fill = TRUE, 
-#     comment.char="#")
-#   dataType <- parameterCdFile[1,]
-#   parameterCdFile <- parameterCdFile[-1,]
   
   parameterData <- parameterCdFile[parameterCdFile$parameter_cd %in% parameterCd,]
-#   parameterData <- parameterCdFile[parameterCdFile$parm_cd %in% parameterCd,]
 
   return(parameterData)
 }
+
+#' USGS Parameter Data Retrieval
+#'
+#' This function is being deprecated for \code{\link{getNWISPcodeInfo}}.
+#' 
+#' @param parameterCd vector of USGS parameter codes.  This is usually an 5 digit number.
+#' @param interactive logical Option for interactive mode.  If true, there is user interaction for error handling and data checks.
+#' @keywords data import USGS web service
+#' @return parameterData dataframe with all information from the USGS about the particular parameter (usually code, name, short name, units, and CAS registry numbers)
+#' @export
+#' @examples
+#' # These examples require an internet connection to run
+#' paramINFO <- getParameterInfo (c('01075','00060','00931'))
+getParameterInfo  <- function(parameterCd,interactive=TRUE){
+  
+  warning("This function is being deprecated, please use getNWISPcodeInfo")
+  
+  parameterCd <- formatCheckParameterCd(parameterCd, interactive=interactive)
+  
+  parameterData <- parameterCdFile[parameterCdFile$parameter_cd %in% parameterCd,]
+  
+  return(parameterData)
+}
\ No newline at end of file
diff --git a/R/getQWDataFromFile.r b/R/getQWDataFromFile.r
deleted file mode 100644
index c005ea65..00000000
--- a/R/getQWDataFromFile.r
+++ /dev/null
@@ -1,46 +0,0 @@
-#' Basic Data Import
-#'
-#' Imports data from user-supplied data file. Specifically used to import water quality data for use in the WRTDS package.
-#' For WRTDS usage, the first column is expected to be dates, the second column remarks (specifically < if censored data),
-#' and the third column is measured values.  There can be additional columns of data, for each column of data, there should
-#' be a remark column preceeding.
-#'
-#' @param filePath string specifying the path to the file
-#' @param fileName string name of file to open
-#' @param hasHeader logical true if the first row of data is the column headers
-#' @param separator string character that separates data cells
-#' @keywords data import file
-#' @return retval dataframe
-#' @export
-#' @examples
-#' # Examples of how to use getQWDataFromFile:
-#' # Change the file path and file name to something meaningful:
-#' filePath <- system.file("extdata", package="dataRetrieval")
-#' filePath <- paste(filePath,"/",sep="")
-#' fileName <- 'ChoptankRiverNitrate.csv'
-#' rawSampleData <- getQWDataFromFile(filePath,fileName, separator=";")
-getQWDataFromFile <- function (filePath,fileName,hasHeader=TRUE,separator=","){
-  totalPath <- paste(filePath,fileName,sep="")
-  tmp <- read.delim(  
-    totalPath, 
-    header = hasHeader,
-    sep=separator,
-    colClasses=c('character'),
-    fill = TRUE, 
-    comment.char="#")
-  
-  retval <- as.data.frame(tmp, stringsAsFactors=FALSE)
-  names(retval)[1:3] <- c("dateTime","code","value")
-  
-  if(dateFormatCheck(retval$dateTime[1])){
-    retval$dateTime <- as.Date(retval$dateTime)
-    
-    compressedData <- compressData(retval)
-    Sample <- populateSampleColumns(compressedData)
-    return (Sample)    
-  } else {
-    warning("Please adjust date formatting to 'YYYY-MM-DD'")
-    return(NA)
-  }
-
-}
diff --git a/R/getRawQWData.r b/R/getRawQWData.r
index 2a034385..5815213b 100644
--- a/R/getRawQWData.r
+++ b/R/getRawQWData.r
@@ -19,7 +19,7 @@
 #' @export
 #' @import RCurl
 #' @seealso \code{\link{getWQPData}}, \code{\link{getWQPSites}}, 
-#' \code{\link{getSTORETSampleData}}, \code{\link{retrieveNWISqwData}}, and \code{\link{basicWQPData}}
+#' \code{\link{getSTORETSampleData}}, \code{\link{retrieveNWISqwData}}, and \code{\link{readWQPData}}
 #' @examples
 #' # These examples require an internet connection to run
 #' rawSample <- retrieveWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
@@ -29,7 +29,7 @@
 retrieveWQPqwData <- function(siteNumber,parameterCd,startDate,endDate,interactive=TRUE){
 
   url <- constructNWISURL(siteNumber,parameterCd,startDate,endDate,"wqp",interactive=interactive)
-  retVal <- basicWQPData(url)
+  retVal <- readWQPData(url)
   return(retVal)
   
 }
diff --git a/R/getSTORETSampleData.R b/R/getSTORETSampleData.R
index f1a3fbe3..4a5e1f66 100644
--- a/R/getSTORETSampleData.R
+++ b/R/getSTORETSampleData.R
@@ -1,3 +1,47 @@
+#' Import Sample Data for WRTDS
+#'
+#' This function is being deprecated for \code{\link{getWQPSample}}.
+#' 
+#' @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.
+#' @keywords data import USGS WRTDS
+#' @export
+#' @return Sample dataframe
+#' @seealso \code{\link{getWQPSample}}
+#' @examples
+#' # These examples require an internet connection to run
+#' \dontrun{Sample_01075 <- getSTORETSampleData('USGS-01594440','Chloride', '', '')}
+#' \dontrun{Sample_All <- getSTORETSampleData('WIDNR_WQX-10032762','Specific conductance', '', '')}
+getSTORETSampleData <- function(siteNumber,characteristicName,startDate,endDate,interactive=TRUE){
+  
+  warning("This function is being deprecated, please use getWQPSample")
+  
+  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)
+}
+
 #' Import Sample Data for WRTDS
 #'
 #' 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}
@@ -13,13 +57,13 @@
 #' @export
 #' @return Sample dataframe
 #' @seealso \code{\link{getWQPData}}, \code{\link{getWQPSites}}, 
-#' \code{\link{retrieveWQPqwData}}, \code{\link{retrieveNWISqwData}}, and \code{\link{basicWQPData}}, 
+#' \code{\link{retrieveWQPqwData}}, \code{\link{retrieveNWISqwData}}, and \code{\link{readWQPData}}, 
 #' \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){
+#' Sample_01075 <- getWQPSample('USGS-01594440','Chloride', '', '')
+#' Sample_All <- getWQPSample('WIDNR_WQX-10032762','Specific conductance', '', '')
+getWQPSample <- function(siteNumber,characteristicName,startDate,endDate,interactive=TRUE){
   
   retval <- retrieveWQPqwData(siteNumber=siteNumber,
                               parameterCd=characteristicName,
diff --git a/R/getSampleData.r b/R/getSampleData.r
index 0ddf73fa..0f14b9fe 100644
--- a/R/getSampleData.r
+++ b/R/getSampleData.r
@@ -1,5 +1,37 @@
 #' Import Sample Data for WRTDS
 #'
+#' This function is being deprecated for \code{\link{getNWISSample}}.
+#'
+#' @param siteNumber string USGS site number.  This is usually an 8 digit number
+#' @param parameterCd string USGS parameter code.  This is usually an 5 digit number.
+#' @param startDate string starting date for data retrieval in the form YYYY-MM-DD.
+#' @param endDate string ending date for data retrieval in the form YYYY-MM-DD.
+#' @param interactive logical Option for interactive mode.  If true, there is user interaction for error handling and data checks.
+#' @keywords data import USGS WRTDS
+#' @export
+#' @return Sample dataframe
+#' @seealso \code{\link{compressData}}, \code{\link{populateSampleColumns}}, \code{\link{getNWISSample}}
+#' @examples
+#' 
+#' # These examples require an internet connection to run
+#' \dontrun{Sample_01075 <- getSampleData('01594440','01075', '1985-01-01', '1985-03-31')}
+#' \dontrun{Sample_All <- getSampleData('05114000','00915;00931', '1985-01-01', '1985-03-31')}
+#' \dontrun{Sample_Select <- getSampleData('05114000','00915;00931', '', '')}
+getSampleData <- function(siteNumber,parameterCd,startDate,endDate,interactive=TRUE){
+  
+  warning("This function is being deprecated, please use getNWISSample")
+  
+  rawSample <- retrieveNWISqwData(siteNumber,parameterCd,startDate,endDate)
+  #rawSample$dateTime <- strptime(rawSample$dateTime,"%Y-%m-%d %H:%M:%S")
+  rawSample$dateTime <- as.Date(rawSample$dateTime)
+  rawSample$site <- NULL
+  compressedData <- compressData(rawSample, interactive=interactive)
+  Sample <- populateSampleColumns(compressedData)
+  return(Sample)
+}
+
+#' Import NWIS Sample Data for EGRET analysis
+#'
 #' Imports data from NWIS web service. This function gets the data from here: \url{http://nwis.waterdata.usgs.gov/nwis/qwdata/}
 #' A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
 #' A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
@@ -14,13 +46,14 @@
 #' @keywords data import USGS WRTDS
 #' @export
 #' @return Sample dataframe
-#' @seealso \code{\link{compressData}}, \code{\link{populateSampleColumns}}
+#' @seealso \code{\link{compressData}}, \code{\link{populateSampleColumns}}, , \code{\link{getNWISSample}}
 #' @examples
 #' # These examples require an internet connection to run
-#' Sample_01075 <- getSampleData('01594440','01075', '1985-01-01', '1985-03-31')
-#' Sample_All <- getSampleData('05114000','00915;00931', '1985-01-01', '1985-03-31')
-#' Sample_Select <- getSampleData('05114000','00915;00931', '', '')
-getSampleData <- function(siteNumber,parameterCd,startDate,endDate,interactive=TRUE){
+#' Sample_01075 <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31')
+#' Sample_All <- getNWISSample('05114000','00915;00931', '1985-01-01', '1985-03-31')
+#' Sample_Select <- getNWISSample('05114000','00915;00931', '', '')
+getNWISSample <- function(siteNumber,parameterCd,startDate,endDate,interactive=TRUE){
+  
   rawSample <- retrieveNWISqwData(siteNumber,parameterCd,startDate,endDate)
   #rawSample$dateTime <- strptime(rawSample$dateTime,"%Y-%m-%d %H:%M:%S")
   rawSample$dateTime <- as.Date(rawSample$dateTime)
@@ -29,3 +62,5 @@ getSampleData <- function(siteNumber,parameterCd,startDate,endDate,interactive=T
   Sample <- populateSampleColumns(compressedData)
   return(Sample)
 }
+
+
diff --git a/R/getSampleDataFromFile.r b/R/getSampleDataFromFile.r
index c5b83012..89d90742 100644
--- a/R/getSampleDataFromFile.r
+++ b/R/getSampleDataFromFile.r
@@ -1,5 +1,33 @@
 #' Import Sample Data for WRTDS
 #'
+#' This function is being deprecated for \code{\link{getUserSample}}.
+#'
+#' @param filePath string specifying the path to the file
+#' @param fileName string name of file to open
+#' @param hasHeader logical true if the first row of data is the column headers
+#' @param separator string character that separates data cells
+#' @param interactive logical Option for interactive mode.  If true, there is user interaction for error handling and data checks.
+#' @keywords data import file
+#' @keywords data import USGS WRTDS
+#' @export
+#' @return Sample dataframe
+#' @examples
+#' filePath <- system.file("extdata", package="dataRetrieval")
+#' filePath <- paste(filePath,"/",sep="")
+#' fileName <- 'ChoptankRiverNitrate.csv'
+#' \dontrun{Sample <- getSampleDataFromFile(filePath,fileName, separator=";",interactive=FALSE)}
+getSampleDataFromFile <- function (filePath,fileName,hasHeader=TRUE,separator=",", interactive=TRUE){
+  
+  warning("This function is being deprecated, please use getUserSample")
+  
+  data <- getDataFromFile(filePath,fileName,hasHeader=hasHeader,separator=separator)
+  compressedData <- compressData(data, interactive=interactive)
+  Sample <- populateSampleColumns(compressedData)
+  return(Sample)
+}
+
+#' Import user sample data for EGRET analysis
+#'
 #' Imports data from a user-supplied file, and converts it to a Sample data frame (including summing multiple constituents), appropriate for WRTDS calculations. See
 #' section 3.4 of the vignette for more details.
 #'
@@ -10,15 +38,16 @@
 #' @param interactive logical Option for interactive mode.  If true, there is user interaction for error handling and data checks.
 #' @keywords data import file
 #' @keywords data import USGS WRTDS
+#' @seealso \code{\link{compressData}}, \code{\link{populateSampleColumns}}
 #' @export
 #' @return Sample dataframe
 #' @examples
 #' filePath <- system.file("extdata", package="dataRetrieval")
 #' filePath <- paste(filePath,"/",sep="")
 #' fileName <- 'ChoptankRiverNitrate.csv'
-#' Sample <- getSampleDataFromFile(filePath,fileName, separator=";",interactive=FALSE)
-getSampleDataFromFile <- function (filePath,fileName,hasHeader=TRUE,separator=",", interactive=TRUE){
-  data <- getQWDataFromFile(filePath,fileName,hasHeader=hasHeader,separator=separator)
+#' Sample <- getUserSample(filePath,fileName, separator=";",interactive=FALSE)
+getUserSample <- function (filePath,fileName,hasHeader=TRUE,separator=",", interactive=TRUE){
+  data <- getDataFromFile(filePath,fileName,hasHeader=hasHeader,separator=separator)
   compressedData <- compressData(data, interactive=interactive)
   Sample <- populateSampleColumns(compressedData)
   return(Sample)
diff --git a/R/getSiteFileData.r b/R/getSiteFileData.r
index c8f71f56..bc70fa58 100644
--- a/R/getSiteFileData.r
+++ b/R/getSiteFileData.r
@@ -8,9 +8,9 @@
 #' @export
 #' @examples
 #' # These examples require an internet connection to run
-#' siteINFO <- getSiteFileData('05114000')
-#' siteINFOMulti <- getSiteFileData(c('05114000','09423350'))
-getSiteFileData <- function(siteNumber){
+#' siteINFO <- getNWISSiteInfo('05114000')
+#' siteINFOMulti <- getNWISSiteInfo(c('05114000','09423350'))
+getNWISSiteInfo <- function(siteNumber){
   
   siteNumber <- paste(siteNumber,collapse=",")
   urlSitefile <- paste("http://waterservices.usgs.gov/nwis/site/?format=rdb&siteOutput=Expanded&sites=",siteNumber,sep = "")
@@ -55,3 +55,64 @@ getSiteFileData <- function(siteNumber){
     return(NA)
   }
 }
+
+
+#' USGS Site File Data Retrieval
+#'
+#' This function is being deprecated for \code{\link{getNWISSiteInfo}}.
+#' 
+#' @param siteNumber string USGS site number.  This is usually an 8 digit number
+#' @keywords data import USGS web service
+#' @return retval dataframe with all information found in the expanded site file
+#' @export
+#' @examples
+#' # These examples require an internet connection to run
+#' \dontrun{siteINFO <- getSiteFileData('05114000')}
+#' \dontrun{siteINFOMulti <- getSiteFileData(c('05114000','09423350'))}
+getSiteFileData <- function(siteNumber){
+  
+  warning("This function is being deprecated, please use getNWISSiteInfo")
+  
+  siteNumber <- paste(siteNumber,collapse=",")
+  urlSitefile <- paste("http://waterservices.usgs.gov/nwis/site/?format=rdb&siteOutput=Expanded&sites=",siteNumber,sep = "")
+  
+  doc = tryCatch({
+    h <- basicHeaderGatherer()
+    doc <- getURL(urlSitefile, headerfunction = h$update)
+    
+  }, warning = function(w) {
+    message(paste("URL caused a warning:", urlSitefile))
+    message(w)
+  }, error = function(e) {
+    message(paste("URL does not seem to exist:", urlSitefile))
+    message(e)
+    return(NA)
+  }) 
+  
+  if(h$value()["Content-Type"] == "text/plain;charset=UTF-8"){
+    
+    SiteFile <- read.delim(
+      textConnection(doc),
+      header = TRUE,
+      quote="\"",
+      dec=".",
+      sep='\t',
+      colClasses=c('character'),
+      fill = TRUE,
+      comment.char="#")
+    
+    INFO <- SiteFile[-1,]
+    names(INFO) <- gsub("_",".",names(INFO))
+    
+    INFO$queryTime <- Sys.time()
+    INFO$dec.lat.va <- as.numeric(INFO$dec.lat.va)
+    INFO$dec.long.va <- as.numeric(INFO$dec.long.va)
+    INFO$alt.va <- as.numeric(INFO$alt.va)
+    
+    return(INFO)
+  } else {
+    message(paste("URL caused an error:", urlSitefile))
+    message("Content-Type=",h$value()["Content-Type"])
+    return(NA)
+  }
+}
diff --git a/R/getWQPData.r b/R/getWQPData.r
index 2a6c567d..cd9902d5 100644
--- a/R/getWQPData.r
+++ b/R/getWQPData.r
@@ -34,7 +34,7 @@ getWQPData <- function(...){
                    urlCall,
                    "&mimeType=tsv",sep = "")
 
-  retVal <- basicWQPData(urlCall)
+  retVal <- readWQPData(urlCall)
   return(retVal)
   
 }
\ No newline at end of file
diff --git a/R/populateParameterINFO.r b/R/populateParameterINFO.r
index 36f80943..f1a5e802 100644
--- a/R/populateParameterINFO.r
+++ b/R/populateParameterINFO.r
@@ -9,9 +9,9 @@
 #' @export
 #' @examples
 #' #This example requires an internet connection to run
-#' INFO <- getSiteFileData('01594440')
+#' INFO <- getNWISSiteInfo('01594440')
 #' parameterCd <- "01075"
-#' parameterData <- getParameterInfo(parameterCd)
+#' parameterData <- getNWISPcodeInfo(parameterCd)
 #' INFO$param.nm <- parameterData$parameter_nm
 #' INFO$param.units <- parameterData$parameter_units
 #' INFO$paramShortName <- parameterData$srsname
diff --git a/R/populateSiteINFO.r b/R/populateSiteINFO.r
index 49f8f0e2..caa9ce5f 100644
--- a/R/populateSiteINFO.r
+++ b/R/populateSiteINFO.r
@@ -9,7 +9,7 @@
 #' @export
 #' @examples
 #' #This example requires an internet connection to run
-#' INFO <- getSiteFileData('01594440')
+#' INFO <- getNWISSiteInfo('01594440')
 #' siteNumber <- "01594440"
 #' siteINFO <- populateSiteINFO(INFO, siteNumber)
 populateSiteINFO <- function(INFO, siteNumber,interactive=TRUE){
diff --git a/R/renameColumns.R b/R/renameColumns.R
index e1a4cf7f..9ec3a6ff 100644
--- a/R/renameColumns.R
+++ b/R/renameColumns.R
@@ -26,7 +26,7 @@ renameColumns <- function(rawData){
   pCodes <- sapply(strsplit(dataCol_names, "_"), function(x) x[2])
   statCd <- sapply(strsplit(dataCol_names, "_"), function(x) x[3])
   
-  pcodeINFO <- getParameterInfo(pCodes,interactive=FALSE)
+  pcodeINFO <- getNWISPcodeInfo(pCodes,interactive=FALSE)
   multipleCodes <- anyDuplicated(pCodes)
   
   statCd <- sub("00001", "_Max", statCd)
-- 
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