diff --git a/R/checkStartEndDate.r b/R/checkStartEndDate.r
deleted file mode 100644
index 4754012283b3526d16f9c91248aaa9e2726dce69..0000000000000000000000000000000000000000
--- a/R/checkStartEndDate.r
+++ /dev/null
@@ -1,37 +0,0 @@
-#' checkStartEndDate
-#'
-#' Checks that the start date is before the end date. If not, it will give the user the opportunity to correct, otherwise will create a warning.
-#'
-#' @param startDate string
-#' @param endDate string
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords WRTDS flow
-#' @return vector where first value is startDate, second is endDate
-#' @export
-#' @examples
-#' startDate <- '1985-01-01'
-#' endDate <- '1990-01-01'
-#' checkStartEndDate(startDate, endDate)
-checkStartEndDate <- function(startDate, endDate,interactive=TRUE){
- start <- as.Date("1850-01-01")
- end <- as.Date(Sys.Date())
-
- if (nzchar(startDate)) start <- as.Date(startDate)
- if (nzchar(endDate)) end <- as.Date(endDate)
- if (start > end) {
- if (interactive){
- cat ("Start date must be before end date, you entered Start = ", startDate, " End = ", endDate, "\n")
- cat ("please re-enter startDate (YYYY-MM-DD) - hit Enter for earliest date as startDate: \n")
- startDate <- readline()
- cat("Please re-enter endDate (YYYY-MM-DD) - hit Enter for latest date as endDate: \n")
- endDate <- readline()
- } else {
- warningMessage <- "Starting date was not before ending date, dates will be ignored"
- warning(warningMessage)
- startDate <- as.Date("1851-01-01")
- endDate <- as.Date(Sys.Date())
- }
-
- }
- return(c(startDate,endDate))
-}
diff --git a/R/compressData.r b/R/compressData.r
deleted file mode 100644
index 8f944da52846869945b42f8565cead6fa3089854..0000000000000000000000000000000000000000
--- a/R/compressData.r
+++ /dev/null
@@ -1,93 +0,0 @@
-#' Compress sample data frame
-#'
-#' Using raw data that has at least dateTime, value, code, populates the measured data portion of the Sample data frame used in WRTDS
-#' ConcLow = Lower bound for an observed concentration
-#' ConcHigh = Upper bound for an observed concentration
-#' ConcAve = Average of ConcLow and ConcHigh. If ConcLow is NA, then ConcAve = ConcHigh/2
-#' Uncen = 1 if uncensored, 0 if censored
-#'
-#' @param data dataframe contains at least dateTime, value, code columns
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords WRTDS flow
-#' @return dataframe returnDataFrame data frame containing dateTime, ConcHigh, ConcLow, Uncen, ConcAve
-#' @export
-#' @examples
-#' dateTime <- c('1985-01-01', '1985-01-02', '1985-01-03')
-#' comment1 <- c("","","")
-#' value1 <- c(1,2,3)
-#' comment2 <- c("","<","")
-#' value2 <- c(2,3,4)
-#' comment3 <- c("","","<")
-#' value3 <- c(3,4,5)
-#' dataInput <- data.frame(dateTime, comment1, value1,
-#' comment2, value2,
-#' comment3, value3, stringsAsFactors=FALSE)
-#' compressData(dataInput)
-compressData <- function(data, interactive=TRUE){
-
- data <- as.data.frame(data, stringsAsFactors=FALSE)
- numColumns <- ncol(data)
- numDataColumns <- (numColumns-1)/2
- lowConcentration <- rep(0,nrow(data))
- highConcentration <- rep(0,nrow(data))
- uncensored <- rep(0,nrow(data))
-
- i <- 1
- while (i <= numDataColumns) {
- code <- data[2*i]
- value <- data[2*i+1]
- value <- as.numeric(unlist(value))
- value[is.na(value)] <- 0
- returnDataFrame <- as.data.frame(matrix(ncol=2,nrow=nrow(code)))
- colnames(returnDataFrame) <- c('code','value')
- returnDataFrame$code <- code[[1]]
- returnDataFrame$code <- ifelse(is.na(returnDataFrame$code),"",returnDataFrame$code)
- returnDataFrame$value <- value
- concentrationColumns <- populateConcentrations(returnDataFrame)
- lowConcentration <- lowConcentration + concentrationColumns$ConcLow
- highConcentration <- highConcentration + concentrationColumns$ConcHigh
- i <- i + 1
- }
-
- names(data) <- c('dateTime', 'code', 'value')
- returnDataFrame <- as.data.frame(matrix(ncol=3,nrow=nrow(data)))
- names(returnDataFrame) <- c('dateTime', 'ConcLow', 'ConcHigh')
-
- data$dateTime <- as.character(data$dateTime)
- if(dateFormatCheck(data$dateTime)){
- returnDataFrame$dateTime <- as.Date(data$dateTime)
- } else {
- data$dateTime <- as.Date(data$dateTime,format="%m/%d/%Y")
- returnDataFrame$dateTime <- as.Date(data$dateTime,format="%m/%d/%Y")
- }
- returnDataFrame$ConcLow <- as.numeric(lowConcentration)
- returnDataFrame$ConcHigh <- as.numeric(highConcentration)
- Uncen1<-ifelse(returnDataFrame$ConcLow==returnDataFrame$ConcHigh,1,0)
- returnDataFrame$Uncen<-ifelse(is.na(returnDataFrame$ConcLow),0,Uncen1)
-
- flaggedData1 <- returnDataFrame[(returnDataFrame$ConcLow == 0 & returnDataFrame$ConcHigh == 0),]
- returnDataFrame <- returnDataFrame[!(returnDataFrame$ConcLow == 0 & returnDataFrame$ConcHigh == 0),]
-
- if (nrow(flaggedData1) > 0){
- WarningMessage <- paste("Deleted ", nrow(flaggedData1), " rows of data because concentration was reported as 0.0, the program is unable to interpret that result and is therefore deleting it.", sep="")
- warning(WarningMessage)
- if (interactive){
- cat("Deleted Rows:\n")
- print(flaggedData1)
- }
- }
-
- flaggedData2 <- returnDataFrame[(returnDataFrame$ConcLow > returnDataFrame$ConcHigh),]
- returnDataFrame <- returnDataFrame[(returnDataFrame$ConcLow <= returnDataFrame$ConcHigh),]
-
- if (nrow(flaggedData2) > 0){
- WarningMessage <- paste("Deleted ", nrow(flaggedData2), " rows of data because the high concentration was reported lower than the low concentration, the program is unable to interpret that result and is therefore deleting it.", sep="")
- warning(WarningMessage)
- if (interactive){
- cat("Deleted Rows:\n")
- print(flaggedData2)
- }
- }
-
- return(returnDataFrame)
-}
diff --git a/R/dataOverview.r b/R/dataOverview.r
deleted file mode 100644
index 85c811376875aa5a37e7cbbfcacfb79d010c3b18..0000000000000000000000000000000000000000
--- a/R/dataOverview.r
+++ /dev/null
@@ -1,37 +0,0 @@
-#' Data Overview for WRTDS
-#'
-#' Gives a summary of data to be used for WRTDS analysis
-#'
-#' @param Daily dataframe
-#' @param Sample dataframe
-#' @keywords data import USGS WRTDS
-#' @export
-#' @seealso \code{\link{mergeReport}}
-#' @examples
-#' # These examples require an internet connection to run
-#' exDaily <- getNWISDaily('01594440','00060', '1985-01-01', '1985-03-31', interactive=FALSE)
-#' exSample <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31', interactive=FALSE)
-#' dataOverview(Daily = exDaily, Sample = exSample)
-dataOverview <- function(Daily, Sample ){
-
- numDays<-length(Daily$Date)
- numSamples<-length(Sample$Date)
- numYears<-round(numDays/365.25,digits=0)
- cat("\n Discharge Record is",numDays,"days long, which is",numYears,"years")
- cat("\n First day of the discharge record is", as.character(Daily$Date[1]),"and last day is",as.character(Daily$Date[numDays]))
- cat("\n The water quality record has",numSamples,"samples")
- cat("\n The first sample is from", as.character(Sample$Date[1]),"and the last sample is from",as.character(Sample$Date[numSamples]))
- if(Sample$Date[1]<Daily$Date[1]) cat("\n WE HAVE A PROBLEM first sample is from before the first daily discharge")
- if(Sample$Date[numSamples]>Daily$Date[numDays]) cat("\n WE HAVE A PROBLEM last sample is from after the last daily discharge")
- Qmin<-signif(min(Daily$Q),digits=3)
- Qmean<-signif(mean(Daily$Q),digits=3)
- Qmax<-signif(max(Daily$Q),digits=3)
- Cmin<-signif(min(Sample$ConcHigh),digits=2)
- Cmean<-signif(mean(Sample$ConcHigh),digits=2)
- Cmax<-signif(max(Sample$ConcHigh),digits=2)
- cat("\n Discharge: Minimum, mean and maximum",Qmin,Qmean,Qmax)
- cat("\n Concentration: Minimum, mean and maximum",Cmin,Cmean,Cmax)
- pct<-sum(Sample$Uncen)
- pct<-((numSamples-pct)/numSamples)*100
- cat("\n Percentage of the sample values that are censored is",signif(pct,digits=2),"%")
-}
diff --git a/R/dateFormatCheck.r b/R/dateFormatCheck.r
deleted file mode 100644
index c3f9dbdf3858a14b51d145347446955280f5b3f1..0000000000000000000000000000000000000000
--- a/R/dateFormatCheck.r
+++ /dev/null
@@ -1,30 +0,0 @@
-#' Check date format
-#'
-#' Checks to see if format is YYYY-MM-DD. Also performs a few other date checks.
-#'
-#' @param date string
-#' @keywords WRTDS flow
-#' @return condition logical if TRUE,
-#' @export
-#' @examples
-#' date <- '1985-01-01'
-#' dateFormatCheck(date)
-#' dateWrong <- '1999/1/7'
-#' dateFormatCheck(dateWrong)
-dateFormatCheck <- function(date){ # checks for the format YYYY-MM-DD
- parts <- strsplit(date,"-",fixed=TRUE)
- condition <- FALSE
- if (length(parts[[1]])>1) {
- if (nchar(parts[[1]][1]) == 4 && nchar(parts[[1]][2]) == 2 && nchar(parts[[1]][3]) == 2){
- testYear <- as.numeric(parts[[1]][1])
- testMonth <- as.numeric(parts[[1]][2])
- testDay <- as.numeric(parts[[1]][3])
- if (!is.na(testYear) && !is.na(testMonth) && !is.na(testDay)){
- if (testMonth <= 12 && testDay <= 31){
- condition <- TRUE
- }
- }
- }
- }
- return(condition)
-}
diff --git a/R/formatCheckDate.r b/R/formatCheckDate.r
deleted file mode 100644
index 6d32a0027fa8c628b59dda55e2f6636b52319414..0000000000000000000000000000000000000000
--- a/R/formatCheckDate.r
+++ /dev/null
@@ -1,30 +0,0 @@
-#' formatCheckDate
-#'
-#' Response to the date format checker. If the date is not formated correctly, it will give the user the opportunity to correct, otherwise will create a warning.
-#'
-#' @param Date string
-#' @param dateString string used in either error message or interactive message. An example would be "startDate"
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords WRTDS flow
-#' @return condition logical if TRUE,
-#' @export
-#' @examples
-#' Date <- '1985-01-01'
-#' dateString <- 'startDate'
-#' formatCheckDate(Date, dateString, interactive = FALSE)
-formatCheckDate <- function(Date, dateString,interactive=TRUE){
- if(nzchar(Date)){
- if (!dateFormatCheck(Date)){
- if (interactive){
- cat("Date must be entered in the form YYYY-MM-DD (no quotes), you entered: ", Date, "as the startDate.\n")
- cat("Please re-enter ", dateString, ":\n")
- Date <- readline()
- } else {
- warningMessage <- paste(dateString, " must be entered in the form YYYY-MM-DD, you entered: ", Date, ". ", dateString, " will be ignored",sep="")
- warning(warningMessage)
- Date <- ""
- }
- }
- }
- return(Date)
-}
diff --git a/R/formatCheckParameterCd.r b/R/formatCheckParameterCd.r
deleted file mode 100644
index 20b1ee0763ffc6b4fe803f05fdb3d81449f557be..0000000000000000000000000000000000000000
--- a/R/formatCheckParameterCd.r
+++ /dev/null
@@ -1,44 +0,0 @@
-#' formatCheckParameterCd
-#'
-#' Checks that the parameter code is 5 digits. If it is less, it will pad the string with zeros. If more, ask the user to re-enter.
-#'
-#' @param parameterCd string to check
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords WRTDS flow
-#' @return parameterCd string
-#' @export
-#' @examples
-#' pCode <- '01234'
-#' formatCheckParameterCd(pCode)
-formatCheckParameterCd <- function(parameterCd, interactive=TRUE){ #checks for a 5 digit number
-
- pCodeReturn <- rep(NA,length(parameterCd))
- index <- 1
-
- for (i in parameterCd){
-
- if (nchar(i) < 5){
- if (interactive){
- message("Most USGS parameter codes are 5 digits long, you entered a ", nchar(i), " digit number = ", i , ".\n")
-
- i <- padVariable(i,5)
- message("The following parameter code will be used instead:",i,"\n")
- message("If you would like to change the parameter code, enter it here (no quotes), otherwise hit return:\n")
- tempparameterCd <- readline()
- if (nzchar(tempparameterCd)){
- i <- tempparameterCd
- }
- } else {
- tempText <- padVariable(i,5)
- warningMessage <- paste("Most USGS parameter codes are 5 digits long, you entered ",
- i , ".\n",tempText," will be used instead", sep="")
- warning(warningMessage)
- i <- padVariable(i,5)
- }
-
- }
- pCodeReturn[index] <- i
- index <- index + 1
- }
- return(pCodeReturn)
-}
diff --git a/R/getDVData.r b/R/getDVData.r
deleted file mode 100644
index 8ddc694c1806d11e2b83053cd6c37249d651f98d..0000000000000000000000000000000000000000
--- a/R/getDVData.r
+++ /dev/null
@@ -1,39 +0,0 @@
-#' 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}
-#'
-#' @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{getNWISdvData}}, \code{\link{populateDaily}}
-#' @examples
-#' # These examples require an internet connection to run
-#' 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 <- getNWISdvData(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)
-}
diff --git a/R/getDailyDataFromFile.r b/R/getDailyDataFromFile.r
deleted file mode 100644
index e435fc20d887af5c4d81d581da56c16fa7a3fb79..0000000000000000000000000000000000000000
--- a/R/getDailyDataFromFile.r
+++ /dev/null
@@ -1,65 +0,0 @@
-#' Import Daily Data for WRTDS
-#'
-#' 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
-#' @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"
-#' \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]
- 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")
- }
- names(data) <- c("dateTime", "value")
- localDaily <- populateDaily(data,qConvert, interactive=interactive)
- localDaily <- localDaily[!is.na(localDaily$Q),]
- return(localDaily)
-}
diff --git a/R/getDataFromFile.r b/R/getDataFromFile.r
deleted file mode 100644
index 1bffc892f363f1626142202417723b937cf8c94f..0000000000000000000000000000000000000000
--- a/R/getDataFromFile.r
+++ /dev/null
@@ -1,46 +0,0 @@
-#' Basic Data Import for Water Flow Data
-#'
-#' Imports data from user-supplied data file. Specifically used to import water flow data for use in the WRTDS package.
-#' For WRTDS usage, the first column is expected to be dates, the second column measured values.
-#' The third column is optional, it contains any remark codes.
-#'
-#' @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 with dateTime, value, and code columns
-#' @export
-#' @examples
-#' # Examples of how to use getDataFromFile:
-#' # Change the file path and file name to something meaningful:
-#' filePath <- system.file("extdata", package="dataRetrieval")
-#' filePath <- paste(filePath,"/",sep="")
-#' fileName <- 'ChoptankRiverFlow.txt'
-#' ChopData <- getDataFromFile(filePath,fileName, separator="\t")
-getDataFromFile <- function (filePath,fileName,hasHeader=TRUE,separator=","){
- totalPath <- paste(filePath,fileName,sep="");
- retval <- read.delim(
- totalPath,
- header = hasHeader,
- sep=separator,
- colClasses=c('character'),
- fill = TRUE,
- comment.char="#")
-
- if(ncol(retval) == 2){
- numCol <- 2
- } else {
- numCol <- seq(from = 3,to = ncol(retval), by = 2)
- }
-
- if(dateFormatCheck(retval[,1])){
- retval[,1] <- as.Date(retval[,1])
- } else {
- retval[,1] <- as.Date(retval[,1],format="%m/%d/%Y")
- }
-
- retval[,numCol] <- sapply(numCol, function(x) as.numeric(retval[,x]))
-
- return (retval)
-}
diff --git a/R/getMetaData.r b/R/getMetaData.r
deleted file mode 100644
index 281d558c75afa9b0e76675df357857c2ca0ba032..0000000000000000000000000000000000000000
--- a/R/getMetaData.r
+++ /dev/null
@@ -1,255 +0,0 @@
-#' Import Metadata for USGS Data
-#'
-#' Populates INFO data frame for EGRET study. If either station number or parameter code supplied, imports data about a particular USGS site 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/}
-#' If either station number or parameter code is not supplied, the user will be asked to input data.
-#' Additionally, the user will be asked for:
-#' staAbbrev - station abbreviation, will be used in naming output files and for structuring batch jobs
-#' constitAbbrev - constitute abbreviation
-#'
-#' @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 interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords data import USGS web service
-#' @export
-#' @return INFO dataframe with at least param.nm, param.units, parameShortName, paramNumber
-#' @examples
-#' # These examples require an internet connection to run
-#' # Automatically gets information about site 05114000 and temperature, no interaction with user
-#' INFO <- getNWISInfo('05114000','00010')
-getNWISInfo <- function(siteNumber, parameterCd,interactive=TRUE){
- if (nzchar(siteNumber)){
- INFO <- getNWISSiteInfo(siteNumber)
- } else {
- INFO <- as.data.frame(matrix(ncol = 2, nrow = 1))
- names(INFO) <- c('site.no', 'shortName')
- }
- INFO <- populateSiteINFO(INFO, siteNumber, interactive=interactive)
-
- if (nzchar(parameterCd)){
- parameterData <- getNWISPcodeInfo(parameterCd,interactive=interactive)
- INFO$param.nm <- parameterData$parameter_nm
- INFO$param.units <- parameterData$parameter_units
- INFO$paramShortName <- parameterData$srsname
- INFO$paramNumber <- parameterData$parameter_cd
- }
-
- INFO <- populateParameterINFO(parameterCd, INFO, interactive=interactive)
- INFO$paStart <- 10
- INFO$paLong <- 12
-
- return(INFO)
-}
-
-#' Import Metadata for Water Quality Portal Data
-#'
-#' Populates INFO data frame for EGRET study. If siteNumber or parameter code (for USGS) or characteristic name
-#' (for non-USGS) is provided, the function will make a call to the Water Quality Portal to get metadata information.
-#' staAbbrev - station abbreviation, will be used in naming output files and for structuring batch jobs
-#' constitAbbrev - constitute abbreviation
-#'
-#' @param siteNumber string site number.
-#' @param parameterCd string USGS parameter code or characteristic name.
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords data import USGS web service WRTDS
-#' @export
-#' @return INFO dataframe with agency, site, dateTime, value, and code columns
-#' @examples
-#' # These examples require an internet connection to run
-#' # Automatically gets information about site 01594440 and temperature, no interaction with user
-#' nameToUse <- 'Specific conductance'
-#' pcodeToUse <- '00095'
-#' \dontrun{
-#' INFO <- getWQPInfo('USGS-04024315',pcodeToUse,interactive=TRUE)
-#' INFO2 <- getWQPInfo('WIDNR_WQX-10032762',nameToUse)
-#' # To adjust the label names:
-#' INFO$shortName <- "Little"
-#' INFO$paramShortName <- "SC"
-#' }
-getWQPInfo <- function(siteNumber, parameterCd, interactive=FALSE){
-
- #Check for pcode:
- pCodeLogic <- (all(nchar(parameterCd) == 5) & suppressWarnings(all(!is.na(as.numeric(parameterCd)))))
-
- if (pCodeLogic){
-
- siteInfo <- getWQPSites(siteid=siteNumber, pCode=parameterCd)
-
- parameterData <- getNWISPcodeInfo(parameterCd = parameterCd)
-
- siteInfo$param.nm <- parameterData$parameter_nm
- siteInfo$param.units <- parameterData$parameter_units
- siteInfo$paramShortName <- parameterData$srsname
- siteInfo$paramNumber <- parameterData$parameter_cd
- siteInfo$constitAbbrev <- parameterData$parameter_cd
-
- } else {
- siteInfo <- getWQPSites(siteid=siteNumber, characteristicName=parameterCd)
-
- siteInfo$param.nm <- parameterCd
- siteInfo$param.units <- ""
- siteInfo$paramShortName <- parameterCd
- siteInfo$paramNumber <- ""
- siteInfo$constitAbbrev <- parameterCd
- }
-
- siteInfo$station.nm <- siteInfo$MonitoringLocationName
- siteInfo$shortName <- siteInfo$station.nm
- siteInfo$site.no <- siteInfo$MonitoringLocationIdentifier
-
- if(interactive){
- cat("Your site for data is", as.character(siteInfo$site.no),".\n")
- if (!nzchar(siteInfo$station.nm)){
- cat("No station name was listed for site: ", siteInfo$site.no, ". Please enter a station name here(no quotes): \n")
- siteInfo$station.nm <- readline()
- }
- cat("Your site name is", siteInfo$station.nm,",")
- cat("but you can modify this to a short name in a style you prefer. \nThis name will be used to label graphs and tables. \n")
- cat("If you want the program to use the name given above, just do a carriage return, otherwise enter the preferred short name(no quotes):\n")
- siteInfo$shortName <- readline()
- if (!nzchar(siteInfo$shortName)) siteInfo$shortName <- siteInfo$station.nm
-
- cat("Your water quality data are for parameter number", siteInfo$paramNumber, "which has the name:'", siteInfo$param.nm, "'.\n")
- cat("Typically you will want a shorter name to be used in graphs and tables. The suggested short name is:'", siteInfo$paramShortName, "'.\n")
- cat("If you would like to change the short name, enter it here, otherwise just hit enter (no quotes):")
- shortNameTemp <- readline()
- if (nchar(shortNameTemp)>0) siteInfo$paramShortName <- shortNameTemp
- cat("The units for the water quality data are: ", siteInfo$param.units, ".\n")
- cat("It is helpful to set up a constiuent abbreviation when doing multi-constituent studies, enter a unique id (three or four characters should work something like tn or tp or NO3).\nIt is case sensitive. Even if you don't feel you need an abbreviation you need to enter something (no quotes):\n")
- siteInfo$constitAbbrev <- readline()
- }
-
- if (interactive){
- cat("It is helpful to set up a station abbreviation when doing multi-site studies, enter a unique id (three or four characters should work).\nIt is case sensitive. Even if you don't feel you need an abbreviation for your site you need to enter something(no quotes):\n")
- siteInfo$staAbbrev <- readline()
- } else {
- siteInfo$staAbbrev <- NA
- }
-
- if(siteInfo$DrainageAreaMeasure.MeasureUnitCode == "sq mi"){
- siteInfo$drainSqKm <- as.numeric(siteInfo$DrainageAreaMeasure.MeasureValue) * 2.5899881
- } else {
- warning("Please check the units for drainage area. The value for INFO$drainSqKm needs to be in square kilometers,")
- siteInfo$drainSqKm <- as.numeric(siteInfo$DrainageAreaMeasure.MeasureValue)
- }
-
- if(interactive){
- if(is.na(siteInfo$drainSqKm)){
- cat("No drainage area was listed in the WQP site file for this site.\n")
- cat("Please enter the drainage area, you can enter it in the units of your choice.\nEnter the area, then enter drainage area code, \n1 is square miles, \n2 is square kilometers, \n3 is acres, \n4 is hectares.\n")
- cat("Area(no quotes):\n")
- siteInfo$drain.area.va <- readline()
- siteInfo$drain.area.va <- as.numeric(siteInfo$drain.area.va)
- cat("Unit Code (1-4, no quotes):")
- qUnit <- readline()
- qUnit <- as.numeric(qUnit)
- conversionVector <- c(2.5899881, 1.0, 0.0040468564, 0.01)
- siteInfo$drainSqKm <- siteInfo$drain.area.va * conversionVector[qUnit]
- }
- }
-
- siteInfo$queryTime <- Sys.time()
- siteInfo$paStart <- 10
- siteInfo$paLong <- 12
-
- return(siteInfo)
-}
-
-
-
-#' Import Metadata from User-Generated File
-#'
-#' Populates INFO data frame for EGRET study. Accepts a user generated file with any metadata that might
-#' be important for the analysis.
-#' Additionally, EGRET analysis requires:"drainSqKm", "staAbbrev", "constitAbbrev",
-#' "param.units", "paramShortName","shortName". If interactive=TRUE, the function will ask for these
-#' fields if they aren't supplied in the file.
-#'
-#' @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 USGS web service WRTDS
-#' @export
-#' @return INFO dataframe with agency, site, dateTime, value, and code columns
-#' @examples
-#' filePath <- system.file("extdata", package="dataRetrieval")
-#' filePath <- paste(filePath,"/",sep="")
-#' fileName <- 'infoTest.csv'
-#' INFO <- getUserInfo(filePath,fileName, separator=",",interactive=FALSE)
-getUserInfo <- function(filePath,fileName,hasHeader=TRUE,separator=",",interactive=FALSE){
-
- totalPath <- paste(filePath,fileName,sep="");
- siteInfo <- read.delim(
- totalPath,
- header = hasHeader,
- sep=separator,
- colClasses=c('character'),
- fill = TRUE,
- comment.char="#")
-
- if(interactive){
-
- if (!nzchar(siteInfo$station.nm)){
- cat("No station name was listed. Please enter a station name here(no quotes): \n")
- siteInfo$station.nm <- readline()
- }
- cat("Your site name is", siteInfo$station.nm,",")
- cat("but you can modify this to a short name in a style you prefer. \nThis name will be used to label graphs and tables. \n")
- cat("If you want the program to use the name given above, just do a carriage return, otherwise enter the preferred short name(no quotes):\n")
- siteInfo$shortName <- readline()
- if (!nzchar(siteInfo$shortName)) siteInfo$shortName <- siteInfo$station.nm
-
- if (!nzchar(siteInfo$param.nm)){
- cat("No water quality parameter name was listed.\nPlease enter the name here(no quotes): \n")
- siteInfo$param.nm <- readline()
- }
-
- cat("Your water quality data are for '", siteInfo$param.nm, "'.\n")
- cat("Typically you will want a shorter name to be used in graphs and tables. The suggested short name is:'", siteInfo$paramShortName, "'.\n")
- cat("If you would like to change the short name, enter it here, otherwise just hit enter (no quotes):")
- shortNameTemp <- readline()
-
- if (nchar(shortNameTemp)>0) siteInfo$paramShortName <- shortNameTemp
-
- if (!nzchar(siteInfo$param.units)){
- cat("No water quality parameter unit was listed.\nPlease enter the units here(no quotes): \n")
- siteInfo$param.nm <- readline()
- }
- cat("The units for the water quality data are: ", siteInfo$param.units, ".\n")
- cat("It is helpful to set up a constiuent abbreviation when doing multi-constituent studies, enter a unique id (three or four characters should work something like tn or tp or NO3).\nIt is case sensitive. Even if you don't feel you need an abbreviation you need to enter something (no quotes):\n")
- siteInfo$constitAbbrev <- readline()
-
- cat("It is helpful to set up a station abbreviation when doing multi-site studies, enter a unique id (three or four characters should work).\nIt is case sensitive. Even if you don't feel you need an abbreviation for your site you need to enter something(no quotes):\n")
- siteInfo$staAbbrev <- readline()
-
- if(is.na(siteInfo$drainSqKm)){
- cat("No drainage area was listed as a column named 'drainSqKm'.\n")
- cat("Please enter the drainage area, you can enter it in the units of your choice.\nEnter the area, then enter drainage area code, \n1 is square miles, \n2 is square kilometers, \n3 is acres, \n4 is hectares.\n")
- cat("Area(no quotes):\n")
- siteInfo$drain.area.va <- readline()
- siteInfo$drain.area.va <- as.numeric(siteInfo$drain.area.va)
- cat("Unit Code (1-4, no quotes):")
- qUnit <- readline()
- qUnit <- as.numeric(qUnit)
- conversionVector <- c(2.5899881, 1.0, 0.0040468564, 0.01)
- siteInfo$drainSqKm <- siteInfo$drain.area.va * conversionVector[qUnit]
- }
- } else {
- requiredColumns <- c("drainSqKm", "staAbbrev", "constitAbbrev",
- "param.units", "paramShortName","shortName")
- if(!all(requiredColumns %in% names(siteInfo))){
- message("The following columns are expected in the EGRET package:\n")
- message(requiredColumns[!(requiredColumns %in% names(siteInfo))])
- }
- }
-
- siteInfo$queryTime <- Sys.time()
- siteInfo$paStart <- 10
- siteInfo$paLong <- 12
-
- return(siteInfo)
-}
-
diff --git a/R/getSTORETSampleData.R b/R/getSTORETSampleData.R
deleted file mode 100644
index a343d693e65398c63b36a94cb14b26d39464e509..0000000000000000000000000000000000000000
--- a/R/getSTORETSampleData.R
+++ /dev/null
@@ -1,47 +0,0 @@
-#' 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}
-#' For raw data, use getWQPData. This function will retrieve the raw data, and compress it (summing constituents). See
-#' chapter 7 of the EGRET user guide for more details, then converts it to the Sample dataframe structure.
-#'
-#' @param siteNumber string site number. If USGS, it should be in the form :'USGS-XXXXXXXXX...'
-#' @param characteristicName string
-#' @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{getWQPData}}, \code{\link{getWQPSites}},
-#' \code{\link{getWQPqwData}}, \code{\link{getNWISqwData}}, and \code{\link{readWQPData}},
-#' \code{\link{compressData}}, \code{\link{populateSampleColumns}}
-#' @examples
-#' # These examples require an internet connection to run
-#' \dontrun{
-#' Sample_01075 <- getWQPSample('USGS-01594440','Chloride', '', '')
-#' Sample_All <- getWQPSample('WIDNR_WQX-10032762','Specific conductance', '', '')
-#' }
-getWQPSample <- function(siteNumber,characteristicName,startDate,endDate,interactive=TRUE){
-
- retval <- getWQPqwData(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/getSampleData.r b/R/getSampleData.r
deleted file mode 100644
index a32670102220a4bfa1c46df2fe0b68f19ffeb337..0000000000000000000000000000000000000000
--- a/R/getSampleData.r
+++ /dev/null
@@ -1,35 +0,0 @@
-#' 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}
-#' For raw data, use getQWData. This function will retrieve the raw data, and compress it (summing constituents). See
-#' section 3.4 of the vignette for more details.
-#'
-#' @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
-#' Sample_01075 <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31')
-#' Sample_All2 <- getNWISSample('05114000',c('00915','00931'), '1985-01-01', '1985-03-31')
-#' Sample_Select <- getNWISSample('05114000',c('00915','00931'), '', '')
-getNWISSample <- function(siteNumber,parameterCd,startDate,endDate,interactive=TRUE){
-
- rawSample <- getNWISqwData(siteNumber,parameterCd,startDate,endDate)
- dataColumns <- grep("p\\d{5}",names(rawSample))
- remarkColumns <- grep("r\\d{5}",names(rawSample))
- totalColumns <-c(grep("sample_dt",names(rawSample)), dataColumns, remarkColumns)
- totalColumns <- totalColumns[order(totalColumns)]
- compressedData <- compressData(rawSample[,totalColumns], interactive=interactive)
- Sample <- populateSampleColumns(compressedData)
- return(Sample)
-}
-
-
diff --git a/R/getSampleDataFromFile.r b/R/getSampleDataFromFile.r
deleted file mode 100644
index 2b6e0d37c5e6537ad56a94ec5c2e1a25d0664547..0000000000000000000000000000000000000000
--- a/R/getSampleDataFromFile.r
+++ /dev/null
@@ -1,24 +0,0 @@
-#' 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.
-#'
-#' @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
-#' @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 <- 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/mergeReport.r b/R/mergeReport.r
deleted file mode 100644
index 8be574094d75fab6e70fb5fd7cc53cf313d93d22..0000000000000000000000000000000000000000
--- a/R/mergeReport.r
+++ /dev/null
@@ -1,26 +0,0 @@
-#' Merge Sample and Daily Data for WRTDS
-#'
-#' Merges the flow data from the daily record into the sample record.
-#'
-#' @param Daily dataframe containing the daily data, default is Daily
-#' @param Sample dataframe containing the sample data, default is Sample
-#' @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 newSample dataframe with merged flow information
-#' @seealso \code{\link{getNWISDaily}}, \code{\link{getNWISSample}}
-#' @examples
-#' # These examples require an internet connection to run
-#' Daily <- getNWISDaily('01594440','00060', '1985-01-01', '1985-03-31')
-#' Sample <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31')
-#' Sample <- mergeReport(Daily, Sample)
-mergeReport<-function(Daily, Sample, interactive=TRUE){
-
- if (interactive){
- dataOverview(Daily, Sample)
- }
-
- newSample <- merge(Daily[,c("Date","Q","LogQ")],Sample,by = "Date",all.y = TRUE)
-
- return(newSample)
-}
diff --git a/R/populateConcentrations.r b/R/populateConcentrations.r
deleted file mode 100644
index 582e1d70ba616853eb256c13ebf5578cdd84eba5..0000000000000000000000000000000000000000
--- a/R/populateConcentrations.r
+++ /dev/null
@@ -1,22 +0,0 @@
-#' Populate Concentration Columns
-#'
-#' Creates ConcLow, ConcHigh, Uncen (0 if censored, 1 if uncensored) columns for Sample data frame for WRTDS study.
-#'
-#' @param rawData vector with value and code columns
-#' @return concentrationColumns dataframe
-#' @export
-#' @examples
-#' code <- c("","<","")
-#' value <- c(1,2,3)
-#' dataInput <- data.frame(value, code, stringsAsFactors=FALSE)
-#' concentrationDF <- populateConcentrations(dataInput)
-populateConcentrations <- function(rawData){ # rawData is a dataframe with value, code
- concentrationColumns <- as.data.frame(matrix(ncol=3,nrow=length(rawData$value)))
- colnames(concentrationColumns) <- c('ConcLow','ConcHigh','Uncen')
- concentrationColumns$ConcLow <- as.numeric(ifelse((rawData$code!="<" | is.na(rawData$code)),rawData$value,0))
- concentrationColumns$ConcHigh <- as.numeric(rawData$value)
- tempConcLow<-ifelse((rawData$code!="<" | is.na(rawData$code)),rawData$value,0)
- concentrationColumns$Uncen <- ifelse(tempConcLow==0,0,1)
- #Add if value = NA?
- return (concentrationColumns) # returns ConcLow, ConcHigh, Uncen (0 if censored, 1 if uncensored)
-}
diff --git a/R/populateDaily.r b/R/populateDaily.r
deleted file mode 100644
index 2ec2d3ed66d39e59db1361729859076842e20ff2..0000000000000000000000000000000000000000
--- a/R/populateDaily.r
+++ /dev/null
@@ -1,114 +0,0 @@
-#' Populate Daily data frame
-#'
-#' Using raw data that has at least dateTime, value, code, populates the rest of the basic Daily data frame used in WRTDS
-#'
-#' @param rawData dataframe contains at least dateTime, value, code columns
-#' @param qConvert string conversion to cubic meters per second
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords WRTDS flow
-#' @author Robert M. Hirsch \email{rhirsch@@usgs.gov}
-#' @import zoo
-#' @return dataframe Daily
-#' @export
-#' @import zoo
-#' @examples
-#' dateTime <- c('1985-01-01', '1985-01-02', '1985-01-03')
-#' value <- c(1,2,3)
-#' code <- c("","","")
-#' dataInput <- data.frame(dateTime, value, code, stringsAsFactors=FALSE)
-#' Daily <- populateDaily(dataInput, 2)
-populateDaily <- function(rawData,qConvert,interactive=TRUE){ # rawData is a dataframe with at least dateTime, value, code
-
-# require(zoo)
-
- localDaily <- as.data.frame(matrix(ncol=2,nrow=length(rawData$value)))
- colnames(localDaily) <- c('Date','Q')
- localDaily$Date <- rawData$dateTime
-
- # need to convert to cubic meters per second to store the values
- localDaily$Q <- rawData$value/qConvert
-
- dateFrame <- populateDateColumns(rawData$dateTime)
- localDaily <- cbind(localDaily, dateFrame[,-1])
-
- localDaily$Date <- as.Date(localDaily$Date)
-
- if(length(rawData$code) != 0) localDaily$Qualifier <- rawData$code
-
- localDaily$i <- 1:nrow(localDaily)
-
- noDataValue <- -999999
-
- nd <- localDaily$Q==noDataValue
-
- localDaily$Q<-ifelse(nd,NA,localDaily$Q)
-
- zeros<-which(localDaily$Q<=0)
-
- nz<-length(zeros)
-
- if(nz>0) {
-
- qshift<- 0.001*mean(localDaily$Q, na.rm=TRUE)
- if (interactive){
-
- zeroNums <- length(which(localDaily$Q == 0))
-
- if (zeroNums > 0){
- cat("There were", as.character(zeroNums), "zero flow days \n")
- }
-
- cat("All days had",as.character(qshift),"cms added to the discharge value.\n")
-
- }
- } else {
- qshift<-0.0
- }
-
- negNums <- length(which(localDaily$Q<0))
- if (negNums > 0) {
- cat("There were", as.character(negNums), "negative flow days \n")
- cat("Negative values are not supported in the EGRET package\n")
- }
-
- localDaily$Q<-localDaily$Q+qshift
-
- localDaily$LogQ <- log(localDaily$Q)
-
- Qzoo<-zoo(localDaily$Q)
-
- if (length(rawData$dateTime) < 30){
- if (interactive){
- cat("This program requires at least 30 data points. You have only provided:", length(rawData$dateTime),"Rolling means will not be calculated.\n")
- }
- warning("This program requires at least 30 data points. Rolling means will not be calculated.")
- } else {
- localDaily$Q7<-as.numeric(rollapply(Qzoo,7,mean,na.rm=FALSE,fill=NA,align="right"))
- localDaily$Q30<-as.numeric(rollapply(Qzoo,30,mean,na.rm=FALSE,fill=NA,align="right"))
- }
-
- dataPoints <- nrow(localDaily)
- difference <- (localDaily$Julian[dataPoints] - localDaily$Julian[1])+1
- if (interactive){
- cat("There are", as.character(dataPoints), "data points, and", as.character(difference), "days.\n")
-
- #these next two lines show the user where the gaps in the data are if there are any
- n<-nrow(localDaily)
- for(i in 2:n) {
- if((localDaily$Julian[i]-localDaily$Julian[i-1])>1) cat("\n discharge data jumps from",as.character(localDaily$Date[i-1]),"to",as.character(localDaily$Date[i]))
- }
-
- numNAs <- sum(is.na(localDaily$Q))
- if(numNAs > 0){
- cat(numNAs, "discharge measurements are not reported (NA's). \nMany of the EGRET functions will not work with missing discharge measurements.")
- if (localDaily$Julian[max(which(is.na(localDaily$Q)),na.rm = TRUE)]-
- localDaily$Julian[min(which(is.na(localDaily$Q)),na.rm = TRUE)]+1 == numNAs){
- cat("\nNA gap is from",as.character(localDaily$Date[min(which(is.na(localDaily$Q)),na.rm = TRUE)]),"to",
- as.character(localDaily$Date[max(which(is.na(localDaily$Q)),na.rm = TRUE)]))
- }
- }
-
- }
-
- return (localDaily)
-}
diff --git a/R/populateDateColumns.r b/R/populateDateColumns.r
deleted file mode 100644
index 9e0503cd43443b8af4bdf045a389bda40739aac9..0000000000000000000000000000000000000000
--- a/R/populateDateColumns.r
+++ /dev/null
@@ -1,36 +0,0 @@
-#' Populate Date Columns
-#'
-#' Creates various date columns for WRTDS study.
-#'
-#' @param rawData vector with dateTime
-#' @return DateFrame dataframe
-#' @importFrom lubridate decimal_date
-#' @export
-#' @examples
-#' dateTime <- c('1984-02-28 13:56', '1984-03-01', '1986-03-01')
-#' expandedDateDF <- populateDateColumns(dateTime)
-populateDateColumns <- function(rawData){ # rawData is a vector of dates
- DateFrame <- as.data.frame(matrix(ncol=1,nrow=length(rawData)))
- colnames(DateFrame) <- c('Date')
- DateFrame$Date <- rawData
- dateTime <- as.POSIXlt(rawData)
- DateFrame$Julian <- as.numeric(julian(dateTime,origin=as.Date("1850-01-01")))
- DateFrame$Month <- dateTime$mon + 1
- DateFrame$Day <- dateTime$yday + 1
- year <- dateTime$year + 1900
- hour <- dateTime$hour
- minute <- dateTime$min
-
- if (sum(hour) == 0 & sum(minute) == 0){
- dateTime$hour <- rep(12,length(dateTime))
- }
-
- leapOffset <- ifelse((year%%4 == 0) & ((year%%100 != 0) | (year%%400 == 0)), 0,1)
-
- DateFrame$Day[DateFrame$Day > 59] <- DateFrame$Day[DateFrame$Day > 59] + leapOffset[DateFrame$Day > 59]
-
- DateFrame$DecYear <- decimal_date(dateTime)
- DateFrame$MonthSeq <- ((year-1850)*12)+DateFrame$Month
- return (DateFrame)
-
-}
diff --git a/R/populateParameterINFO.r b/R/populateParameterINFO.r
deleted file mode 100644
index c21ecc6c81a5ff30aa7a3d40bd8317274f0edee4..0000000000000000000000000000000000000000
--- a/R/populateParameterINFO.r
+++ /dev/null
@@ -1,55 +0,0 @@
-#' Populate Parameter Information Columns
-#'
-#' Populates INFO data frame with additional user-supplied information concerning the measured parameter.
-#'
-#' @param INFO dataframe with value and code columns. Default is INFO
-#' @param parameterCd string USGS parameter code
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @return INFO dataframe
-#' @export
-#' @examples
-#' #This example requires an internet connection to run
-#' INFO <- getNWISSiteInfo('01594440')
-#' parameterCd <- "01075"
-#' parameterData <- getNWISPcodeInfo(parameterCd)
-#' INFO$param.nm <- parameterData$parameter_nm
-#' INFO$param.units <- parameterData$parameter_units
-#' INFO$paramShortName <- parameterData$srsname
-#' INFO$paramNumber <- parameterData$parameter_cd
-#' INFO <- populateParameterINFO(parameterCd, INFO)
-populateParameterINFO <- function(parameterCd, INFO, interactive=TRUE){
- if (nzchar(parameterCd)){
- if(interactive){
- cat("Your water quality data are for parameter number", INFO$paramNumber, "which has the name:'", INFO$param.nm, "'.\n")
- cat("Typically you will want a shorter name to be used in graphs and tables. The suggested short name is:'", INFO$paramShortName, "'.\n")
- cat("If you would like to change the short name, enter it here, otherwise just hit enter (no quotes):")
- shortNameTemp <- readline()
- if (nchar(shortNameTemp)>0) INFO$paramShortName <- shortNameTemp
- cat("The units for the water quality data are: ", INFO$param.units, ".\n")
- cat("It is helpful to set up a constiuent abbreviation when doing multi-constituent studies, enter a unique id (three or four characters should work something like tn or tp or NO3).\nIt is case sensitive. Even if you don't feel you need an abbreviation you need to enter something (no quotes):\n")
- INFO$constitAbbrev <- readline()
- } else {
- INFO$constitAbbrev <- INFO$paramShortName
- }
- } else {
- if (interactive){
- INFO$paramNumber <- NA
- cat("Enter a long name for the water quality data (no quotes):\n")
- INFO$param.nm <- readline()
- cat("Enter a short name to be used in graphs and tables(no quotes):\n")
- INFO$paramShortName <- readline()
- cat("It is helpful to set up a constiuent abbreviation when doing multi-constituent studies, enter a unique id (three or four characters should work something like tn or tp or NO3).\nIt is case sensitive. Even if you don't feel you need an abbreviation you need to enter something (no quotes):\n")
- INFO$constitAbbrev <- readline()
- cat("Enter the units of the water quality data(no quotes):\n")
- INFO$param.units <- readline()
- } else {
- INFO$paramNumber <- NA
- INFO$param.nm <- NA
- INFO$paramShortName <- NA
- INFO$constitAbbrev <- NA
- INFO$param.units <- NA
- }
- }
-
- return(INFO)
-}
diff --git a/R/populateSampleColumns.r b/R/populateSampleColumns.r
deleted file mode 100644
index 38461e7169e75d75d986e7bd0142768b8ccd9a38..0000000000000000000000000000000000000000
--- a/R/populateSampleColumns.r
+++ /dev/null
@@ -1,32 +0,0 @@
-#' Populate Sample Columns
-#'
-#' Creates ConcAve and ConcLow based on Uncen. Removes any samples with NA values in ConcHigh
-#'
-#' @param rawData dataframe with dateTime, ConcLow, ConcHigh, Uncen
-#' @return Sample2 dataframe
-#' @export
-#' @examples
-#' dateTime <- c('1985-01-01', '1985-01-02', '1985-01-03')
-#' ConcLow <- c(1,2,0)
-#' ConcHigh <- c(1,2,3)
-#' Uncen <- c(1,1,0)
-#' dataInput <- data.frame(dateTime, ConcLow, ConcHigh, Uncen, stringsAsFactors=FALSE)
-#' Sample <- populateSampleColumns(dataInput)
-populateSampleColumns <- function(rawData){ # rawData is a dataframe with dateTime, ConcLow, ConcHigh, Uncen
- Sample <- as.data.frame(matrix(ncol=3,nrow=length(rawData$dateTime)))
- colnames(Sample) <- c('Date', 'ConcLow','ConcHigh')
- Sample$Date <- rawData$dateTime
- Sample$ConcLow <- rawData$ConcLow
- Sample$ConcHigh <- rawData$ConcHigh
- Sample$Uncen <- rawData$Uncen
- Sample$ConcAve <- (Sample$ConcLow+Sample$ConcHigh)/2
- Sample$ConcLow <- ifelse((rawData$ConcLow == 0.0 & rawData$Uncen == 0),NA,rawData$ConcLow)
-
- dateFrame <- populateDateColumns(rawData$dateTime)
- Sample <- cbind(Sample, dateFrame[,-1])
-
- Sample$SinDY <- sin(2*pi*Sample$DecYear)
- Sample$CosDY <- cos(2*pi*Sample$DecYear)
- Sample2 <- subset(Sample, (!is.na(Sample$ConcHigh))) # Was just ConcHigh.....
- return (Sample2)
-}
diff --git a/R/populateSiteINFO.r b/R/populateSiteINFO.r
deleted file mode 100644
index 6a57df2ae484237ee7927aca447b783353082596..0000000000000000000000000000000000000000
--- a/R/populateSiteINFO.r
+++ /dev/null
@@ -1,104 +0,0 @@
-#' Populate Site Information Columns
-#'
-#' Populates INFO data frame with additional user-supplied information. Also removes fields not related to WRTDS study.
-#'
-#' @param INFO dataframe with value and code columns
-#' @param siteNumber string USGS site number
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @return INFO dataframe
-#' @export
-#' @examples
-#' #This example requires an internet connection to run
-#' INFO <- getNWISSiteInfo('01594440')
-#' siteNumber <- "01594440"
-#' siteINFO <- populateSiteINFO(INFO, siteNumber)
-populateSiteINFO <- function(INFO, siteNumber,interactive=TRUE){
- if (nzchar(siteNumber)){
-
- if (!nzchar(INFO$site.no)) {
- INFO$site.no <- siteNumber
- }
-
- if (interactive){
- cat("Your site for streamflow data is", as.character(INFO$site.no),".\n")
- if (!nzchar(INFO$station.nm)){
- cat("No station name was listed in the USGS site file for site: ", INFO$site.no, ". Please enter a station name here(no quotes): \n")
- INFO$station.nm <- readline()
- }
- cat("Your site name is", INFO$station.nm,",")
- cat("but you can modify this to a short name in a style you prefer. \nThis name will be used to label graphs and tables. \n")
- cat("If you want the program to use the name given above, just do a carriage return, otherwise enter the preferred short name(no quotes):\n")
- INFO$shortName <- readline()
- if (!nzchar(INFO$shortName)) INFO$shortName <- INFO$station.nm
- if (!nzchar(INFO$dec.lat.va) || !nzchar(INFO$dec.long.va)){
- cat("No latitude or longitude was listed in the USGS site file for this site.\n")
- cat("Please enter a latitude and longitude in decimal degrees, positive latitudes are north, negative are south, positive longitudes are east, \nnegative longitudes are west, so for example a site in the northeastern US might look like, 40.1, -83.2\nThese only need to be sufficiently accurate to place them on a map of the study area.\n\n")
- cat("Latitude(no quotes):\n")
- INFO$dec.lat.va <- readline()
- cat("Longitude(no quotes):\n")
- INFO$dec.long.va <- readline()
- }
- cat("The latitude and longitude of the site are: ",INFO$dec.lat.va, ", ", INFO$dec.long.va, "(degrees north and west).\n")
- if (!nzchar(INFO$drain.area.va)){
- cat("No drainage area was listed in the USGS site file for this site.\n")
- cat("Please enter the drainage area, you can enter it in the units of your choice.\nEnter the area, then enter drainage area code, \n1 is square miles\n2 is square kilometers\n3 is acres\n4 is hectares.\n")
- cat("Area(no quotes):\n")
- INFO$drain.area.va <- readline()
- INFO$drain.area.va <- as.numeric(INFO$drain.area.va)
- cat("Unit Code (1-4, no quotes):")
- qUnit <- readline()
- qUnit <- as.numeric(qUnit)
- conversionVector <- c(2.5899881, 1.0, 0.0040468564, 0.01)
- INFO$drainSqKm <- INFO$drain.area.va * conversionVector[qUnit]
- } else {
- INFO$drain.area.va <- as.numeric(INFO$drain.area.va)
- INFO$contrib.drain.area.va <- as.numeric(INFO$contrib.drain.area.va)
- INFO$drainSqKm <- INFO$drain.area.va * 2.5899881
- }
- cat("The drainage area at this site is ", INFO$drain.area.va, "square miles which is being stored as", INFO$drainSqKm, "square kilometers.\n")
- } else {
- INFO$drain.area.va <- as.numeric(INFO$drain.area.va)
- INFO$contrib.drain.area.va <- as.numeric(INFO$contrib.drain.area.va)
- INFO$drainSqKm <- INFO$drain.area.va * 2.5899881
- INFO$shortName <- INFO$station.nm
- }
- } else {
- if (interactive){
- cat("The program needs to know a site number or id, please enter that here (don't use quotes) - Enter to leave blank:")
- INFO$site.no <- readline()
- cat("Please enter a site name that will be used to label all graphs and tables(no quotes):\n")
- INFO$shortName <- readline()
- cat("Please enter a latitude and longitude in decimal degrees, positive latitudes are north, negative are south, positive longitudes are east, \nnegative longitudes are west, so for example a site in the northeastern US might look like, 40.1, -83.2\nThese only need to be sufficiently accurate to place them on a map of the study area.\n\n")
- cat("Latitude(no quotes):\n")
- INFO$dec.lat.va <- readline()
- cat("Longitude(no quotes):\n")
- INFO$dec.long.va <- readline()
- INFO$dec.lat.va <- as.numeric(INFO$dec.lat.va)
- INFO$dec.long.va <- as.numeric(INFO$dec.long.va)
- cat("Please enter the drainage area, you can enter it in the units of your choice.\nEnter the area, then enter drainage area code, 1 is square miles, 2 is square kilometers, 3 is acres, and 4 is hectares.\n")
- cat("Area(no quotes):\n")
- INFO$drain.area.va <- readline()
- INFO$drain.area.va <- as.numeric(INFO$drain.area.va)
- cat("Unit Code (1-4, no quotes)\nrepresenting \n1: sq mi \n2: sq km \n3: sq m\n4: sq 100*km):")
- qUnit <- readline()
- qUnit <- as.numeric(qUnit)
- conversionVector <- c(2.5899881, 1.0, 0.0040468564, 0.01)
- INFO$drainSqKm <- INFO$drain.area.va * conversionVector[qUnit]
- cat("The drainage area is being stored as", INFO$drainSqKm, "square kilometers.\n")
- } else {
- INFO$site.no <- NA
- INFO$shortName <- NA
- INFO$dec.lat.va <- NA
- INFO$dec.long.va <- NA
- INFO$drain.area.va <- NA
- INFO$drainSqKm <- NA
- }
- }
- if (interactive){
- cat("It is helpful to set up a station abbreviation when doing multi-site studies, enter a unique id (three or four characters should work).\nIt is case sensitive. Even if you don't feel you need an abbreviation for your site you need to enter something(no quotes):\n")
- INFO$staAbbrev <- readline()
- } else {
- INFO$staAbbrev <- NA
- }
- return(INFO)
-}
diff --git a/R/processQWData.r b/R/processQWData.r
deleted file mode 100644
index 329374effcd4cc93368afc6a1ea3aa95887cb3ca..0000000000000000000000000000000000000000
--- a/R/processQWData.r
+++ /dev/null
@@ -1,54 +0,0 @@
-#' Processing of USGS NWIS Water Quality Data
-#'
-#' Processes water quality portal data. This function looks at detection limit and detection
-#' conditions to determine if a value is left censored or not. Censored values are given the qualifier
-#' "<". The dataframe is also converted from a long to wide format.
-#'
-#' @param data dataframe from Water Quality Portal
-#' @param pCode logical if TRUE, assume data came from a pCode search, if FALSE, characteristic name.
-#' @keywords data import USGS web service
-#' @return data dataframe with first column dateTime, and at least one qualifier and value columns
-#' (subsequent qualifier/value columns could follow depending on the number of parameter codes)
-#' @export
-#' @examples
-#' # These examples require an internet connection to run
-#' \dontrun{
-#' rawSample <- getWQPqwData('USGS-01594440','', '', '')
-#' rawSampleSelect <- processQWData(rawSample)
-#' }
-processQWData <- function(data,pCode=TRUE){
-
- qualifier <- ifelse((data$ResultDetectionConditionText == "Not Detected" |
- data$ResultDetectionConditionText == "Detected Not Quantified" |
- data$ResultMeasureValue < data$DetectionQuantitationLimitMeasure.MeasureValue),"<","")
-
- correctedData<-ifelse((nchar(qualifier)==0),data$ResultMeasureValue,data$DetectionQuantitationLimitMeasure.MeasureValue)
- test <- data.frame(data$USGSPCode)
-
- test$dateTime <- data$ActivityStartDate
-
- originalLength <- nrow(test)
- test$qualifier <- qualifier
- test$value <- as.numeric(correctedData)
-
- test <- test[!is.na(test$dateTime),]
- newLength <- nrow(test)
- if (originalLength != newLength){
- numberRemoved <- originalLength - newLength
- warningMessage <- paste(numberRemoved, " rows removed because no date was specified", sep="")
- warning(warningMessage)
- }
-
- if (pCode){
- colnames(test)<- c("USGSPCode","dateTime","qualifier","value")
- newTimeVar <- "USGSPCode"
- } else {
- colnames(test)<- c("CharacteristicName","dateTime","qualifier","value")
- newTimeVar <- "CharacteristicName"
- }
-
- data <- suppressWarnings(reshape(test, idvar="dateTime", timevar = newTimeVar, direction="wide"))
- data$dateTime <- format(data$dateTime, "%Y-%m-%d")
- data$dateTime <- as.Date(data$dateTime)
- return(data)
-}
diff --git a/R/removeDuplicates.r b/R/removeDuplicates.r
deleted file mode 100644
index 00687cc10f8a30b2168b0192ca262daa8c7e8f0f..0000000000000000000000000000000000000000
--- a/R/removeDuplicates.r
+++ /dev/null
@@ -1,17 +0,0 @@
-#' Remove Duplicates
-#'
-#' Removes observations from the data frame Sample when the observation has the identical date and value as another observation
-#'
-#' @param Sample dataframe with at least DecYear and ConcHigh, default name is Sample
-#' @export
-#' @return Sample1 dataframe
-#' @examples
-#' DecYear <- c('1985.01', '1985.01', '1985.02', '1985.02', '1985.03')
-#' ConcHigh <- c(1,2,3,3,5)
-#' dataInput <- data.frame(DecYear, ConcHigh, stringsAsFactors=FALSE)
-#' removeDuplicates(dataInput)
-removeDuplicates <- function(Sample) {
- Sample1 <- Sample[!duplicated(Sample[c("DecYear","ConcHigh")]),]
-
- return(Sample1)
-}
diff --git a/inst/extdata/ChoptankRiverFlow.txt b/inst/extdata/ChoptankRiverFlow.txt
deleted file mode 100644
index 1aa92f002be518b6d369904d6acac643f62764d2..0000000000000000000000000000000000000000
--- a/inst/extdata/ChoptankRiverFlow.txt
+++ /dev/null
@@ -1,4384 +0,0 @@
-date Qdaily
-10/1/1999 3.029902561
-10/2/1999 2.406931941
-10/3/1999 2.152080324
-10/4/1999 2.152080324
-10/5/1999 3.19980364
-10/6/1999 2.775050944
-10/7/1999 2.350298249
-10/8/1999 2.152080324
-10/9/1999 1.925545553
-10/10/1999 1.86891186
-10/11/1999 2.605149866
-10/12/1999 2.095446631
-10/13/1999 2.010496092
-10/14/1999 1.982179246
-10/15/1999 1.86891186
-10/16/1999 2.237030863
-10/17/1999 2.18039717
-10/18/1999 2.152080324
-10/19/1999 1.982179246
-10/20/1999 2.944952022
-10/21/1999 4.020992184
-10/22/1999 4.700596497
-10/23/1999 4.44574488
-10/24/1999 4.417428034
-10/25/1999 3.992675338
-10/26/1999 3.369704718
-10/27/1999 3.001585715
-10/28/1999 2.775050944
-10/29/1999 2.57683302
-10/30/1999 2.463565634
-10/31/1999 2.350298249
-11/1/1999 2.831684637
-11/2/1999 2.49188248
-11/3/1999 2.831684637
-11/4/1999 2.973268869
-11/5/1999 2.746734098
-11/6/1999 2.49188248
-11/7/1999 2.378615095
-11/8/1999 2.293664556
-11/9/1999 2.208714017
-11/10/1999 2.18039717
-11/11/1999 2.123763478
-11/12/1999 2.067129785
-11/13/1999 2.038812939
-11/14/1999 1.982179246
-11/15/1999 1.982179246
-11/16/1999 1.925545553
-11/17/1999 1.86891186
-11/18/1999 1.812278168
-11/19/1999 1.755644475
-11/20/1999 1.727327628
-11/21/1999 1.755644475
-11/22/1999 1.755644475
-11/23/1999 1.727327628
-11/24/1999 1.727327628
-11/25/1999 1.755644475
-11/26/1999 1.812278168
-11/27/1999 3.82277426
-11/28/1999 5.323567117
-11/29/1999 4.615645958
-11/30/1999 3.51128895
-12/1/1999 3.001585715
-12/2/1999 2.746734098
-12/3/1999 2.605149866
-12/4/1999 2.520199327
-12/5/1999 2.435248788
-12/6/1999 2.548516173
-12/7/1999 3.426338411
-12/8/1999 3.313071025
-12/9/1999 2.973268869
-12/10/1999 2.88831833
-12/11/1999 3.454655257
-12/12/1999 3.51128895
-12/13/1999 3.228120486
-12/14/1999 4.898814422
-12/15/1999 11.80812494
-12/16/1999 11.49663963
-12/17/1999 7.334063209
-12/18/1999 5.606735581
-12/19/1999 4.785547036
-12/20/1999 4.389111187
-12/21/1999 4.44574488
-12/22/1999 4.474061726
-12/23/1999 4.190893263
-12/24/1999 3.907724799
-12/25/1999 3.652873182
-12/26/1999 3.426338411
-12/27/1999 3.398021564
-12/28/1999 3.284754179
-12/29/1999 3.143169947
-12/30/1999 3.001585715
-12/31/1999 2.944952022
-1/1/2000 2.80336779
-1/2/2000 2.661783559
-1/3/2000 2.633466712
-1/4/2000 2.746734098
-1/5/2000 4.728913344
-1/6/2000 5.748319813
-1/7/2000 4.700596497
-1/8/2000 4.077625877
-1/9/2000 3.737823721
-1/10/2000 3.737823721
-1/11/2000 4.049309031
-1/12/2000 3.964358492
-1/13/2000 3.596239489
-1/14/2000 3.341387872
-1/15/2000 2.973268869
-1/16/2000 2.860001483
-1/17/2000 2.831684637
-1/18/2000 2.661783559
-1/19/2000 2.775050944
-1/20/2000 2.718417251
-1/21/2000 2.661783559
-1/22/2000 2.49188248
-1/23/2000 2.690100405
-1/24/2000 2.520199327
-1/25/2000 2.435248788
-1/26/2000 2.746734098
-1/27/2000 2.633466712
-1/28/2000 2.293664556
-1/29/2000 2.265347709
-1/30/2000 2.265347709
-1/31/2000 3.454655257
-2/1/2000 4.275843802
-2/2/2000 4.417428034
-2/3/2000 3.936041645
-2/4/2000 3.82277426
-2/5/2000 3.766140567
-2/6/2000 3.652873182
-2/7/2000 3.567922642
-2/8/2000 3.794457413
-2/9/2000 3.907724799
-2/10/2000 4.247526955
-2/11/2000 5.635052427
-2/12/2000 7.56059798
-2/13/2000 7.475647441
-2/14/2000 6.824359975
-2/15/2000 10.84535216
-2/16/2000 11.24178801
-2/17/2000 7.730499059
-2/18/2000 6.880993668
-2/19/2000 15.51763181
-2/20/2000 22.20040755
-2/21/2000 14.61149273
-2/22/2000 9.627727765
-2/23/2000 7.362380056
-2/24/2000 6.597825204
-2/25/2000 5.521785042
-2/26/2000 5.69168612
-2/27/2000 6.31465674
-2/28/2000 6.00317143
-2/29/2000 5.748319813
-3/1/2000 5.238616578
-3/2/2000 4.842180729
-3/3/2000 4.44574488
-3/4/2000 4.105942723
-3/5/2000 3.907724799
-3/6/2000 3.709506874
-3/7/2000 3.454655257
-3/8/2000 3.313071025
-3/9/2000 3.313071025
-3/10/2000 3.228120486
-3/11/2000 3.086536254
-3/12/2000 3.369704718
-3/13/2000 3.539605796
-3/14/2000 3.313071025
-3/15/2000 3.114853101
-3/16/2000 3.029902561
-3/17/2000 4.077625877
-3/18/2000 4.955448115
-3/19/2000 4.332477494
-3/20/2000 3.82277426
-3/21/2000 8.070301215
-3/22/2000 66.54458897
-3/23/2000 56.9168612
-3/24/2000 23.44634879
-3/25/2000 15.80080027
-3/26/2000 13.08238302
-3/27/2000 11.83644178
-3/28/2000 27.80714313
-3/29/2000 29.44952022
-3/30/2000 16.33882035
-3/31/2000 11.55327332
-4/1/2000 8.778222374
-4/2/2000 7.419013749
-4/3/2000 6.654458897
-4/4/2000 6.597825204
-4/5/2000 7.079211592
-4/6/2000 6.739409436
-4/7/2000 5.974854584
-4/8/2000 5.295250271
-4/9/2000 6.31465674
-4/10/2000 7.64554852
-4/11/2000 7.107528439
-4/12/2000 5.918220891
-4/13/2000 5.0687155
-4/14/2000 4.530695419
-4/15/2000 4.44574488
-4/16/2000 5.266933425
-4/17/2000 12.96911564
-4/18/2000 19.4819903
-4/19/2000 19.1138713
-4/20/2000 14.7813938
-4/21/2000 11.92139232
-4/22/2000 15.23446335
-4/23/2000 15.2061465
-4/24/2000 11.12852062
-4/25/2000 8.608321296
-4/26/2000 8.664954989
-4/27/2000 8.749905528
-4/28/2000 7.730499059
-4/29/2000 6.62614205
-4/30/2000 5.861587198
-5/1/2000 5.097032346
-5/2/2000 4.643962804
-5/3/2000 4.304160648
-5/4/2000 3.936041645
-5/5/2000 3.709506874
-5/6/2000 3.369704718
-5/7/2000 3.171486793
-5/8/2000 3.029902561
-5/9/2000 2.831684637
-5/10/2000 2.520199327
-5/11/2000 2.746734098
-5/12/2000 2.463565634
-5/13/2000 2.406931941
-5/14/2000 2.973268869
-5/15/2000 2.661783559
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-9/5/2011 5.720002966
-9/6/2011 5.38020081
-9/7/2011 7.702182212
-9/8/2011 13.22396725
-9/9/2011 20.30317885
-9/10/2011 19.96337669
-9/11/2011 12.17624394
-9/12/2011 9.061390838
-9/13/2011 8.013667522
-9/14/2011 6.909310514
-9/15/2011 6.00317143
-9/16/2011 5.097032346
-9/17/2011 4.530695419
-9/18/2011 4.190893263
-9/19/2011 3.964358492
-9/20/2011 3.82277426
-9/21/2011 3.794457413
-9/22/2011 3.624556335
-9/23/2011 3.766140567
-9/24/2011 4.898814422
-9/25/2011 5.550101888
-9/26/2011 4.728913344
-9/27/2011 4.304160648
-9/28/2011 8.58000445
-9/29/2011 13.90357157
-9/30/2011 9.457826687
diff --git a/inst/extdata/ChoptankRiverNitrate.csv b/inst/extdata/ChoptankRiverNitrate.csv
deleted file mode 100644
index 7bd463448294cf6487a7b15c9b73178e1bfcf332..0000000000000000000000000000000000000000
--- a/inst/extdata/ChoptankRiverNitrate.csv
+++ /dev/null
@@ -1,8 +0,0 @@
-cdate;remarkCode;Nitrate;remarkCode2;Nitrate2
-1999-10-07;;1.4;;1.2
-1999-11-04;<;0.99;<;0.25
-1999-12-30;;1.42;;1.4
-2000-01-04;;1.59;;2.1
-2000-02-03;;1.54;;1.0
-2000-02-15;;1.37;<;.50
-2000-02-19;<;1.24;;1.4
diff --git a/man/checkStartEndDate.Rd b/man/checkStartEndDate.Rd
deleted file mode 100644
index 8f4519b56e87c0c7f92c09c6d73c02dc2178ab67..0000000000000000000000000000000000000000
--- a/man/checkStartEndDate.Rd
+++ /dev/null
@@ -1,28 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{checkStartEndDate}
-\alias{checkStartEndDate}
-\title{checkStartEndDate}
-\usage{
-checkStartEndDate(startDate, endDate, interactive = TRUE)
-}
-\arguments{
-\item{startDate}{string}
-
-\item{endDate}{string}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-vector where first value is startDate, second is endDate
-}
-\description{
-Checks that the start date is before the end date. If not, it will give the user the opportunity to correct, otherwise will create a warning.
-}
-\examples{
-startDate <- '1985-01-01'
-endDate <- '1990-01-01'
-checkStartEndDate(startDate, endDate)
-}
-\keyword{WRTDS}
-\keyword{flow}
-
diff --git a/man/compressData.Rd b/man/compressData.Rd
deleted file mode 100644
index 5782f8d5dc6b13a024a8cfb16222eebba6b25d58..0000000000000000000000000000000000000000
--- a/man/compressData.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{compressData}
-\alias{compressData}
-\title{Compress sample data frame}
-\usage{
-compressData(data, interactive = TRUE)
-}
-\arguments{
-\item{data}{dataframe contains at least dateTime, value, code columns}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-dataframe returnDataFrame data frame containing dateTime, ConcHigh, ConcLow, Uncen, ConcAve
-}
-\description{
-Using raw data that has at least dateTime, value, code, populates the measured data portion of the Sample data frame used in WRTDS
-ConcLow = Lower bound for an observed concentration
-ConcHigh = Upper bound for an observed concentration
-ConcAve = Average of ConcLow and ConcHigh. If ConcLow is NA, then ConcAve = ConcHigh/2
-Uncen = 1 if uncensored, 0 if censored
-}
-\examples{
-dateTime <- c('1985-01-01', '1985-01-02', '1985-01-03')
-comment1 <- c("","","")
-value1 <- c(1,2,3)
-comment2 <- c("","<","")
-value2 <- c(2,3,4)
-comment3 <- c("","","<")
-value3 <- c(3,4,5)
-dataInput <- data.frame(dateTime, comment1, value1,
- comment2, value2,
- comment3, value3, stringsAsFactors=FALSE)
-compressData(dataInput)
-}
-\keyword{WRTDS}
-\keyword{flow}
-
diff --git a/man/dataOverview.Rd b/man/dataOverview.Rd
deleted file mode 100644
index e8fdb6c6cc17af832e76549f5403e98bb8a34950..0000000000000000000000000000000000000000
--- a/man/dataOverview.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{dataOverview}
-\alias{dataOverview}
-\title{Data Overview for WRTDS}
-\usage{
-dataOverview(Daily, Sample)
-}
-\arguments{
-\item{Daily}{dataframe}
-
-\item{Sample}{dataframe}
-}
-\description{
-Gives a summary of data to be used for WRTDS analysis
-}
-\examples{
-# These examples require an internet connection to run
-exDaily <- getNWISDaily('01594440','00060', '1985-01-01', '1985-03-31', interactive=FALSE)
-exSample <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31', interactive=FALSE)
-dataOverview(Daily = exDaily, Sample = exSample)
-}
-\seealso{
-\code{\link{mergeReport}}
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-
diff --git a/man/dateFormatCheck.Rd b/man/dateFormatCheck.Rd
deleted file mode 100644
index 5800f638b3e0f91691724019061fc454b7f5613f..0000000000000000000000000000000000000000
--- a/man/dateFormatCheck.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{dateFormatCheck}
-\alias{dateFormatCheck}
-\title{Check date format}
-\usage{
-dateFormatCheck(date)
-}
-\arguments{
-\item{date}{string}
-}
-\value{
-condition logical if TRUE,
-}
-\description{
-Checks to see if format is YYYY-MM-DD. Also performs a few other date checks.
-}
-\examples{
-date <- '1985-01-01'
-dateFormatCheck(date)
-dateWrong <- '1999/1/7'
-dateFormatCheck(dateWrong)
-}
-\keyword{WRTDS}
-\keyword{flow}
-
diff --git a/man/formatCheckDate.Rd b/man/formatCheckDate.Rd
deleted file mode 100644
index a2c6843499ada9b47f91349c8dbdfd8b828bc2ef..0000000000000000000000000000000000000000
--- a/man/formatCheckDate.Rd
+++ /dev/null
@@ -1,28 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{formatCheckDate}
-\alias{formatCheckDate}
-\title{formatCheckDate}
-\usage{
-formatCheckDate(Date, dateString, interactive = TRUE)
-}
-\arguments{
-\item{Date}{string}
-
-\item{dateString}{string used in either error message or interactive message. An example would be "startDate"}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-condition logical if TRUE,
-}
-\description{
-Response to the date format checker. If the date is not formated correctly, it will give the user the opportunity to correct, otherwise will create a warning.
-}
-\examples{
-Date <- '1985-01-01'
-dateString <- 'startDate'
-formatCheckDate(Date, dateString, interactive = FALSE)
-}
-\keyword{WRTDS}
-\keyword{flow}
-
diff --git a/man/formatCheckParameterCd.Rd b/man/formatCheckParameterCd.Rd
deleted file mode 100644
index 4af747f0bbf7f1ca80ed6356952e882f2097b445..0000000000000000000000000000000000000000
--- a/man/formatCheckParameterCd.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{formatCheckParameterCd}
-\alias{formatCheckParameterCd}
-\title{formatCheckParameterCd}
-\usage{
-formatCheckParameterCd(parameterCd, interactive = TRUE)
-}
-\arguments{
-\item{parameterCd}{string to check}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-parameterCd string
-}
-\description{
-Checks that the parameter code is 5 digits. If it is less, it will pad the string with zeros. If more, ask the user to re-enter.
-}
-\examples{
-pCode <- '01234'
-formatCheckParameterCd(pCode)
-}
-\keyword{WRTDS}
-\keyword{flow}
-
diff --git a/man/getDailyDataFromFile.Rd b/man/getDailyDataFromFile.Rd
deleted file mode 100644
index 62e5346a65d29d075faeffecfc9a574b6e994041..0000000000000000000000000000000000000000
--- a/man/getDailyDataFromFile.Rd
+++ /dev/null
@@ -1,39 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getDailyDataFromFile}
-\alias{getDailyDataFromFile}
-\title{Import Daily Data for WRTDS}
-\usage{
-getDailyDataFromFile(filePath, fileName, hasHeader = TRUE, separator = ",",
- qUnit = 1, interactive = TRUE)
-}
-\arguments{
-\item{filePath}{string specifying the path to the file}
-
-\item{fileName}{string name of file to open}
-
-\item{hasHeader}{logical true if the first row of data is the column headers}
-
-\item{separator}{string character that separates data cells}
-
-\item{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}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-Daily dataframe
-}
-\description{
-This function is being deprecated for \code{\link{getUserDaily}}.
-}
-\examples{
-filePath <- system.file("extdata", package="dataRetrieval")
-filePath <- paste(filePath,"/",sep="")
-fileName <- "ChoptankRiverFlow.txt"
-\dontrun{Daily <- getDailyDataFromFile(filePath,fileName,separator="\\t")}
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{file}
-\keyword{import}
-
diff --git a/man/getDataFromFile.Rd b/man/getDataFromFile.Rd
deleted file mode 100644
index a138b286029a9940716b129bb12feef972330986..0000000000000000000000000000000000000000
--- a/man/getDataFromFile.Rd
+++ /dev/null
@@ -1,36 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getDataFromFile}
-\alias{getDataFromFile}
-\title{Basic Data Import for Water Flow Data}
-\usage{
-getDataFromFile(filePath, fileName, hasHeader = TRUE, separator = ",")
-}
-\arguments{
-\item{filePath}{string specifying the path to the file}
-
-\item{fileName}{string name of file to open}
-
-\item{hasHeader}{logical true if the first row of data is the column headers}
-
-\item{separator}{string character that separates data cells}
-}
-\value{
-retval dataframe with dateTime, value, and code columns
-}
-\description{
-Imports data from user-supplied data file. Specifically used to import water flow data for use in the WRTDS package.
-For WRTDS usage, the first column is expected to be dates, the second column measured values.
-The third column is optional, it contains any remark codes.
-}
-\examples{
-# Examples of how to use getDataFromFile:
-# Change the file path and file name to something meaningful:
-filePath <- system.file("extdata", package="dataRetrieval")
-filePath <- paste(filePath,"/",sep="")
-fileName <- 'ChoptankRiverFlow.txt'
-ChopData <- getDataFromFile(filePath,fileName, separator="\\t")
-}
-\keyword{data}
-\keyword{file}
-\keyword{import}
-
diff --git a/man/getNWISDaily.Rd b/man/getNWISDaily.Rd
deleted file mode 100644
index aa269cc7101aa18df8c0deb5093fc6ecda4644c0..0000000000000000000000000000000000000000
--- a/man/getNWISDaily.Rd
+++ /dev/null
@@ -1,49 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getNWISDaily}
-\alias{getNWISDaily}
-\title{Import NWIS Daily Data for EGRET analysis}
-\usage{
-getNWISDaily(siteNumber, parameterCd, startDate, endDate, interactive = TRUE,
- convert = TRUE, format = "tsv")
-}
-\arguments{
-\item{siteNumber}{string USGS site number. This is usually an 8 digit number}
-
-\item{parameterCd}{string USGS parameter code. This is usually an 5 digit number.}
-
-\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{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.}
-
-\item{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".}
-}
-\value{
-Daily dataframe
-}
-\description{
-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}
-}
-\examples{
-# These examples require an internet connection to run
-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')
-}
-\seealso{
-\code{\link{getNWISdvData}}, \code{\link{populateDaily}}
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-
diff --git a/man/getNWISInfo.Rd b/man/getNWISInfo.Rd
deleted file mode 100644
index 10f3bdf529b1df517280064a395102ac7903d895..0000000000000000000000000000000000000000
--- a/man/getNWISInfo.Rd
+++ /dev/null
@@ -1,37 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getNWISInfo}
-\alias{getNWISInfo}
-\title{Import Metadata for USGS Data}
-\usage{
-getNWISInfo(siteNumber, parameterCd, interactive = TRUE)
-}
-\arguments{
-\item{siteNumber}{string USGS site number. This is usually an 8 digit number}
-
-\item{parameterCd}{string USGS parameter code. This is usually an 5 digit number.}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-INFO dataframe with at least param.nm, param.units, parameShortName, paramNumber
-}
-\description{
-Populates INFO data frame for EGRET study. If either station number or parameter code supplied, imports data about a particular USGS site 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/}
-If either station number or parameter code is not supplied, the user will be asked to input data.
-Additionally, the user will be asked for:
-staAbbrev - station abbreviation, will be used in naming output files and for structuring batch jobs
-constitAbbrev - constitute abbreviation
-}
-\examples{
-# These examples require an internet connection to run
-# Automatically gets information about site 05114000 and temperature, no interaction with user
-INFO <- getNWISInfo('05114000','00010')
-}
-\keyword{USGS}
-\keyword{data}
-\keyword{import}
-\keyword{service}
-\keyword{web}
-
diff --git a/man/getNWISSample.Rd b/man/getNWISSample.Rd
deleted file mode 100644
index e6caf8a67373caa53a117d331660ddf0b139e019..0000000000000000000000000000000000000000
--- a/man/getNWISSample.Rd
+++ /dev/null
@@ -1,42 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getNWISSample}
-\alias{getNWISSample}
-\title{Import NWIS Sample Data for EGRET analysis}
-\usage{
-getNWISSample(siteNumber, parameterCd, startDate, endDate, interactive = TRUE)
-}
-\arguments{
-\item{siteNumber}{string USGS site number. This is usually an 8 digit number}
-
-\item{parameterCd}{string USGS parameter code. This is usually an 5 digit number.}
-
-\item{startDate}{string starting date for data retrieval in the form YYYY-MM-DD.}
-
-\item{endDate}{string ending date for data retrieval in the form YYYY-MM-DD.}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-Sample dataframe
-}
-\description{
-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}
-For raw data, use getQWData. This function will retrieve the raw data, and compress it (summing constituents). See
-section 3.4 of the vignette for more details.
-}
-\examples{
-# These examples require an internet connection to run
-Sample_01075 <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31')
-Sample_All2 <- getNWISSample('05114000',c('00915','00931'), '1985-01-01', '1985-03-31')
-Sample_Select <- getNWISSample('05114000',c('00915','00931'), '', '')
-}
-\seealso{
-\code{\link{compressData}}, \code{\link{populateSampleColumns}}, , \code{\link{getNWISSample}}
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-
diff --git a/man/getUserDaily.Rd b/man/getUserDaily.Rd
deleted file mode 100644
index 64ed42aac10cfc9198f999d6e989a9fe2b094ae9..0000000000000000000000000000000000000000
--- a/man/getUserDaily.Rd
+++ /dev/null
@@ -1,39 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getUserDaily}
-\alias{getUserDaily}
-\title{Import user daily data for EGRET analysis}
-\usage{
-getUserDaily(filePath, fileName, hasHeader = TRUE, separator = ",",
- qUnit = 1, interactive = TRUE)
-}
-\arguments{
-\item{filePath}{string specifying the path to the file}
-
-\item{fileName}{string name of file to open}
-
-\item{hasHeader}{logical true if the first row of data is the column headers}
-
-\item{separator}{string character that separates data cells}
-
-\item{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}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-Daily dataframe
-}
-\description{
-Imports data from a user-supplied file, and converts it to a Daily data frame, appropriate for WRTDS calculations.
-}
-\examples{
-filePath <- system.file("extdata", package="dataRetrieval")
-filePath <- paste(filePath,"/",sep="")
-fileName <- "ChoptankRiverFlow.txt"
-Daily <- getUserDaily(filePath,fileName,separator="\\t")
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{file}
-\keyword{import}
-
diff --git a/man/getUserInfo.Rd b/man/getUserInfo.Rd
deleted file mode 100644
index c7dcd25cad4af30bd2950e9dd9291eecd6a173a6..0000000000000000000000000000000000000000
--- a/man/getUserInfo.Rd
+++ /dev/null
@@ -1,42 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getUserInfo}
-\alias{getUserInfo}
-\title{Import Metadata from User-Generated File}
-\usage{
-getUserInfo(filePath, fileName, hasHeader = TRUE, separator = ",",
- interactive = FALSE)
-}
-\arguments{
-\item{filePath}{string specifying the path to the file}
-
-\item{fileName}{string name of file to open}
-
-\item{hasHeader}{logical true if the first row of data is the column headers}
-
-\item{separator}{string character that separates data cells}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-INFO dataframe with agency, site, dateTime, value, and code columns
-}
-\description{
-Populates INFO data frame for EGRET study. Accepts a user generated file with any metadata that might
-be important for the analysis.
-Additionally, EGRET analysis requires:"drainSqKm", "staAbbrev", "constitAbbrev",
-"param.units", "paramShortName","shortName". If interactive=TRUE, the function will ask for these
-fields if they aren't supplied in the file.
-}
-\examples{
-filePath <- system.file("extdata", package="dataRetrieval")
-filePath <- paste(filePath,"/",sep="")
-fileName <- 'infoTest.csv'
-INFO <- getUserInfo(filePath,fileName, separator=",",interactive=FALSE)
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-\keyword{service}
-\keyword{web}
-
diff --git a/man/getUserSample.Rd b/man/getUserSample.Rd
deleted file mode 100644
index b6b9844172b1facfd8dc8b76691cc2658ade562f..0000000000000000000000000000000000000000
--- a/man/getUserSample.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getUserSample}
-\alias{getUserSample}
-\title{Import user sample data for EGRET analysis}
-\usage{
-getUserSample(filePath, fileName, hasHeader = TRUE, separator = ",",
- interactive = TRUE)
-}
-\arguments{
-\item{filePath}{string specifying the path to the file}
-
-\item{fileName}{string name of file to open}
-
-\item{hasHeader}{logical true if the first row of data is the column headers}
-
-\item{separator}{string character that separates data cells}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-Sample dataframe
-}
-\description{
-Imports data from a user-supplied file, and converts it to a Sample data frame (including summing multiple constituents), appropriate for WRTDS calculations.
-}
-\examples{
-filePath <- system.file("extdata", package="dataRetrieval")
-filePath <- paste(filePath,"/",sep="")
-fileName <- 'ChoptankRiverNitrate.csv'
-Sample <- getUserSample(filePath,fileName, separator=";",interactive=FALSE)
-}
-\seealso{
-\code{\link{compressData}}, \code{\link{populateSampleColumns}}
-}
-\keyword{data}
-\keyword{file}
-\keyword{import}
-
diff --git a/man/getWQPInfo.Rd b/man/getWQPInfo.Rd
deleted file mode 100644
index 46eb210ed08aa5c83c1e4035c4e2581013163f22..0000000000000000000000000000000000000000
--- a/man/getWQPInfo.Rd
+++ /dev/null
@@ -1,43 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getWQPInfo}
-\alias{getWQPInfo}
-\title{Import Metadata for Water Quality Portal Data}
-\usage{
-getWQPInfo(siteNumber, parameterCd, interactive = FALSE)
-}
-\arguments{
-\item{siteNumber}{string site number.}
-
-\item{parameterCd}{string USGS parameter code or characteristic name.}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-INFO dataframe with agency, site, dateTime, value, and code columns
-}
-\description{
-Populates INFO data frame for EGRET study. If siteNumber or parameter code (for USGS) or characteristic name
-(for non-USGS) is provided, the function will make a call to the Water Quality Portal to get metadata information.
-staAbbrev - station abbreviation, will be used in naming output files and for structuring batch jobs
-constitAbbrev - constitute abbreviation
-}
-\examples{
-# These examples require an internet connection to run
-# Automatically gets information about site 01594440 and temperature, no interaction with user
-nameToUse <- 'Specific conductance'
-pcodeToUse <- '00095'
-\dontrun{
-INFO <- getWQPInfo('USGS-04024315',pcodeToUse,interactive=TRUE)
-INFO2 <- getWQPInfo('WIDNR_WQX-10032762',nameToUse)
-# To adjust the label names:
-INFO$shortName <- "Little"
-INFO$paramShortName <- "SC"
-}
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-\keyword{service}
-\keyword{web}
-
diff --git a/man/getWQPSample.Rd b/man/getWQPSample.Rd
deleted file mode 100644
index 6418f32a98fce6ad5546d55b35ac9d2b9c78d148..0000000000000000000000000000000000000000
--- a/man/getWQPSample.Rd
+++ /dev/null
@@ -1,44 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getWQPSample}
-\alias{getWQPSample}
-\title{Import Sample Data for WRTDS}
-\usage{
-getWQPSample(siteNumber, characteristicName, startDate, endDate,
- interactive = TRUE)
-}
-\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.}
-}
-\value{
-Sample dataframe
-}
-\description{
-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.
-}
-\examples{
-# These examples require an internet connection to run
-\dontrun{
-Sample_01075 <- getWQPSample('USGS-01594440','Chloride', '', '')
-Sample_All <- getWQPSample('WIDNR_WQX-10032762','Specific conductance', '', '')
-}
-}
-\seealso{
-\code{\link{getWQPData}}, \code{\link{getWQPSites}},
-\code{\link{getWQPqwData}}, \code{\link{getNWISqwData}}, and \code{\link{readWQPData}},
-\code{\link{compressData}}, \code{\link{populateSampleColumns}}
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-
diff --git a/man/mergeReport.Rd b/man/mergeReport.Rd
deleted file mode 100644
index 1ac27dabccc1862005ab7a4133ef3c54e15b02d7..0000000000000000000000000000000000000000
--- a/man/mergeReport.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{mergeReport}
-\alias{mergeReport}
-\title{Merge Sample and Daily Data for WRTDS}
-\usage{
-mergeReport(Daily, Sample, interactive = TRUE)
-}
-\arguments{
-\item{Daily}{dataframe containing the daily data, default is Daily}
-
-\item{Sample}{dataframe containing the sample data, default is Sample}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-newSample dataframe with merged flow information
-}
-\description{
-Merges the flow data from the daily record into the sample record.
-}
-\examples{
-# These examples require an internet connection to run
-Daily <- getNWISDaily('01594440','00060', '1985-01-01', '1985-03-31')
-Sample <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31')
-Sample <- mergeReport(Daily, Sample)
-}
-\seealso{
-\code{\link{getNWISDaily}}, \code{\link{getNWISSample}}
-}
-\keyword{USGS}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-
diff --git a/man/populateConcentrations.Rd b/man/populateConcentrations.Rd
deleted file mode 100644
index 54456d911de59f398ac49c3a80dc45f2f047f20c..0000000000000000000000000000000000000000
--- a/man/populateConcentrations.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{populateConcentrations}
-\alias{populateConcentrations}
-\title{Populate Concentration Columns}
-\usage{
-populateConcentrations(rawData)
-}
-\arguments{
-\item{rawData}{vector with value and code columns}
-}
-\value{
-concentrationColumns dataframe
-}
-\description{
-Creates ConcLow, ConcHigh, Uncen (0 if censored, 1 if uncensored) columns for Sample data frame for WRTDS study.
-}
-\examples{
-code <- c("","<","")
-value <- c(1,2,3)
-dataInput <- data.frame(value, code, stringsAsFactors=FALSE)
-concentrationDF <- populateConcentrations(dataInput)
-}
-
diff --git a/man/populateDaily.Rd b/man/populateDaily.Rd
deleted file mode 100644
index 4672b2dccc1a58f8a708fbedcbc1a017e7757dc2..0000000000000000000000000000000000000000
--- a/man/populateDaily.Rd
+++ /dev/null
@@ -1,33 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{populateDaily}
-\alias{populateDaily}
-\title{Populate Daily data frame}
-\usage{
-populateDaily(rawData, qConvert, interactive = TRUE)
-}
-\arguments{
-\item{rawData}{dataframe contains at least dateTime, value, code columns}
-
-\item{qConvert}{string conversion to cubic meters per second}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-dataframe Daily
-}
-\description{
-Using raw data that has at least dateTime, value, code, populates the rest of the basic Daily data frame used in WRTDS
-}
-\examples{
-dateTime <- c('1985-01-01', '1985-01-02', '1985-01-03')
-value <- c(1,2,3)
-code <- c("","","")
-dataInput <- data.frame(dateTime, value, code, stringsAsFactors=FALSE)
-Daily <- populateDaily(dataInput, 2)
-}
-\author{
-Robert M. Hirsch \email{rhirsch@usgs.gov}
-}
-\keyword{WRTDS}
-\keyword{flow}
-
diff --git a/man/populateDateColumns.Rd b/man/populateDateColumns.Rd
deleted file mode 100644
index 423f0d0c8dc26163885bfa466b594a02cc07ad68..0000000000000000000000000000000000000000
--- a/man/populateDateColumns.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{populateDateColumns}
-\alias{populateDateColumns}
-\title{Populate Date Columns}
-\usage{
-populateDateColumns(rawData)
-}
-\arguments{
-\item{rawData}{vector with dateTime}
-}
-\value{
-DateFrame dataframe
-}
-\description{
-Creates various date columns for WRTDS study.
-}
-\examples{
-dateTime <- c('1984-02-28 13:56', '1984-03-01', '1986-03-01')
-expandedDateDF <- populateDateColumns(dateTime)
-}
-
diff --git a/man/populateParameterINFO.Rd b/man/populateParameterINFO.Rd
deleted file mode 100644
index bfd5aa1f083a76c230f0e78fb2cd1f0e14451a9d..0000000000000000000000000000000000000000
--- a/man/populateParameterINFO.Rd
+++ /dev/null
@@ -1,32 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{populateParameterINFO}
-\alias{populateParameterINFO}
-\title{Populate Parameter Information Columns}
-\usage{
-populateParameterINFO(parameterCd, INFO, interactive = TRUE)
-}
-\arguments{
-\item{parameterCd}{string USGS parameter code}
-
-\item{INFO}{dataframe with value and code columns. Default is INFO}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-INFO dataframe
-}
-\description{
-Populates INFO data frame with additional user-supplied information concerning the measured parameter.
-}
-\examples{
-#This example requires an internet connection to run
-INFO <- getNWISSiteInfo('01594440')
-parameterCd <- "01075"
-parameterData <- getNWISPcodeInfo(parameterCd)
-INFO$param.nm <- parameterData$parameter_nm
-INFO$param.units <- parameterData$parameter_units
-INFO$paramShortName <- parameterData$srsname
-INFO$paramNumber <- parameterData$parameter_cd
-INFO <- populateParameterINFO(parameterCd, INFO)
-}
-
diff --git a/man/populateSampleColumns.Rd b/man/populateSampleColumns.Rd
deleted file mode 100644
index 48be0d713bb3dd369a7c65a99344d6eaeb1e4953..0000000000000000000000000000000000000000
--- a/man/populateSampleColumns.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{populateSampleColumns}
-\alias{populateSampleColumns}
-\title{Populate Sample Columns}
-\usage{
-populateSampleColumns(rawData)
-}
-\arguments{
-\item{rawData}{dataframe with dateTime, ConcLow, ConcHigh, Uncen}
-}
-\value{
-Sample2 dataframe
-}
-\description{
-Creates ConcAve and ConcLow based on Uncen. Removes any samples with NA values in ConcHigh
-}
-\examples{
-dateTime <- c('1985-01-01', '1985-01-02', '1985-01-03')
-ConcLow <- c(1,2,0)
-ConcHigh <- c(1,2,3)
-Uncen <- c(1,1,0)
-dataInput <- data.frame(dateTime, ConcLow, ConcHigh, Uncen, stringsAsFactors=FALSE)
-Sample <- populateSampleColumns(dataInput)
-}
-
diff --git a/man/populateSiteINFO.Rd b/man/populateSiteINFO.Rd
deleted file mode 100644
index b5da355c14252cdc91400d3dc2de654dea8e6c21..0000000000000000000000000000000000000000
--- a/man/populateSiteINFO.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{populateSiteINFO}
-\alias{populateSiteINFO}
-\title{Populate Site Information Columns}
-\usage{
-populateSiteINFO(INFO, siteNumber, interactive = TRUE)
-}
-\arguments{
-\item{INFO}{dataframe with value and code columns}
-
-\item{siteNumber}{string USGS site number}
-
-\item{interactive}{logical Option for interactive mode. If true, there is user interaction for error handling and data checks.}
-}
-\value{
-INFO dataframe
-}
-\description{
-Populates INFO data frame with additional user-supplied information. Also removes fields not related to WRTDS study.
-}
-\examples{
-#This example requires an internet connection to run
-INFO <- getNWISSiteInfo('01594440')
-siteNumber <- "01594440"
-siteINFO <- populateSiteINFO(INFO, siteNumber)
-}
-
diff --git a/man/processQWData.Rd b/man/processQWData.Rd
deleted file mode 100644
index c68559e050ba0d224f575a3781b27c1e53f95fc7..0000000000000000000000000000000000000000
--- a/man/processQWData.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{processQWData}
-\alias{processQWData}
-\title{Processing of USGS NWIS Water Quality Data}
-\usage{
-processQWData(data, pCode = TRUE)
-}
-\arguments{
-\item{data}{dataframe from Water Quality Portal}
-
-\item{pCode}{logical if TRUE, assume data came from a pCode search, if FALSE, characteristic name.}
-}
-\value{
-data dataframe with first column dateTime, and at least one qualifier and value columns
-(subsequent qualifier/value columns could follow depending on the number of parameter codes)
-}
-\description{
-Processes water quality portal data. This function looks at detection limit and detection
-conditions to determine if a value is left censored or not. Censored values are given the qualifier
-"<". The dataframe is also converted from a long to wide format.
-}
-\examples{
-# These examples require an internet connection to run
-\dontrun{
-rawSample <- getWQPqwData('USGS-01594440','', '', '')
-rawSampleSelect <- processQWData(rawSample)
-}
-}
-\keyword{USGS}
-\keyword{data}
-\keyword{import}
-\keyword{service}
-\keyword{web}
-
diff --git a/man/readWQPData.Rd b/man/readWQPData.Rd
deleted file mode 100644
index aa1e2f15549d6e4bae241e45abfd913caf54ee07..0000000000000000000000000000000000000000
--- a/man/readWQPData.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{readWQPData}
-\alias{readWQPData}
-\title{Basic Water Quality Portal Data grabber}
-\usage{
-readWQPData(url)
-}
-\arguments{
-\item{url}{string URL to Water Quality Portal#'}
-}
-\value{
-retval dataframe raw data returned from the Water Quality Portal. Additionally, a POSIXct dateTime column is supplied for
-start and end times.
-}
-\description{
-Imports data from the Water Quality Portal based on a specified url.
-}
-\examples{
-# These examples require an internet connection to run
-\dontrun{
-## Examples take longer than 5 seconds:
-rawSampleURL <- constructNWISURL('USGS-01594440','01075', '1985-01-01', '1985-03-31',"wqp")
-rawSample <- readWQPData(rawSampleURL)
-}
-}
-\keyword{USGS}
-\keyword{data}
-\keyword{import}
-\keyword{service}
-\keyword{web}
-
diff --git a/man/removeDuplicates.Rd b/man/removeDuplicates.Rd
deleted file mode 100644
index 6eed234002f01221fa02e3777404c815c3a31f34..0000000000000000000000000000000000000000
--- a/man/removeDuplicates.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{removeDuplicates}
-\alias{removeDuplicates}
-\title{Remove Duplicates}
-\usage{
-removeDuplicates(Sample)
-}
-\arguments{
-\item{Sample}{dataframe with at least DecYear and ConcHigh, default name is Sample}
-}
-\value{
-Sample1 dataframe
-}
-\description{
-Removes observations from the data frame Sample when the observation has the identical date and value as another observation
-}
-\examples{
-DecYear <- c('1985.01', '1985.01', '1985.02', '1985.02', '1985.03')
-ConcHigh <- c(1,2,3,3,5)
-dataInput <- data.frame(DecYear, ConcHigh, stringsAsFactors=FALSE)
-removeDuplicates(dataInput)
-}
-
diff --git a/vignettes/Rhelp.png b/vignettes/Rhelp.png
deleted file mode 100644
index 2267f63983342275a92bf41a3f9b9f99fd0b76fd..0000000000000000000000000000000000000000
Binary files a/vignettes/Rhelp.png and /dev/null differ
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
deleted file mode 100644
index 78cf8512f5ecde9e75efe4d6874c7177b27885d8..0000000000000000000000000000000000000000
--- a/vignettes/dataRetrieval-concordance.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\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 8 1 9 0 %
-24 1 3 0 21 1 4 0 6 1 8 0 18 1 3 0 25 1 1 4 19 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 39 0 10 1 9 0 20 1 4 0 14 1 4 0 33 1 13 %
-0 39 1 14 0 18 1 2 0 14 1 2 0 49 1 4 0 7 1 4 0 11 1 2 %
-0 17 1 7 0 22 1 8 0 21 1 4 0 9 1 4 0 79 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 26 0 152 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 43 1}
diff --git a/vignettes/dataRetrieval.Rnw b/vignettes/dataRetrieval.Rnw
deleted file mode 100644
index bc52720f90eaacf7ffe93f134999ff849f5be8b5..0000000000000000000000000000000000000000
--- a/vignettes/dataRetrieval.Rnw
+++ /dev/null
@@ -1,1276 +0,0 @@
-%\VignetteIndexEntry{Introduction to the dataRetrieval package}
-%\VignetteEngine{knitr::knitr}
-%\VignetteDepends{}
-%\VignetteSuggests{xtable,EGRET}
-%\VignetteImports{zoo, XML, RCurl, reshape2,lubridate}
-%\VignettePackage{dataRetrieval}
-
-\documentclass[a4paper,11pt]{article}
-
-\usepackage{amsmath}
-\usepackage{times}
-\usepackage{hyperref}
-\usepackage[numbers, round]{natbib}
-\usepackage[american]{babel}
-\usepackage{authblk}
-\usepackage{subfig}
-\usepackage{placeins}
-\usepackage{footnote}
-\usepackage{tabularx}
-\usepackage{threeparttable}
-\usepackage{parskip}
-
-\usepackage{csquotes}
-\usepackage{setspace}
-
-% \doublespacing
-
-\renewcommand{\topfraction}{0.85}
-\renewcommand{\textfraction}{0.1}
-\usepackage{graphicx}
-
-
-\usepackage{mathptmx}% Times Roman font
-\usepackage[scaled=.90]{helvet}% Helvetica, served as a model for arial
-
-% \usepackage{indentfirst}
-% \setlength\parindent{20pt}
-\setlength{\parskip}{0pt}
-
-\usepackage{courier}
-
-\usepackage{titlesec}
-\usepackage{titletoc}
-
-\titleformat{\section}
- {\normalfont\sffamily\bfseries\LARGE}
- {\thesection}{0.5em}{}
-\titleformat{\subsection}
- {\normalfont\sffamily\bfseries\Large}
- {\thesubsection}{0.5em}{}
-\titleformat{\subsubsection}
- {\normalfont\sffamily\large}
- {\thesubsubsection}{0.5em}{}
-
-\titlecontents{section}
-[2em] % adjust left margin
-{\sffamily} % font formatting
-{\contentslabel{2.3em}} % section label and offset
-{\hspace*{-2.3em}}
-{\titlerule*[0.25pc]{.}\contentspage}
-
-\titlecontents{subsection}
-[4.6em] % adjust left margin
-{\sffamily} % font formatting
-{\contentslabel{2.3em}} % section label and offset
-{\hspace*{-2.3em}}
-{\titlerule*[0.25pc]{.}\contentspage}
-
-\titlecontents{subsubsection}
-[6.9em] % adjust left margin
-{\sffamily} % font formatting
-{\contentslabel{2.3em}} % section label and offset
-{\hspace*{-2.3em}}
-{\titlerule*[0.25pc]{.}\contentspage}
-
-\titlecontents{table}
-[0em] % adjust left margin
-{\sffamily} % font formatting
-{Table\hspace*{2em} \contentslabel {2em}} % section label and offset
-{\hspace*{4em}}
-{\titlerule*[0.25pc]{.}\contentspage}
-
-\titlecontents{figure}
-[0em] % adjust left margin
-{\sffamily} % font formatting
-{Figure\hspace*{2em} \contentslabel {2em}} % section label and offset
-{\hspace*{4em}}
-{\titlerule*[0.25pc]{.}\contentspage}
-
-%Italisize and change font of urls:
-\urlstyle{sf}
-\renewcommand\UrlFont\itshape
-
-\usepackage{caption}
-\captionsetup{
- font={sf},
- labelfont={bf,sf},
- labelsep=period,
- justification=justified,
- singlelinecheck=false
-}
-
-
-
-\textwidth=6.2in
-\textheight=8.5in
-\parskip=.3cm
-\oddsidemargin=.1in
-\evensidemargin=.1in
-\headheight=-.3in
-
-
-%------------------------------------------------------------
-% newcommand
-%------------------------------------------------------------
-\newcommand{\scscst}{\scriptscriptstyle}
-\newcommand{\scst}{\scriptstyle}
-\newcommand{\Robject}[1]{{\texttt{#1}}}
-\newcommand{\Rfunction}[1]{{\texttt{#1}}}
-\newcommand{\Rclass}[1]{\textit{#1}}
-\newcommand{\Rpackage}[1]{\textit{#1}}
-\newcommand{\Rexpression}[1]{\texttt{#1}}
-\newcommand{\Rmethod}[1]{{\texttt{#1}}}
-\newcommand{\Rfunarg}[1]{{\texttt{#1}}}
-
-\begin{document}
-
-<<openLibrary, echo=FALSE>>=
-library(xtable)
-options(continue=" ")
-options(width=60)
-library(knitr)
-
-@
-
-\renewenvironment{knitrout}{\begin{singlespace}}{\end{singlespace}}
-\renewcommand*\listfigurename{Figures}
-
-\renewcommand*\listtablename{Tables}
-
-
-%------------------------------------------------------------
-\title{The dataRetrieval R package}
-%------------------------------------------------------------
-\author[1]{Laura De Cicco}
-\author[1]{Robert Hirsch}
-\affil[1]{United States Geological Survey}
-
-
-<<include=TRUE ,echo=FALSE,eval=TRUE>>=
-opts_chunk$set(highlight=TRUE, tidy=TRUE, keep.space=TRUE, keep.blank.space=FALSE, keep.comment=TRUE, tidy=FALSE,comment="")
-knit_hooks$set(inline = function(x) {
- if (is.numeric(x)) round(x, 3)})
-knit_hooks$set(crop = hook_pdfcrop)
-
-bold.colHeaders <- function(x) {
- x <- gsub("\\^(\\d)","$\\^\\1$",x)
- x <- gsub("\\%","\\\\%",x)
- x <- gsub("\\_"," ",x)
- returnX <- paste("\\multicolumn{1}{c}{\\textbf{\\textsf{", x, "}}}", sep = "")
-}
-addSpace <- function(x) ifelse(x != "1", "[5pt]","")
-@
-
-\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} or \url{http://dx.doi.org/10.3133/tm4A10} 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 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:userFiles} 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:
-
-<<workflow, echo=TRUE,eval=FALSE>>=
-library(dataRetrieval)
-# Choptank River near Greensboro, MD
-siteNumber <- "01491000"
-ChoptankInfo <- getNWISSiteInfo(siteNumber)
-parameterCd <- "00060"
-
-#Raw daily data:
-rawDailyData <- getNWISdvData(siteNumber,parameterCd,
- "1980-01-01","2010-01-01")
-# Data compiled for EGRET analysis
-Daily <- getNWISDaily(siteNumber,parameterCd,
- "1980-01-01","2010-01-01")
-
-# Sample data Nitrate:
-parameterCd <- "00618"
-Sample <- getNWISSample(siteNumber,parameterCd,
- "1980-01-01","2010-01-01")
-
-# Metadata on site and nitrate:
-INFO <- getNWISInfo(siteNumber,parameterCd)
-
-# Merge discharge and nitrate data to one dataframe:
-Sample <- mergeReport()
-
-@
-
-
-%------------------------------------------------------------
-\section{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. 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 (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 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}.
-
-
-<<tableParameterCodes, echo=FALSE,results='asis'>>=
-pCode <- c('00060', '00065', '00010','00045','00400')
-shortName <- c("Discharge [ft$^3$/s]","Gage height [ft]","Temperature [C]", "Precipitation [in]", "pH")
-
-data.df <- data.frame(pCode, shortName, stringsAsFactors=FALSE)
-
-print(xtable(data.df,
- label="tab:params",
- caption="Common USGS Parameter Codes"),
- caption.placement="top",
- size = "\\footnotesize",
- latex.environment=NULL,
- sanitize.text.function = function(x) {x},
- sanitize.colnames.function = bold.colHeaders,
- sanitize.rownames.function = addSpace
- )
-
-@
-
-A complete list (as of September 25, 2013) is available as data attached to the package. It is accessed by the following:
-
-<<tableParameterCodesDataRetrieval>>=
-library(dataRetrieval)
-parameterCdFile <- parameterCdFile
-names(parameterCdFile)
-@
-
-
-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}.
-
-<<tableStatCodes, echo=FALSE,results='asis'>>=
-StatCode <- c('00001', '00002', '00003','00008')
-shortName <- c("Maximum","Minimum","Mean", "Median")
-
-data.df <- data.frame(StatCode, shortName, stringsAsFactors=FALSE)
-
-print(xtable(data.df,label="tab:stat",
- caption="Commonly used USGS Stat Codes"),
- caption.placement="top",
- size = "\\footnotesize",
- latex.environment=NULL,
- sanitize.colnames.function = bold.colHeaders,
- sanitize.rownames.function = addSpace
- )
-
-@
-
-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{getNWISSiteInfo}
-\label{sec:usgsSiteFileData}
-%------------------------------------------------------------
-Use the \texttt{getNWISSiteInfo} function to obtain all of the information available for a particular USGS site such as full station name, drainage area, latitude, and longitude. \texttt{getNWISSiteInfo} can also access information about multiple sites with a vector input.
-
-
-<<getSite, echo=TRUE>>=
-siteNumbers <- c("01491000","01645000")
-siteINFO <- getNWISSiteInfo(siteNumbers)
-@
-
-A specific example piece of information can be retrieved, in this case a station name, as follows:
-
-<<siteNames2, echo=TRUE>>=
-siteINFO$station.nm
-@
-Site information is obtained from \url{http://waterservices.usgs.gov/rest/Site-Test-Tool.html}
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsubsection{getNWISDataAvailability}
-\label{sec:usgsDataAvailability}
-%------------------------------------------------------------
-To discover what data is available for a particular USGS site, including measured parameters, period of record, and number of samples (count), use the \texttt{getNWISDataAvailability} function. It is possible to limit the retrieval information to a subset of types (\texttt{"}dv\texttt{"}, \texttt{"}uv\texttt{"}, or \texttt{"}qw\texttt{"}). In the following example, we limit the retrieved Choptank data to only daily data. Leaving the \texttt{"}type\texttt{"} argument blank returns all of the available data for that site.
-
-
-<<getSiteExtended, echo=TRUE>>=
-# Continuing from the previous example:
-# This pulls out just the daily data:
-
-dailyDataAvailable <- getNWISDataAvailability(siteNumbers,
- type="dv")
-
-@
-
-<<tablegda, echo=FALSE,results='asis'>>=
-tableData <- with(dailyDataAvailable,
- data.frame(
- siteNumber= site_no,
- srsname=srsname,
- startDate=as.character(startDate),
- endDate=as.character(endDate),
- count=as.character(count),
- units=parameter_units,
- statCd = statCd,
- stringsAsFactors=FALSE)
- )
-
-tableData$units[which(tableData$units == "ft3/s")] <- "ft$^3$/s"
-tableData$units[which(tableData$units == "uS/cm @25C")] <- "$\\mu$S/cm @25C"
-
-
-print(xtable(tableData,label="tab:gda",
- caption="Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]"),
- caption.placement="top",
- size = "\\footnotesize",
- latex.environment=NULL,
- sanitize.text.function = function(x) {x},
- sanitize.colnames.function = bold.colHeaders,
- sanitize.rownames.function = addSpace
- )
-
-@
-
-
-
-See Section \ref{app:createWordTable} for instructions on converting an R dataframe to a table in Microsoft\textregistered\ software Excel or Word to display a data availability table similar to Table \ref{tab:gda}. Excel, Microsoft, PowerPoint, Windows, and Word are registered trademarks of Microsoft Corporation in the United States and other countries.
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsection{Parameter Information}
-\label{sec:usgsParams}
-%------------------------------------------------------------
-To obtain all of the available information concerning a measured parameter (or multiple parameters), use the \texttt{getNWISPcodeInfo} function:
-
-<<label=getPCodeInfo, echo=TRUE>>=
-# Using defaults:
-parameterCd <- "00618"
-parameterINFO <- getNWISPcodeInfo(parameterCd)
-colnames(parameterINFO)
-@
-
-A specific example piece of information, in this case parameter name, can be obtained as follows:
-
-<<siteNames, echo=TRUE>>=
-parameterINFO$parameter_nm
-@
-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{getNWISdvData} 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.
-
-<<label=getNWISDaily, echo=TRUE, eval=TRUE>>=
-
-# Continuing with our Choptank River example
-siteNumber <- "01491000"
-parameterCd <- "00060" # Discharge
-startDate <- "" # Will request earliest date
-endDate <- "" # Will request latest date
-
-discharge <- getNWISdvData(siteNumber,
- parameterCd, startDate, endDate)
-names(discharge)
-@
-
-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:
-<<label=getNWIStemperature, echo=TRUE>>=
-
-parameterCd <- c("00010","00060") # Temperature and discharge
-statCd <- c("00001","00003") # Mean and maximum
-startDate <- "2012-01-01"
-endDate <- "2012-05-01"
-
-temperatureAndFlow <- getNWISdvData(siteNumber, parameterCd,
- startDate, endDate, statCd=statCd)
-
-@
-
-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.
-
-<<label=renameColumns, echo=TRUE>>=
-names(temperatureAndFlow)
-
-temperatureAndFlow <- renameColumns(temperatureAndFlow)
-names(temperatureAndFlow)
-@
-
-An example of plotting the above data (Figure \ref{fig:getNWIStemperaturePlot}):
-
-<<getNWIStemperaturePlot, echo=TRUE, fig.cap="Temperature and discharge plot of Choptank River in 2012.",out.width='1\\linewidth',out.height='1\\linewidth',fig.show='hold'>>=
-par(mar=c(5,5,5,5)) #sets the size of the plot window
-
-with(temperatureAndFlow, plot(
- datetime, Temperature_water_degrees_Celsius_Max_01,
- xlab="Date",ylab="Max Temperature [C]"
- ))
-par(new=TRUE)
-with(temperatureAndFlow, plot(
- datetime, Discharge_cubic_feet_per_second,
- col="red",type="l",xaxt="n",yaxt="n",xlab="",ylab="",axes=FALSE
- ))
-axis(4,col="red",col.axis="red")
-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))
-@
-
-
-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{getNWISunitData}. 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.
-
-<<label=getNWISUnit, echo=TRUE>>=
-
-parameterCd <- "00060" # Discharge
-startDate <- "2012-05-12"
-endDate <- "2012-05-13"
-dischargeToday <- getNWISunitData(siteNumber, parameterCd,
- startDate, endDate)
-@
-
-The retrieval produces the following dataframe:
-
-<<dischargeData, echo=FALSE>>=
-head(dischargeToday)
-@
-
-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{getNWISqwData}, with the input arguments: siteNumber, parameterCd, startDate, endDate, and interactive (similar to \texttt{getNWISunitData} and \texttt{getNWISdvData}). 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). Expanded = TRUE includes such columns as remark codes, value qualifying text, and detection level.
-
-
-<<label=getQW, echo=TRUE>>=
-
-# Dissolved Nitrate parameter codes:
-parameterCd <- c("00618","71851")
-startDate <- "1985-10-01"
-endDate <- "2012-09-30"
-
-dissolvedNitrate <- getNWISqwData(siteNumber, parameterCd,
- startDate, endDate, expanded=TRUE)
-names(dissolvedNitrate)
-
-
-@
-
-
-<<getQWtemperaturePlot, echo=TRUE, fig.cap=paste(parameterINFO$parameter_nm, "at", siteINFO$station.nm[1])>>=
-with(dissolvedNitrate, plot(
- startDateTime, result_va_00618,
- xlab="Date",ylab = paste(parameterINFO$srsname,
- "[",parameterINFO$parameter_units,"]")
- ))
-title(siteINFO$station.nm[1])
-@
-
-\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).
-
-
-<<label=geturl, echo=TRUE, eval=FALSE>>=
-# Dissolved Nitrate parameter codes:
-pCode <- c("00618","71851")
-startDate <- "1964-06-11"
-endDate <- "2012-12-18"
-url_qw <- constructNWISURL(siteNumber,pCode,startDate,endDate,'qw')
-url_dv <- constructNWISURL(siteNumber,"00060",startDate,endDate,
- 'dv',statCd="00003")
-url_uv <- constructNWISURL(siteNumber,"00060",startDate,endDate,'uv')
-@
-
-
-
-%------------------------------------------------------------
-\section{Water Quality Portal Web 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 database (data from EPA), NWIS database (data from USGS), STEWARDS database (data from USDA), and additional databases are slated to be included. Because only USGS uses parameter codes, a \texttt{"}characteristic name\texttt{"} must be supplied. The \texttt{getWQPqwData} function can take either a USGS parameter code, or a more general characteristic 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, eval=FALSE>>=
-specificCond <- getWQPqwData('WIDNR_WQX-10032762',
- 'Specific conductance','2011-05-01','2011-09-30')
-@
-
-Guidance for finding characteristic names can be found at: \url{http://www.waterqualitydata.us/webservices_documentation.jsp}.
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\section{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{NWIS sites}
-\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¶meterCd=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{NWIS data}
-\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{Water Quality Portal sites}
-\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{Water Quality Portal data}
-\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
-
-%------------------------------------------------------------
-\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 \enquote{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{getNWISInfo}, \texttt{getWQPInfo}, and \texttt{getUserInfo} functions obtain metadata, or data about the streamgage and measured parameters. Any number of columns can be included in this dataframe. Table \ref{tab:INFOtable} describes fields are required for EGRET functions.
-
-\begin{table}[!ht]
-\begin{minipage}{\linewidth}
-{\footnotesize
-\caption{INFO columns required in EGRET functions}
-\label{tab:INFOtable}
-\begin{tabular}{lll}
- \hline
-\multicolumn{1}{c}{\textbf{\textsf{Column Name}}} &
-\multicolumn{1}{c}{\textbf{\textsf{Type}}} &
-\multicolumn{1}{c}{\textbf{\textsf{Description}}} \\ [0pt]
- \hline
- constitAbbrev & string & Constituent abbreviation, used for saving the workspace in EGRET\\
- [5pt] drainSqKm & numeric & Drainage area in square kilometers \\
- [5pt] paramShortName & string & Parameter name to use on graphs \\
- [5pt] param.units & string & Parameter units \\
- [5pt] shortName & string & Station name to use on graphs\\
- [5pt] staAbbrev & string & Station Abbreviation \\
- \hline
-\end{tabular}
-}
-\end{minipage}
-\end{table}
-
-The function \texttt{getNWISInfo} combines \texttt{getNWISSiteInfo} and \texttt{getNWISPcodeInfo}, producing one dataframe called INFO.
-
-<<ThirdExample>>=
-parameterCd <- "00618"
-INFO <- getNWISInfo(siteNumber,parameterCd, interactive=FALSE)
-@
-
-It is also possible to create the INFO dataframe using information from the Water Quality Portal:
-
-<<WQPInfo, eval=FALSE>>=
-parameterCd <- "00618"
-INFO_WQP <- getWQPInfo("USGS-01491000",parameterCd)
-@
-
-Finally, the function \texttt{getUserInfo} can be used to convert comma separated files into an INFO dataframe.
-
-Any supplemental column that would be useful can be added to the INFO dataframe.
-
-<<addInfo, eval=TRUE, echo=TRUE>>=
-
-INFO$riverInfo <- "Major tributary of the Chesapeake Bay"
-INFO$GreensboroPopulation <- 1931
-
-@
-
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsection{Daily Data}
-\label{Dailysubsection}
-%------------------------------------------------------------
-The \texttt{getNWISDaily} 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.
-
-<<firstExample>>=
-siteNumber <- "01491000"
-startDate <- "2000-01-01"
-endDate <- "2013-01-01"
-# This call will get NWIS (ft3/s) data , and convert it to m3/s:
-Daily <- getNWISDaily(siteNumber, "00060", startDate, endDate)
-@
-
-
-
-<<colNamesDaily, echo=FALSE,results='asis'>>=
-ColumnName <- c("Date", "Q", "Julian","Month","Day","DecYear","MonthSeq","Qualifier","i","LogQ","Q7","Q30")
-Type <- c("Date", "number", "number","integer","integer","number","integer","string","integer","number","number","number")
-Description <- c("Date", "Discharge in m$^3$/s", "Number of days since January 1, 1850", "Month of the year [1-12]", "Day of the year [1-366]", "Decimal year", "Number of months since January 1, 1850", "Qualifying code", "Index of days, starting with 1", "Natural logarithm of Q", "7 day running average of Q", "30 day running average of Q")
-Units <- c("date", "m$^3$/s","days", "months","days","years","months", "character","days","numeric","m$^3$/s","m$^3$/s")
-
-DF <- data.frame(ColumnName,Type,Description,Units)
-
-print(xtable(DF, caption="Daily dataframe",label="tab:DailyDF1"),
- caption.placement="top",
- size = "\\footnotesize",
- latex.environment=NULL,
- sanitize.text.function = function(x) {x},
- sanitize.colnames.function = bold.colHeaders,
- sanitize.rownames.function = addSpace
-
- )
-
-@
-
-
-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.
-
-User-generated Sample dataframes can also be created using the \texttt{getUserDaily} function. This is discused in detail in section \ref{sec:DailyFile}.
-
-\FloatBarrier
-
-%------------------------------------------------------------
-\subsection{Sample Data}
-\label{Samplesubsection}
-%------------------------------------------------------------
-The \texttt{getNWISSample} 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{getWQPqwData} or \texttt{getWQPData} as described in the previous section.
-
-<<secondExample>>=
-parameterCd <- "00618"
-Sample <-getNWISSample(siteNumber,parameterCd,
- startDate, endDate)
-@
-
-The \texttt{getWQPSample} function retrieves Water Quality Portal sample data (STORET, NWIS, STEWARDS). The arguments for this function are siteNumber, characteristicName, startDate, endDate, interactive. Table \ref{tab:SampleDataframe} lists details of the Sample data frame.
-
-<<STORET,echo=TRUE,eval=FALSE>>=
-site <- 'WIDNR_WQX-10032762'
-characteristicName <- 'Specific conductance'
-Sample <-getWQPSample(site,characteristicName,
- startDate, endDate)
-@
-
-User-generated Sample dataframes can also be created using the \texttt{getUserSample} function. This is discused in detail in section \ref{sec:SampleFile}.
-
-\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{getNWISSample} 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}.
-
-
-
-<<label=tab:exampleComplexQW, echo=FALSE, eval=TRUE,results='asis'>>=
-cdate <- c("2003-02-15","2003-06-30","2004-09-15","2005-01-30","2005-05-30","2005-10-30")
-rdp <- c("", "<","<","","","")
-dp <- c(0.02,0.01,0.005,NA,NA,NA)
-rpp <- c("", "","<","","","")
-pp <- c(0.5,0.3,0.2,NA,NA,NA)
-rtp <- c("","","","","<","<")
-tp <- c(NA,NA,NA,0.43,0.05,0.02)
-
-DF <- data.frame(cdate,rdp,dp,rpp,pp,rtp,tp,stringsAsFactors=FALSE)
-
-xTab <- xtable(DF, caption="Example data",digits=c(0,0,0,3,0,3,0,3),label="tab:exampleComplexQW")
-
-print(xTab,
- caption.placement="top",
- size = "\\footnotesize",
- latex.environment=NULL,
- sanitize.colnames.function = bold.colHeaders,
- sanitize.rownames.function = addSpace
- )
-
-@
-
-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 getNWISSample, getWQPSample, or getUserSample. The raw data functions: \texttt{getWQPData}, \texttt{getNWISqwData}, \texttt{getWQPqwData}, \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:
-
-<<thirdExample,echo=FALSE>>=
- compressedData <- compressData(DF)
- Sample <- populateSampleColumns(compressedData)
-@
-
-<<thirdExampleView,echo=TRUE>>=
- Sample
-@
-
-Section \ref{sec:userFiles} discusses inputting user-generated files. The functions \texttt{getUserSample} and \texttt{getNWISSample} 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{getUserDaily}
-\label{sec:DailyFile}
-%------------------------------------------------------------
-The \texttt{getUserDaily} 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:
-<<openDaily, eval = FALSE>>=
-fileName <- "ChoptankRiverFlow.txt"
-filePath <- "C:/RData/"
-Daily <-getFileDaily(filePath,fileName,
- separator="\t")
-@
-
-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{getUserSample}
-\label{sec:SampleFile}
-%------------------------------------------------------------
-
-The \texttt{getUserSample} 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:
-<<openSample, eval = FALSE>>=
-fileName <- "ChoptankRiverNitrate.csv"
-filePath <- "C:/RData/"
-Sample <-getUserSample(filePath,fileName,
- separator=",")
-@
-
-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}
-
-
-<<openSample2, eval = FALSE>>=
-fileName <- "ChoptankPhosphorus.txt"
-filePath <- "C:/RData/"
-Sample <-getUserSample(filePath,fileName,
- separator="\t")
-@
-
-
-\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.
-
-
-<<mergeExample>>=
-siteNumber <- "01491000"
-parameterCd <- "00631" # Nitrate
-startDate <- "2000-01-01"
-endDate <- "2013-01-01"
-
-Daily <- getNWISDaily(siteNumber, "00060", startDate, endDate)
-Sample <- getNWISSample(siteNumber,parameterCd, startDate, endDate)
-Sample <- mergeReport(Daily,Sample)
-names(Sample)
-@
-
-\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.
-%
-% <<egretEx, echo=TRUE, eval=TRUE, fig.cap="Default \\texttt{multiPlotDataOverview}">>=
-% # Continuing Choptank example from the previous sections
-% library(EGRET)
-% multiPlotDataOverview()
-% @
-%
-% \FloatBarrier
-% \clearpage
-
-
-%------------------------------------------------------------
-\section{Summary}
-\label{sec:summary}
-%------------------------------------------------------------
-
-Tables \ref{tab:dataRetrievalFunctions1},\ref{tab:dataRetrievalOrg}, 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{getNWISdvData} & Raw USGS daily data \\
- [5pt]Daily & \texttt{getNWISData} & Raw USGS data in generalized query \\
- [5pt]Daily\tnote{1} & \texttt{getNWISDaily} & USGS daily values \\
- [5pt]Daily\tnote{1} & \texttt{getUserDaily} & User-generated daily data \\
- [5pt]Sample & \texttt{getNWISqwData} & Raw USGS water quality data \\
- [5pt]Sample & \texttt{getWQPqwData} & Raw Water Quality Data Portal data \\
- [5pt]Sample & \texttt{getWQPData} & Raw Water Quality Portal data in generalized query\\
- [5pt]Sample\tnote{1} & \texttt{getNWISSample} & USGS water quality data\\
- [5pt]Sample\tnote{1} & \texttt{getWQPSample} & Water Quality Data Portal data \\
- [5pt]Sample\tnote{1} & \texttt{getUserSample} & User-generated sample data \\
- [5pt]Unit & \texttt{getNWISunitData} & Raw USGS instantaneous data \\
- [5pt]Information\tnote{1} & \texttt{getNWISInfo} & Station and parameter code information extracted from USGS\\
- [5pt]Information\tnote{1} & \texttt{getWQPInfo} & Station and parameter information extracted from Water Quality Portal \\
- [5pt]Information\tnote{1} & \texttt{getUserInfo} & Station and parameter information extracted from user-generated file \\
- [5pt]Information & \texttt{getNWISPcodeInfo} & USGS parameter code information \\
- [5pt]Information & \texttt{getNWISSiteInfo} & USGS station information \\
- [5pt]Information & \texttt{getNWISDataAvailability} & Data available at USGS stations \\
- [5pt]Information & \texttt{getNWISSites} & USGS station information in generalized query \\
- \hline
-\end{tabular}
-
- \begin{tablenotes}
- \item[1] Indicates that the function creates a data frame suitable for use in EGRET software, otherwise data is returned in the exact form that it was received.
- \end{tablenotes}
- \end{threeparttable}
-}
-\end{table}
-
-
-\begin{table}[!ht]
-\begin{minipage}{\linewidth}
-{\footnotesize
-\begin{threeparttable}[b]
-\caption{dataRetrieval functions organization}
-\label{tab:dataRetrievalOrg}
-\begin{tabular}{|c|ccc|}
-
-\multicolumn{1}{c}{\textbf{\textsf{}}} &
-\multicolumn{1}{c}{\textbf{\textsf{Site Query}}} &
-\multicolumn{1}{c}{\textbf{\textsf{Meta Data}}} &
-\multicolumn{1}{c}{\textbf{\textsf{Data Retrieval}}} \\ [0pt]
-\hline
-\textbf{NWIS:} & \texttt{getNWISSites} & \texttt{getNWISInfo}\tnote{1} & \texttt{getNWISData} \\
-\textit{Daily} & \texttt{getNWISDataAvailability}& \texttt{getNWISSiteInfo} & \texttt{getNWISDaily}\tnote{1} \\
-\textit{Unit/Instantaneous} & & \texttt{getNWISPcodeInfo} & \texttt{getNWISSample}\tnote{1} \\
-\textit{Groundwater} & & & \texttt{getNWISdvData} \\
-\textit{Water Quality} & & & \texttt{getNWISunitData}\\
- & & & \texttt{getNWISqwData} \\
-\hline
-\textbf{Water Quality Portal:} & \texttt{getWQPSites} & \texttt{getWQPInfo}\tnote{1} & \texttt{getWQPSample}\tnote{1}\\
-\textit{USGS} & & & \texttt{getWQPqwData} \\
-\textit{EPA} & & & \texttt{getWQPData} \\
-\textit{USDA} & & & \\
-\hline
-\textbf{User-supplied files:} & & \texttt{getUserInfo}\tnote{1} & \texttt{getUserDaily}\tnote{1} \\
-\textit{Daily} & & & \texttt{getUserSample}\tnote{1} \\
-\textit{Sample} & & & \\
-\textit{Site Information} & & & \\
-
- \hline
-\end{tabular}
- \begin{tablenotes}
- \item[1] Indicates that the function creates a data frame suitable for use in EGRET software, otherwise data is returned in the exact form that it was received.
- \end{tablenotes}
- \end{threeparttable}
-}
-\end{minipage}
-\end{table}
-
-
-
-\begin{table}[!ht]
-\begin{minipage}{\linewidth}
-{\footnotesize
-\caption{Supplemental dataRetrieval 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.
-
-<<helpFunc,eval = FALSE>>=
-?removeDuplicates
-@
-
-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.:
-<<rawFunc,eval = TRUE>>=
-removeDuplicates
-@
-
-
-\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:
-<<seeVignette,eval = FALSE>>=
-vignette(dataRetrieval)
-@
-
-\FloatBarrier
-\clearpage
-%------------------------------------------------------------
-\subsection{R User: Installing dataRetrieval}
-%------------------------------------------------------------
-The following command installs dataRetrieval and subsequent required packages:
-
-<<installFromCran,eval = FALSE>>=
-install.packages("dataRetrieval",
-repos=c("http://usgs-r.github.com","http://cran.us.r-project.org"),
-dependencies=TRUE,
-type="both")
-@
-
-After installing the package, you need to open the library each time you re-start R. This is done with the simple command:
-<<openLibraryTest, eval=FALSE>>=
-library(dataRetrieval)
-@
-
-
-%------------------------------------------------------------
-\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:
-
-<<label=getSiteApp, echo=TRUE>>=
-availableData <- getNWISDataAvailability(siteNumber)
-dailyData <- availableData["dv" == availableData$service,]
-dailyData <- dailyData["00003" == dailyData$statCd,]
-
-tableData <- with(dailyData,
- data.frame(
- shortName=srsname,
- Start=startDate,
- End=endDate,
- Count=count,
- Units=parameter_units)
- )
-tableData
-@
-
-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):
-
-
-<<label=saveData, echo=TRUE, eval=FALSE>>=
-write.table(tableData, file="tableData.tsv",sep="\t",
- row.names = FALSE,quote=FALSE)
-@
-
-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
-
-%-------------------------------------
-\section{Disclaimer}
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-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.
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-
-\end{document}
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