diff --git a/R/getWaterML2Data.r b/R/getWaterML2Data.r
index 45137c609a56d88577e10f7f1c15ed68a7e37346..f0fee9c234caebff41d5f2c948e1af962964b187 100644
--- a/R/getWaterML2Data.r
+++ b/R/getWaterML2Data.r
@@ -6,7 +6,7 @@
#' @return mergedDF a data frame containing columns agency, site, dateTime, values, and remark codes for all requested combinations
#' @export
#' @import XML
-#' @importFrom plyr rbind.fill.matrix
+#' @importFrom dplyr rbind_all
#' @examples
#' URL <- "http://waterservices.usgs.gov/nwis/dv/?format=waterml,2.0&sites=01646500&startDT=2014-09-01&endDT=2014-09-08&statCd=00003¶meterCd=00060"
#' \dontrun{dataReturned3 <- getWaterML2Data(URL)}
@@ -43,7 +43,7 @@ getWaterML2Data <- function(obs_url){
ifelse("qualifier" == xmlName(x),xpathSApply(x,"./@xlink:title",namespaces = ns),"")), #originally I had the "" as xmlAttr(x)
xmlName(x)), namespaces = ns)
- DF2 <- do.call(rbind.fill.matrix, lapply(xp, t))
+ DF2 <- do.call(rbind_all, lapply(xp, t))
DF2 <- as.data.frame(DF2,stringsAsFactors=FALSE)
DF2$time <- gsub(":","",DF2$time)
DF2$time <- with(DF2, ifelse(nchar(time) > 18,as.POSIXct(strptime(time, format="%Y-%m-%dT%H%M%S%z")),
diff --git a/inst/doc/dataRetrieval.pdf b/inst/doc/dataRetrieval.pdf
index 3c9343bb0e734cc31aa0513446f0cc9b147fe02f..697f49b713b84c7c7adbcf1070691ca0b26f6bb1 100644
Binary files a/inst/doc/dataRetrieval.pdf and b/inst/doc/dataRetrieval.pdf differ
diff --git a/man/getDVData.Rd b/man/getDVData.Rd
index a3b8a030c482957e57c4aefc368799b2bc418012..e73c862defb8bbc96d34a69fec2c0d15d6d98cd5 100644
--- a/man/getDVData.Rd
+++ b/man/getDVData.Rd
@@ -29,18 +29,16 @@ but the user must carefully check the results to see if the data returns matches
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}
+This function is being deprecated for \code{\link{getNWISDaily}}.
}
\examples{
# These examples require an internet connection to run
-Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31')
-DailyCFS <- getDVData('01594440','00060', '1985-01-01', '1985-03-31',convert=FALSE)
-DailySuspSediment <- getDVData('01594440','80154', '1985-01-01', '1985-03-31')
+\dontrun{Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31')}
+\dontrun{DailyCFS <- getDVData('01594440','00060', '1985-01-01', '1985-03-31',convert=FALSE)}
+\dontrun{DailySuspSediment <- getDVData('01594440','80154', '1985-01-01', '1985-03-31')}
}
\seealso{
-\code{\link{retrieveNWISdvData}}, \code{\link{populateDaily}}
+\code{\link{retrieveNWISdvData}}, \code{\link{populateDaily}}, \code{\link{getNWISData}}
}
\keyword{USGS}
\keyword{WRTDS}
diff --git a/man/getDailyDataFromFile.Rd b/man/getDailyDataFromFile.Rd
index 737ba4b89784cd6ad393e17329230a38ef6369c1..62e5346a65d29d075faeffecfc9a574b6e994041 100644
--- a/man/getDailyDataFromFile.Rd
+++ b/man/getDailyDataFromFile.Rd
@@ -23,13 +23,13 @@ getDailyDataFromFile(filePath, fileName, hasHeader = TRUE, separator = ",",
Daily dataframe
}
\description{
-Imports data from a user-supplied file, and converts it to a Daily data frame, appropriate for WRTDS calculations.
+This function is being deprecated for \code{\link{getUserDaily}}.
}
\examples{
filePath <- system.file("extdata", package="dataRetrieval")
filePath <- paste(filePath,"/",sep="")
fileName <- "ChoptankRiverFlow.txt"
-Daily <- getDailyDataFromFile(filePath,fileName,separator="\\t")
+\dontrun{Daily <- getDailyDataFromFile(filePath,fileName,separator="\\t")}
}
\keyword{USGS}
\keyword{WRTDS}
diff --git a/man/getDataAvailability.Rd b/man/getDataAvailability.Rd
index 805ccf8849b0acdf49348cf83413ef1ee9d9258e..b4955943661147c9fb24bc6c8fac9d533c3e9893 100644
--- a/man/getDataAvailability.Rd
+++ b/man/getDataAvailability.Rd
@@ -14,14 +14,14 @@ getDataAvailability(siteNumber, type = c("uv", "dv", "qw"))
retval dataframe with all information found in the expanded site file
}
\description{
-Imports a table of available parameters, period of record, and count.
+This function is being deprecated for \code{\link{getNWISDataAvailability}}.
}
\examples{
# These examples require an internet connection to run
-availableData <- getDataAvailability('05114000')
+\dontrun{availableData <- getDataAvailability('05114000')}
# To find just unit value ('instantaneous') data:
-uvData <- getDataAvailability('05114000',type="uv")
-uvDataMulti <- getDataAvailability(c('05114000','09423350'),type="uv")
+\dontrun{uvData <- getDataAvailability('05114000',type="uv")}
+\dontrun{uvDataMulti <- getDataAvailability(c('05114000','09423350'),type="uv")}
}
\keyword{USGS}
\keyword{data}
diff --git a/man/getNWISDaily.Rd b/man/getNWISDaily.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..67a69406c90ef266368981fed9438b3f3d56a169
--- /dev/null
+++ b/man/getNWISDaily.Rd
@@ -0,0 +1,49 @@
+% 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{retrieveNWISdvData}}, \code{\link{populateDaily}}
+}
+\keyword{USGS}
+\keyword{WRTDS}
+\keyword{data}
+\keyword{import}
+
diff --git a/man/getNWISDataAvailability.Rd b/man/getNWISDataAvailability.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..8fdb4950a8b29dc6483654c88d26388d7fe91923
--- /dev/null
+++ b/man/getNWISDataAvailability.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2 (4.0.2): do not edit by hand
+\name{getNWISDataAvailability}
+\alias{getNWISDataAvailability}
+\title{USGS data availability}
+\usage{
+getNWISDataAvailability(siteNumber, type = c("uv", "dv", "qw"))
+}
+\arguments{
+\item{siteNumber}{string USGS site number.}
+
+\item{type}{vector string. Options are "uv", "dv", "qw"}
+}
+\value{
+retval dataframe with all information found in the expanded site file
+}
+\description{
+Imports a table of available parameters, period of record, and count.
+}
+\examples{
+# These examples require an internet connection to run
+availableData <- getNWISDataAvailability('05114000')
+# To find just unit value ('instantaneous') data:
+uvData <- getNWISDataAvailability('05114000',type="uv")
+uvDataMulti <- getNWISDataAvailability(c('05114000','09423350'),type="uv")
+}
+\keyword{USGS}
+\keyword{data}
+\keyword{import}
+\keyword{service}
+\keyword{web}
+
diff --git a/man/getNWISPcodeInfo.Rd b/man/getNWISPcodeInfo.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..9dd734f8eae29bc064b6a2f642f40885c307559c
--- /dev/null
+++ b/man/getNWISPcodeInfo.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2 (4.0.2): do not edit by hand
+\name{getNWISPcodeInfo}
+\alias{getNWISPcodeInfo}
+\title{USGS Parameter Data Retrieval}
+\usage{
+getNWISPcodeInfo(parameterCd, interactive = TRUE)
+}
+\arguments{
+\item{parameterCd}{vector of USGS parameter codes. 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{
+parameterData dataframe with all information from the USGS about the particular parameter (usually code, name, short name, units, and CAS registry numbers)
+}
+\description{
+Imports data from NWIS about meaured parameter based on user-supplied parameter code.
+This function gets the data from here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes}
+}
+\examples{
+# These examples require an internet connection to run
+paramINFO <- getNWISPcodeInfo(c('01075','00060','00931'))
+}
+\keyword{USGS}
+\keyword{data}
+\keyword{import}
+\keyword{service}
+\keyword{web}
+
diff --git a/man/getNWISSample.Rd b/man/getNWISSample.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..268c902f0b910fd3752e0c37b29fbbe3a16b5237
--- /dev/null
+++ b/man/getNWISSample.Rd
@@ -0,0 +1,42 @@
+% 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_All <- getNWISSample('05114000','00915;00931', '1985-01-01', '1985-03-31')
+Sample_Select <- getNWISSample('05114000','00915;00931', '', '')
+}
+\seealso{
+\code{\link{compressData}}, \code{\link{populateSampleColumns}}, , \code{\link{getNWISSample}}
+}
+\keyword{USGS}
+\keyword{WRTDS}
+\keyword{data}
+\keyword{import}
+
diff --git a/man/getNWISSiteInfo.Rd b/man/getNWISSiteInfo.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..27d7521730f6949190b9b542169f86f2e71d7fce
--- /dev/null
+++ b/man/getNWISSiteInfo.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2 (4.0.2): do not edit by hand
+\name{getNWISSiteInfo}
+\alias{getNWISSiteInfo}
+\title{USGS Site File Data Retrieval}
+\usage{
+getNWISSiteInfo(siteNumber)
+}
+\arguments{
+\item{siteNumber}{string USGS site number. This is usually an 8 digit number}
+}
+\value{
+retval dataframe with all information found in the expanded site file
+}
+\description{
+Imports data from USGS site file site. This function gets data from here: \url{http://waterservices.usgs.gov/}
+}
+\examples{
+# These examples require an internet connection to run
+siteINFO <- getNWISSiteInfo('05114000')
+siteINFOMulti <- getNWISSiteInfo(c('05114000','09423350'))
+}
+\keyword{USGS}
+\keyword{data}
+\keyword{import}
+\keyword{service}
+\keyword{web}
+
diff --git a/man/getParameterInfo.Rd b/man/getParameterInfo.Rd
index c8d2e6518a439027786a999accb536ff5b3e5be6..1dcd19e33b11ee1834d754cde74ddb2b7c613a88 100644
--- a/man/getParameterInfo.Rd
+++ b/man/getParameterInfo.Rd
@@ -14,12 +14,11 @@ getParameterInfo(parameterCd, interactive = TRUE)
parameterData dataframe with all information from the USGS about the particular parameter (usually code, name, short name, units, and CAS registry numbers)
}
\description{
-Imports data from NWIS about meaured parameter based on user-supplied parameter code.
-This function gets the data from here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes}
+This function is being deprecated for \code{\link{getNWISPcodeInfo}}.
}
\examples{
# These examples require an internet connection to run
-paramINFO <- getParameterInfo(c('01075','00060','00931'))
+paramINFO <- getParameterInfo (c('01075','00060','00931'))
}
\keyword{USGS}
\keyword{data}
diff --git a/man/getQWDataFromFile.Rd b/man/getQWDataFromFile.Rd
deleted file mode 100644
index 4817423c35c02776c47686aa4a72c2995fbce6ae..0000000000000000000000000000000000000000
--- a/man/getQWDataFromFile.Rd
+++ /dev/null
@@ -1,37 +0,0 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{getQWDataFromFile}
-\alias{getQWDataFromFile}
-\title{Basic Data Import}
-\usage{
-getQWDataFromFile(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
-}
-\description{
-Imports data from user-supplied data file. Specifically used to import water quality data for use in the WRTDS package.
-For WRTDS usage, the first column is expected to be dates, the second column remarks (specifically < if censored data),
-and the third column is measured values. There can be additional columns of data, for each column of data, there should
-be a remark column preceeding.
-}
-\examples{
-# Examples of how to use getQWDataFromFile:
-# Change the file path and file name to something meaningful:
-filePath <- system.file("extdata", package="dataRetrieval")
-filePath <- paste(filePath,"/",sep="")
-fileName <- 'ChoptankRiverNitrate.csv'
-rawSampleData <- getQWDataFromFile(filePath,fileName, separator=";")
-}
-\keyword{data}
-\keyword{file}
-\keyword{import}
-
diff --git a/man/getSTORETSampleData.Rd b/man/getSTORETSampleData.Rd
index ef391a0d3c971d7ffe27177ea698031020619cee..b478d3045695cfd4c0a7e74ba975edcde4c1e650 100644
--- a/man/getSTORETSampleData.Rd
+++ b/man/getSTORETSampleData.Rd
@@ -21,19 +21,15 @@ getSTORETSampleData(siteNumber, characteristicName, startDate, endDate,
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.
+This function is being deprecated for \code{\link{getWQPSample}}.
}
\examples{
# These examples require an internet connection to run
-Sample_01075 <- getSTORETSampleData('USGS-01594440','Chloride', '', '')
-Sample_All <- getSTORETSampleData('WIDNR_WQX-10032762','Specific conductance', '', '')
+\dontrun{Sample_01075 <- getSTORETSampleData('USGS-01594440','Chloride', '', '')}
+\dontrun{Sample_All <- getSTORETSampleData('WIDNR_WQX-10032762','Specific conductance', '', '')}
}
\seealso{
-\code{\link{getWQPData}}, \code{\link{getWQPSites}},
-\code{\link{retrieveWQPqwData}}, \code{\link{retrieveNWISqwData}}, and \code{\link{basicWQPData}},
-\code{\link{compressData}}, \code{\link{populateSampleColumns}}
+\code{\link{getWQPSample}}
}
\keyword{USGS}
\keyword{WRTDS}
diff --git a/man/getSampleData.Rd b/man/getSampleData.Rd
index 7daa684639aa93d5ef84b811748afc03336c2e0e..e2f1b497c541d868b58ab1c71a888462d9023351 100644
--- a/man/getSampleData.Rd
+++ b/man/getSampleData.Rd
@@ -20,20 +20,16 @@ getSampleData(siteNumber, parameterCd, startDate, endDate, interactive = TRUE)
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.
+This function is being deprecated for \code{\link{getNWISSample}}.
}
\examples{
# These examples require an internet connection to run
-Sample_01075 <- getSampleData('01594440','01075', '1985-01-01', '1985-03-31')
-Sample_All <- getSampleData('05114000','00915;00931', '1985-01-01', '1985-03-31')
-Sample_Select <- getSampleData('05114000','00915;00931', '', '')
+\dontrun{Sample_01075 <- getSampleData('01594440','01075', '1985-01-01', '1985-03-31')}
+\dontrun{Sample_All <- getSampleData('05114000','00915;00931', '1985-01-01', '1985-03-31')}
+\dontrun{Sample_Select <- getSampleData('05114000','00915;00931', '', '')}
}
\seealso{
-\code{\link{compressData}}, \code{\link{populateSampleColumns}}
+\code{\link{compressData}}, \code{\link{populateSampleColumns}}, \code{\link{getNWISSample}}
}
\keyword{USGS}
\keyword{WRTDS}
diff --git a/man/getSampleDataFromFile.Rd b/man/getSampleDataFromFile.Rd
index d597f75e090a03d2575b0e909afcc868b82b3ce0..293ee4bb90c32b28dcbc7cfb031a2c6a1a458b83 100644
--- a/man/getSampleDataFromFile.Rd
+++ b/man/getSampleDataFromFile.Rd
@@ -21,14 +21,13 @@ getSampleDataFromFile(filePath, fileName, hasHeader = TRUE, separator = ",",
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. See
-section 3.4 of the vignette for more details.
+This function is being deprecated for \code{\link{getUserSample}}.
}
\examples{
filePath <- system.file("extdata", package="dataRetrieval")
filePath <- paste(filePath,"/",sep="")
fileName <- 'ChoptankRiverNitrate.csv'
-Sample <- getSampleDataFromFile(filePath,fileName, separator=";",interactive=FALSE)
+\dontrun{Sample <- getSampleDataFromFile(filePath,fileName, separator=";",interactive=FALSE)}
}
\keyword{USGS}
\keyword{WRTDS}
diff --git a/man/getSiteFileData.Rd b/man/getSiteFileData.Rd
index 6affa0fc76f9340e427f37c43b2dac813bf53e12..7eeecdf26f3377eb490f1904885f4075d6a70a28 100644
--- a/man/getSiteFileData.Rd
+++ b/man/getSiteFileData.Rd
@@ -12,12 +12,12 @@ getSiteFileData(siteNumber)
retval dataframe with all information found in the expanded site file
}
\description{
-Imports data from USGS site file site. This function gets data from here: \url{http://waterservices.usgs.gov/}
+This function is being deprecated for \code{\link{getNWISSiteInfo}}.
}
\examples{
# These examples require an internet connection to run
-siteINFO <- getSiteFileData('05114000')
-siteINFOMulti <- getSiteFileData(c('05114000','09423350'))
+\dontrun{siteINFO <- getSiteFileData('05114000')}
+\dontrun{siteINFOMulti <- getSiteFileData(c('05114000','09423350'))}
}
\keyword{USGS}
\keyword{data}
diff --git a/man/getUserDaily.Rd b/man/getUserDaily.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..64ed42aac10cfc9198f999d6e989a9fe2b094ae9
--- /dev/null
+++ b/man/getUserDaily.Rd
@@ -0,0 +1,39 @@
+% 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/getUserSample.Rd b/man/getUserSample.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..a15153ebb764bbbac5c5ad07c99ecd2decd8713e
--- /dev/null
+++ b/man/getUserSample.Rd
@@ -0,0 +1,41 @@
+% 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. See
+section 3.4 of the vignette for more details.
+}
+\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{USGS}
+\keyword{WRTDS}
+\keyword{data}
+\keyword{file}
+\keyword{import}
+
diff --git a/man/getWQPSample.Rd b/man/getWQPSample.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..333a297b509569e4c4ec729b215617e511e9fa1d
--- /dev/null
+++ b/man/getWQPSample.Rd
@@ -0,0 +1,42 @@
+% 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
+Sample_01075 <- getWQPSample('USGS-01594440','Chloride', '', '')
+Sample_All <- getWQPSample('WIDNR_WQX-10032762','Specific conductance', '', '')
+}
+\seealso{
+\code{\link{getWQPData}}, \code{\link{getWQPSites}},
+\code{\link{retrieveWQPqwData}}, \code{\link{retrieveNWISqwData}}, and \code{\link{readWQPData}},
+\code{\link{compressData}}, \code{\link{populateSampleColumns}}
+}
+\keyword{USGS}
+\keyword{WRTDS}
+\keyword{data}
+\keyword{import}
+
diff --git a/man/populateParameterINFO.Rd b/man/populateParameterINFO.Rd
index cec191cc3f6a2ed95e7c80a5fe8e7f84bb5ef436..29c59aca4158c9081718fc891529449615f9ab5c 100644
--- a/man/populateParameterINFO.Rd
+++ b/man/populateParameterINFO.Rd
@@ -20,9 +20,9 @@ Populates INFO data frame with additional user-supplied information concerning t
}
\examples{
#This example requires an internet connection to run
-INFO <- getSiteFileData('01594440')
+INFO <- getNWISSiteInfo('01594440')
parameterCd <- "01075"
-parameterData <- getParameterInfo(parameterCd)
+parameterData <- getNWISPcodeInfo(parameterCd)
INFO$param.nm <- parameterData$parameter_nm
INFO$param.units <- parameterData$parameter_units
INFO$paramShortName <- parameterData$srsname
diff --git a/man/populateSiteINFO.Rd b/man/populateSiteINFO.Rd
index 9155734eb3dc1b39227a8539abf66016856e475c..b5da355c14252cdc91400d3dc2de654dea8e6c21 100644
--- a/man/populateSiteINFO.Rd
+++ b/man/populateSiteINFO.Rd
@@ -20,7 +20,7 @@ Populates INFO data frame with additional user-supplied information. Also remove
}
\examples{
#This example requires an internet connection to run
-INFO <- getSiteFileData('01594440')
+INFO <- getNWISSiteInfo('01594440')
siteNumber <- "01594440"
siteINFO <- populateSiteINFO(INFO, siteNumber)
}
diff --git a/man/basicWQPData.Rd b/man/readWQPData.Rd
similarity index 86%
rename from man/basicWQPData.Rd
rename to man/readWQPData.Rd
index d7a1768157e0ff9094822ed6de9e8454db8f551d..75a3337fbc7e012eba6935bb725435b9a9b17128 100644
--- a/man/basicWQPData.Rd
+++ b/man/readWQPData.Rd
@@ -1,9 +1,9 @@
% Generated by roxygen2 (4.0.2): do not edit by hand
-\name{basicWQPData}
-\alias{basicWQPData}
+\name{readWQPData}
+\alias{readWQPData}
\title{Basic Water Quality Portal Data grabber}
\usage{
-basicWQPData(url)
+readWQPData(url)
}
\arguments{
\item{url}{string URL to Water Quality Portal#'}
@@ -18,7 +18,7 @@ Imports data from the Water Quality Portal based on a specified url.
\examples{
# These examples require an internet connection to run
rawSampleURL <- constructNWISURL('USGS-01594440','01075', '1985-01-01', '1985-03-31',"wqp")
-rawSample <- basicWQPData(rawSampleURL)
+rawSample <- readWQPData(rawSampleURL)
}
\keyword{USGS}
\keyword{data}
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index 181c612dc70ef26bf5b9524e1b8f541b20fe6410..249761fafbe1f1c3fc437d83153370819b2b5795 100644
--- a/vignettes/dataRetrieval-concordance.tex
+++ b/vignettes/dataRetrieval-concordance.tex
@@ -2,8 +2,8 @@
1 127 1 49 0 1 7 15 1 1 14 55 1 3 0 36 1 2 0 8 1 9 0 %
24 1 3 0 21 1 4 0 6 1 8 0 18 1 3 0 26 1 1 4 17 1 9 0 %
6 1 7 0 22 1 8 0 16 1 2 0 11 1 23 0 22 1 9 0 20 1 3 0 %
-6 1 17 0 28 1 12 0 10 1 9 0 16 1 4 0 18 1 4 0 31 1 17 %
+6 1 17 0 28 1 12 0 10 1 9 0 20 1 4 0 14 1 4 0 32 1 17 %
0 39 1 14 0 18 1 2 0 14 1 2 0 23 1 4 0 17 1 7 0 22 1 %
8 0 19 1 4 0 9 1 4 0 78 1 1 2 9 1 1 4 4 1 20 0 44 1 4 %
-0 30 1 4 0 22 1 4 0 21 1 37 0 13 1 9 0 94 1 4 0 9 1 %
-13 0 13 1 4 0 14 1 4 0 5 1 4 0 23 1 18 0 8 1 4 0 60 1}
+0 30 1 4 0 22 1 4 0 21 1 37 0 13 1 9 0 132 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
index 0e36a3c5ee228ea23ad194192b159a9f2be35f0c..305319c399f4f95f6bdcdd65f863e8bd0f85647f 100644
--- a/vignettes/dataRetrieval.Rnw
+++ b/vignettes/dataRetrieval.Rnw
@@ -184,7 +184,7 @@ addSpace <- function(x) ifelse(x != "1", "[5pt]","")
The dataRetrieval package was created to simplify the process of loading hydrologic data into the R environment. It has been specifically designed to work seamlessly with the EGRET R package: Exploration and Graphics for RivEr Trends. See: \url{https://github.com/USGS-R/EGRET/wiki} for information on EGRET. EGRET is designed to provide analysis of water quality data sets using the Weighted Regressions on Time, Discharge and Season (WRTDS) method as well as analysis of discharge trends using robust time-series smoothing techniques. Both of these capabilities provide both tabular and graphical analyses of long-term data sets.
-The dataRetrieval package is designed to retrieve many of the major data types of U.S. Geological Survey (USGS) hydrologic data that are available on the Web. Users may also load data from other sources (text files, spreadsheets) using dataRetrieval. Section \ref{sec:genRetrievals} provides examples of how one can obtain raw data from USGS sources on the Web and load them into dataframes within the R environment. The functionality described in section \ref{sec:genRetrievals} is for general use and is not tailored for the specific uses of the EGRET package. The functionality described in section \ref{sec:EGRETdfs} is tailored specifically to obtaining input from the Web and structuring it for use in the EGRET package. The functionality described in section \ref{sec:summary} is for converting hydrologic data from user-supplied files and structuring it specifically for use in the EGRET package.
+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.
@@ -194,19 +194,19 @@ A quick workflow for major dataRetrieval functions:
library(dataRetrieval)
# Choptank River near Greensboro, MD
siteNumber <- "01491000"
-ChoptankInfo <- getSiteFileData(siteNumber)
+ChoptankInfo <- getNWISSiteInfo(siteNumber)
parameterCd <- "00060"
#Raw daily data:
rawDailyData <- retrieveNWISdvData(siteNumber,parameterCd,
"1980-01-01","2010-01-01")
# Data compiled for EGRET analysis
-Daily <- getDVData(siteNumber,parameterCd,
+Daily <- getNWISDaily(siteNumber,parameterCd,
"1980-01-01","2010-01-01")
# Sample data Nitrate:
parameterCd <- "00618"
-Sample <- getSampleData(siteNumber,parameterCd,
+Sample <- getNWISSample(siteNumber,parameterCd,
"1980-01-01","2010-01-01")
# Metadata on site and nitrate:
@@ -219,10 +219,10 @@ Sample <- mergeReport()
%------------------------------------------------------------
-\section{General USGS Web Retrievals}
+\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. The siteNumber for this streamgage is 01491000. Daily discharge measurements are available as far back as 1948. Additionally, nitrate has been measured since 1964.
+In this section, five examples of Web retrievals document how to get raw data. This data includes site information (\ref{sec:usgsSite}), measured parameter information (\ref{sec:usgsParams}), historical daily values(\ref{sec:usgsDaily}), unit values (which include real-time data but can also include other sensor data stored at regular time intervals) (\ref{sec:usgsRT}), and water quality data (\ref{sec:usgsWQP}) or (\ref{sec:usgsSTORET}). We will use the Choptank River near Greensboro, MD as an example. Daily discharge measurements are available as far back as 1948. Additionally, nitrate has been measured since 1964.
% %------------------------------------------------------------
% \subsection{Introduction}
@@ -295,15 +295,15 @@ Examples for using these siteNumber's, parameter codes, and stat codes will be p
%------------------------------------------------------------
%------------------------------------------------------------
-\subsubsection{getSiteFileData}
+\subsubsection{getNWISSiteInfo}
\label{sec:usgsSiteFileData}
%------------------------------------------------------------
-Use the \texttt{getSiteFileData} function to obtain all of the information available for a particular USGS site such as full station name, drainage area, latitude, and longitude. \texttt{getSiteFileData} can also access information about multiple sites with a vector input.
+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 <- getSiteFileData(siteNumbers)
+siteINFO <- getNWISSiteInfo(siteNumbers)
@
A specific example piece of information can be retrieved, in this case a station name, as follows:
@@ -315,17 +315,17 @@ Site information is obtained from \url{http://waterservices.usgs.gov/rest/Site-T
\FloatBarrier
%------------------------------------------------------------
-\subsubsection{getDataAvailability}
+\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{getDataAvailability} function. It is possible to limit the retrieval information to a subset of types (\texttt{"}dv\texttt{"}, \texttt{"}uv\texttt{"}, or \texttt{"}qw\texttt{"}). In the following example, we limit the retrieved Choptank data to only daily data. Leaving the \texttt{"}type\texttt{"} argument blank returns all of the available data for that site.
+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 <- getDataAvailability(siteNumbers,
+dailyDataAvailable <- getNWISDataAvailability(siteNumbers,
type="dv")
@
@@ -368,12 +368,12 @@ See Section \ref{app:createWordTable} for instructions on converting an R datafr
\subsection{Parameter Information}
\label{sec:usgsParams}
%------------------------------------------------------------
-To obtain all of the available information concerning a measured parameter (or multiple parameters), use the \texttt{getParameterInfo} function:
+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 <- getParameterInfo(parameterCd)
+parameterINFO <- getNWISPcodeInfo(parameterCd)
colnames(parameterINFO)
@
@@ -520,20 +520,6 @@ title(siteINFO$station.nm[1])
\FloatBarrier
-
-
-%------------------------------------------------------------
-\subsection{STORET Water Quality Retrievals}
-\label{sec:usgsSTORET}
-%------------------------------------------------------------
-There are additional water quality data sets available from the Water Quality Data Portal (\url{http://www.waterqualitydata.us/}). These data sets can be housed in either the STORET (data from EPA), NWIS database (data from USGS), and additional databases are slated to be included. Because only USGS uses parameter codes, a \texttt{"}characteristic name\texttt{"} must be supplied. The \texttt{retrieveWQPqwData} function can take either a USGS parameter code, or a more general cahracteristic name in the parameterCd input argument. The Water Quality Data Portal includes data discovery tools and information on characteristic names. The following example retrieves specific conductance from a DNR site in Wisconsin.
-
-
-<<label=getQWData, echo=TRUE, eval=FALSE>>=
-specificCond <- retrieveWQPqwData('WIDNR_WQX-10032762',
- 'Specific conductance','2011-05-01','2011-09-30')
-@
-
%------------------------------------------------------------
\subsection{URL Construction}
\label{sec:usgsURL}
@@ -552,16 +538,31 @@ url_dv <- constructNWISURL(siteNumber,"00060",startDate,endDate,
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 (data from EPA), NWIS database (data from USGS), STEWARDS database (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{retrieveWQPqwData} function can take either a USGS parameter code, or a more general cahracteristic name in the parameterCd input argument. The Water Quality Data Portal includes data discovery tools and information on characteristic names. The following example retrieves specific conductance from a DNR site in Wisconsin.
+
+
+<<label=getQWData, echo=TRUE, eval=FALSE>>=
+specificCond <- retrieveWQPqwData('WIDNR_WQX-10032762',
+ 'Specific conductance','2011-05-01','2011-09-30')
+@
+
+
\FloatBarrier
%------------------------------------------------------------
-\subsection{Generalized Retrievals}
+\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{Generalized NWIS site retrievals}
+\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:
@@ -585,7 +586,7 @@ nrow(sites)
%------------------------------------------------------------
-\subsubsection{Generalized NWIS data retrievals}
+\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.
@@ -623,7 +624,7 @@ nrow(dischargeWI)
@
%------------------------------------------------------------
-\subsubsection{Generalized Water Quality Portal site retrievals}
+\subsubsection{Water Quality Portal sites}
\label{sec:WQPGenSite}
%------------------------------------------------------------
@@ -642,7 +643,7 @@ sitesNJ <- getWQPSites(statecode="US:34",
%------------------------------------------------------------
-\subsubsection{Generalized Water Quality Portal data retrievals}
+\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:
@@ -662,7 +663,7 @@ dataPH <- getWQPData(statecode="US:55",
\section{Data Retrievals Structured For Use In The EGRET Package}
\label{sec:EGRETdfs}
%------------------------------------------------------------
-Rather than using the raw data as retrieved by the Web, the dataRetrieval package also includes functions that return the data in a structure that has been designed to work with the EGRET R package (\url{https://github.com/USGS-R/EGRET/wiki}). In general, these dataframes may be much more 'R-friendly' than the raw data, and will contain additional date information that allows for efficient data analysis.
+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.
@@ -670,7 +671,7 @@ In this section, we use 3 dataRetrieval functions to get sufficient data to perf
\subsection{INFO Data}
\label{INFOsubsection}
%------------------------------------------------------------
-The \texttt{getMetaData} function obtains metadata, or data about the streamgage and measured parameters. This function combines \texttt{getSiteFileData} and \texttt{getParameterInfo}, producing one dataframe called INFO.
+The \texttt{getMetaData} function obtains metadata, or data about the streamgage and measured parameters. This function combines \texttt{getNWISSiteInfo} and \texttt{getNWISPcodeInfo}, producing one dataframe called INFO.
<<ThirdExample>>=
parameterCd <- "00618"
@@ -684,14 +685,14 @@ INFO <-getMetaData(siteNumber,parameterCd, interactive=FALSE)
\subsection{Daily Data}
\label{Dailysubsection}
%------------------------------------------------------------
-The \texttt{getDVData} function retrieves the daily values (discharge in this case). It requires the inputs siteNumber, parameterCd, startDate, endDate, interactive, and convert. Most of these arguments are described in section \ref{sec:genRetrievals}, however \texttt{"}convert\texttt{"} is a new argument (that defaults to TRUE). The convert argument tells the program to convert the values from cubic feet per second (ft\textsuperscript{3}/s) to cubic meters per second (m\textsuperscript{3}/s) as shown in the example Daily data frame in Table \ref{tab:DailyDF1}. For EGRET applications with NWIS Web retrieval, do not use this argument (the default is TRUE), EGRET assumes that discharge is always stored in units of cubic meters per second. If you don't want this conversion and are not using EGRET, set convert=FALSE in the function call.
+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 <- getDVData(siteNumber, "00060", startDate, endDate)
+Daily <- getNWISDaily(siteNumber, "00060", startDate, endDate)
@
@@ -727,20 +728,20 @@ Notice that the \enquote{Day of the year} column can span from 1 to 366. The 366
\subsection{Sample Data}
\label{Samplesubsection}
%------------------------------------------------------------
-The \texttt{getSampleData} function retrieves USGS sample data from NWIS. The arguments for this function are also siteNumber, parameterCd, startDate, endDate, interactive. These are the same inputs as \texttt{retrieveWQPqwData} or \texttt{getWQPData} as described in the previous section.
+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{retrieveWQPqwData} or \texttt{getWQPData} as described in the previous section.
<<secondExample>>=
parameterCd <- "00618"
-Sample <-getSampleData(siteNumber,parameterCd,
+Sample <-getNWISSample(siteNumber,parameterCd,
startDate, endDate)
@
-The \texttt{getSTORETSampleData} function retrieves STORET sample data (or other non-NWIS data) from the water quality portal. The arguments for this function are siteNumber, characteristicName, startDate, endDate, interactive. Table \ref{tab:SampleDataframe} lists details of the Sample data frame.
+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 <-getSTORETSampleData(site,characteristicName,
+Sample <-getWQPSample(site,characteristicName,
startDate, endDate)
@
@@ -786,7 +787,7 @@ Sample <-getSTORETSampleData(site,characteristicName,
Notice that the \enquote{Day of the year} column can span from 1 to 366. The 366 accounts for leap years. Every day has a consistent day of the year. This means, February 28\textsuperscript{th} is always the 59\textsuperscript{th} day of the year, Feb. 29\textsuperscript{th} is always the 60\textsuperscript{th} day of the year, and March 1\textsuperscript{st} is always the 61\textsuperscript{st} day of the year whether or not it is a leap year.
-Section \ref{sec:cenValues} is about summing multiple constituents, including how interval censoring is used. Since the Sample data frame is structured to only contain one constituent, when more than one parameter codes are requested, the \texttt{getSampleData} function will sum the values of each constituent as described below.
+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
@@ -824,7 +825,7 @@ print(xTab,
@
-The dataRetrieval package will \enquote{add up} all the values in a given row to form the total for that sample when using the Sample dataframe. Thus, you only want to enter data that should be added together. If you want a dataframe with multiple constituents that are not summed, do not use getSampleData, getSTORETSampleData, or getSampleDataFromFile. The raw data functions: \texttt{getWQPData}, \texttt{retrieveNWISqwData}, \texttt{retrieveWQPqwData}, \texttt{getWQPData} will not sum constituents, but leave them in their individual columns.
+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{retrieveNWISqwData}, \texttt{retrieveWQPqwData}, \texttt{getWQPData} will not sum constituents, but leave them in their individual columns.
For example, we might know the value for dp on 5/30/2005, but we don't want to put it in the table because under the rules of this data set, we are not supposed to add it in to the values in 2005.
@@ -841,7 +842,7 @@ For the more complex example case, let us say dp is reported as \verb@<@0.01 and
Sample
@
-Section \ref{sec:userFiles} discusses inputting user-generated files. The functions \texttt{getSampleDataFromFile} and \texttt{getSampleData} assume summation with interval censoring inputs, and are discussed in sections \ref{sec:DailyFile} and \ref{sec:SampleFile}.
+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
@@ -852,10 +853,10 @@ Section \ref{sec:userFiles} discusses inputting user-generated files. The functi
In addition to retrieving data from the USGS Web services, the dataRetrieval package also includes functions to generate the Daily and Sample data frame from local files.
%------------------------------------------------------------
-\subsubsection{getDailyDataFromFile}
+\subsubsection{getUserDaily}
\label{sec:DailyFile}
%------------------------------------------------------------
-The \texttt{getDailyDataFromFile} function will load a user-supplied text file and convert it to the Daily dataframe. The file should have two columns, the first dates, the second values. The dates are formatted either mm/dd/yyyy or yyyy-mm-dd. Using a 4-digit year is required. This function has the following inputs: filePath, fileName,hasHeader (TRUE/FALSE), separator, qUnit, and interactive (TRUE/FALSE). filePath is a string that defines the path to your file, and the string can either be a full path, or path relative to your R working directory. The input fileName is a string that defines the file name (including the extension).
+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.
@@ -881,7 +882,7 @@ The call to open this file, convert the discharge to cubic meters per second, an
<<openDaily, eval = FALSE>>=
fileName <- "ChoptankRiverFlow.txt"
filePath <- "C:/RData/"
-Daily <- getDailyDataFromFile(filePath,fileName,
+Daily <-getFileDaily(filePath,fileName,
separator="\t")
@
@@ -890,11 +891,11 @@ Microsoft\textregistered\ Excel files can be a bit tricky to import into R direc
\FloatBarrier
%------------------------------------------------------------
-\subsubsection{getSampleDataFromFile}
+\subsubsection{getUserSample}
\label{sec:SampleFile}
%------------------------------------------------------------
-The \texttt{getSampleDataFromFile} function will import a user-generated file and populate the Sample dataframe. The difference between sample data and discharge data is that the code requires a third column that contains a remark code, either blank or \verb@"<"@, which will tell the program that the data were \enquote{left-censored} (or, below the detection limit of the sensor). Therefore, the data must be in the form: date, remark, value. An example of a comma-delimited file is:
+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}
@@ -911,7 +912,7 @@ The call to open this file, and populate the Sample dataframe is:
<<openSample, eval = FALSE>>=
fileName <- "ChoptankRiverNitrate.csv"
filePath <- "C:/RData/"
-Sample <- getSampleDataFromFile(filePath,fileName,
+Sample <-getUserSample(filePath,fileName,
separator=",")
@
@@ -933,7 +934,7 @@ date rdp dp rpp pp rtp tp
<<openSample2, eval = FALSE>>=
fileName <- "ChoptankPhosphorus.txt"
filePath <- "C:/RData/"
-Sample <- getSampleDataFromFile(filePath,fileName,
+Sample <-getUserSample(filePath,fileName,
separator="\t")
@
@@ -952,8 +953,8 @@ parameterCd <- "00631" # Nitrate
startDate <- "2000-01-01"
endDate <- "2013-01-01"
-Daily <- getDVData(siteNumber, "00060", startDate, endDate)
-Sample <- getSampleData(siteNumber,parameterCd, startDate, endDate)
+Daily <- getNWISDaily(siteNumber, "00060", startDate, endDate)
+Sample <- getNWISSample(siteNumber,parameterCd, startDate, endDate)
Sample <- mergeReport()
head(Sample)
@
@@ -980,7 +981,7 @@ multiPlotDataOverview()
\label{sec:summary}
%------------------------------------------------------------
-Tables \ref{tab:dataRetrievalFunctions1} and \ref{tab:dataRetrievalMisc} summarize the data retrieval functions:
+Tables \ref{tab:dataRetrievalFunctions1},\ref{tab:dataRetrievalOrg}, and \ref{tab:dataRetrievalMisc} summarize the data retrieval functions:
\begin{table}
{\footnotesize
@@ -995,20 +996,19 @@ Tables \ref{tab:dataRetrievalFunctions1} and \ref{tab:dataRetrievalMisc} summari
\multicolumn{1}{c}{\textbf{\textsf{Description}}} \\ [0pt]
\hline
Daily & \texttt{retrieveNWISdvData} & Raw USGS daily data \\
- [5pt]Daily\tnote{1} & \texttt{getDVData} & USGS daily values \\
- [5pt]Daily\tnote{1} & \texttt{getDailyDataFromFile} & User generated daily data \\
+ [5pt]Daily\tnote{1} & \texttt{getNWISDaily} & USGS daily values \\
+ [5pt]Daily\tnote{1} & \texttt{getUserDaily} & User generated daily data \\
[5pt]Sample & \texttt{retrieveNWISqwData} & Raw USGS water quality data \\
[5pt]Sample & \texttt{retrieveWQPqwData} & Raw Water Quality Data Portal data \\
- [5pt]Sample & \texttt{getQWDataFromFile} & Raw user generated water quality data \\
[5pt]Sample & \texttt{getWQPData} & General Water Quality Portal\\
- [5pt]Sample\tnote{1} & \texttt{getSampleData} & USGS water quality data\\
- [5pt]Sample\tnote{1} & \texttt{getSTORETSampleData} & STORET Water Quality Data Portal data \\
- [5pt]Sample\tnote{1} & \texttt{getSampleDataFromFile} & User generated sample data \\
+ [5pt]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{retrieveNWISunitData} & Raw USGS instantaneous data \\
[5pt]Information\tnote{1} & \texttt{getMetaData} & USGS station and parameter code information \\
- [5pt]Information & \texttt{getParameterInfo} & USGS parameter code information \\
- [5pt]Information & \texttt{getSiteFileData} & USGS station information \\
- [5pt]Information & \texttt{getDataAvailability} & Data available at USGS stations \\
+ [5pt]Information & \texttt{getNWISPcodeInfo} & USGS parameter code information \\
+ [5pt]Information & \texttt{getNWISSiteInfo} & USGS station information \\
+ [5pt]Information & \texttt{getNWISDataAvailability} & Data available at USGS stations \\
\hline
\end{tabular}
@@ -1023,7 +1023,46 @@ Tables \ref{tab:dataRetrievalFunctions1} and \ref{tab:dataRetrievalMisc} summari
\begin{table}[!ht]
\begin{minipage}{\linewidth}
{\footnotesize
-\caption{dataRetrieval miscellaneous functions}
+\caption{dataRetrieval functions organization}
+\label{tab:dataRetrievalOrg}
+\hspace*{-1.5cm}
+\begin{tabular}{|c|cccc|}
+
+\multicolumn{1}{c}{\textbf{\textsf{Source}}} &
+\multicolumn{1}{c}{\textbf{\textsf{Site Query}}} &
+\multicolumn{1}{c}{\textbf{\textsf{Meta Data}}} &
+\multicolumn{1}{c}{\textbf{\textsf{Raw Data}}} &
+\multicolumn{1}{c}{\textbf{\textsf{EGRET Data}}} \\ [0pt]
+\hline
+\textbf{NWIS:} & \texttt{getNWISSites} & & \texttt{getNWISData} & \\
+\textit{Daily} & & \texttt{getNWISSiteInfo} & \texttt{retrieveNWISdvData} & \texttt{getNWISDaily} \\
+\textit{Unit/Instantaneous} & \texttt{getNWISDataAvailability} & \texttt{getNWISPcodeInfo} & \texttt{retrieveNWISunitData} & \\
+\textit{Groundwater} & & \texttt{getNWISInfo} & & \\
+\textit{Water Quality} & & & \texttt{retrieveNWISqwDAta} & \texttt{getNWISSample}\\
+\hline
+\textbf{Water Quality Portal:} & \texttt{getWQPSites} & \texttt{getWQPInfo} & \texttt{retrieveWQPqwData} & \texttt{getWQPSample} \\
+\textit{USGS} & & & \texttt{getWQPData} & \\
+\textit{EPA} & & & & \\
+\textit{USDA} & & & & \\
+\hline
+\textbf{User-supplied files:} & & & & \\
+\textit{Daily} & & & & \texttt{getUserDaily}\\
+\textit{Sample} & & & & \texttt{getUserSample}\\
+\textit{Site Information} & & \texttt{getUserInfo} & & \\
+
+ \hline
+\end{tabular}
+\hspace*{-1.5cm}
+}
+\end{minipage}
+\end{table}
+
+
+
+\begin{table}[!ht]
+\begin{minipage}{\linewidth}
+{\footnotesize
+\caption{dataRetrieval function organization}
\label{tab:dataRetrievalMisc}
\begin{tabular}{ll}
\hline
@@ -1114,7 +1153,7 @@ library(dataRetrieval)
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 <- getDataAvailability(siteNumber)
+availableData <- getNWISDataAvailability(siteNumber)
dailyData <- availableData["dv" == availableData$service,]
dailyData <- dailyData["00003" == dailyData$statCd,]
@@ -1177,22 +1216,5 @@ From Excel, it is simple to copy and paste the tables in other Microsoft\textreg
%------------------------------------
This information is preliminary and is subject to revision. It is being provided to meet the need for timely best science. The information is provided on the condition that neither the U.S. Geological Survey nor the U.S. Government may be held liable for any damages resulting from the authorized or unauthorized use of the information.
-% %------------------------------------------------------------
-% % BIBLIO
-% %------------------------------------------------------------
-% \begin{thebibliography}{10}
-%
-% \bibitem{HirschI}
-% Helsel, D.R. and R. M. Hirsch, 2002. Statistical Methods in Water Resources Techniques of Water Resources Investigations, Book 4, chapter A3. U.S. Geological Survey. 522 pages. \url{http://pubs.usgs.gov/twri/twri4a3/}
-%
-% \bibitem{HirschII}
-% Hirsch, R. M., Moyer, D. L. and Archfield, S. A. (2010), Weighted Regressions on Time, Discharge, and Season (WRTDS), with an Application to Chesapeake Bay River Inputs. JAWRA Journal of the American Water Resources Association, 46: 857-880. doi: 10.1111/j.1752-1688.2010.00482.x \url{http://onlinelibrary.wiley.com/doi/10.1111/j.1752-1688.2010.00482.x/full}
-%
-% \bibitem{HirschIII}
-% Sprague, L. A., Hirsch, R. M., and Aulenbach, B. T. (2011), Nitrate in the Mississippi River and Its Tributaries, 1980 to 2008: Are We Making Progress? Environmental Science \& Technology, 45 (17): 7209-7216. doi: 10.1021/es201221s \url{http://pubs.acs.org/doi/abs/10.1021/es201221s}
-%
-% \end{thebibliography}
-
-% \end{document}
\end{document}
diff --git a/vignettes/dataRetrieval.lof b/vignettes/dataRetrieval.lof
new file mode 100644
index 0000000000000000000000000000000000000000..9624362eb664791c72992a573779ac88ed60c45a
--- /dev/null
+++ b/vignettes/dataRetrieval.lof
@@ -0,0 +1,7 @@
+\select@language {american}
+\contentsline {figure}{\numberline {1}{\ignorespaces Temperature and discharge plot of Choptank River in 2012}}{9}{figure.caption.4}
+\contentsline {figure}{\numberline {2}{\ignorespaces Nitrate, water, filtered, milligrams per liter as nitrogen at CHOPTANK RIVER NEAR GREENSBORO, MD}}{12}{figure.caption.5}
+\contentsline {figure}{\numberline {3}{\ignorespaces Default \texttt {multiPlotDataOverview}}}{24}{figure.caption.11}
+\contentsline {figure}{\numberline {4}{\ignorespaces A simple R help file\relax }}{29}{figure.caption.16}
+\contentsline {figure}{\numberline {5}{\ignorespaces A simple table produced in Microsoft\textregistered \ Excel. Additional formatting will be requried, for example converting u to $\mu $ \relax }}{32}{figure.caption.17}
+\contentsfinish
diff --git a/vignettes/dataRetrieval.log b/vignettes/dataRetrieval.log
new file mode 100644
index 0000000000000000000000000000000000000000..f999a06bdb65ae9010e32600fb70cfb856dc0677
--- /dev/null
+++ b/vignettes/dataRetrieval.log
@@ -0,0 +1,1091 @@
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diff --git a/vignettes/dataRetrieval.lot b/vignettes/dataRetrieval.lot
new file mode 100644
index 0000000000000000000000000000000000000000..a8399f8f622548fc1e2fdd0bccccf39edafb789d
--- /dev/null
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+\select@language {american}
+\contentsline {table}{\numberline {1}{\ignorespaces Common USGS Parameter Codes\relax }}{4}{table.caption.1}
+\contentsline {table}{\numberline {2}{\ignorespaces Commonly used USGS Stat Codes\relax }}{5}{table.caption.2}
+\contentsline {table}{\numberline {3}{\ignorespaces Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]\relax }}{6}{table.caption.3}
+\contentsline {table}{\numberline {4}{\ignorespaces NWIS general data calls\relax }}{14}{table.caption.6}
+\contentsline {table}{\numberline {5}{\ignorespaces Daily dataframe\relax }}{17}{table.caption.7}
+\contentsline {table}{\numberline {6}{\ignorespaces Sample dataframe\relax }}{18}{table.caption.9}
+\contentsline {table}{\numberline {7}{\ignorespaces Example data\relax }}{19}{table.caption.10}
+\contentsline {table}{\numberline {8}{\ignorespaces dataRetrieval functions\relax }}{26}{table.caption.13}
+\contentsline {table}{\numberline {9}{\ignorespaces dataRetrieval functions organization\relax }}{26}{table.caption.14}
+\contentsline {table}{\numberline {10}{\ignorespaces dataRetrieval function organization\relax }}{27}{table.caption.15}
+\contentsfinish
diff --git a/vignettes/dataRetrieval.pdf b/vignettes/dataRetrieval.pdf
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+%\VignetteIndexEntry{Introduction to the dataRetrieval package}
+%\VignetteEngine{knitr::knitr}
+%\VignetteDepends{}
+%\VignetteSuggests{xtable,EGRET}
+%\VignetteImports{zoo, XML, RCurl}
+%\VignettePackage{dataRetrieval}
+
+\documentclass[a4paper,11pt]{article}\usepackage[]{graphicx}\usepackage[]{color}
+%% maxwidth is the original width if it is less than linewidth
+%% otherwise use linewidth (to make sure the graphics do not exceed the margin)
+\makeatletter
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+ \linewidth
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+ \Gin@nat@width
+ \fi
+}
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+
+\usepackage{framed}
+\makeatletter
+\newenvironment{kframe}{%
+ \def\at@end@of@kframe{}%
+ \ifinner\ifhmode%
+ \def\at@end@of@kframe{\end{minipage}}%
+ \begin{minipage}{\columnwidth}%
+ \fi\fi%
+ \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
+ \colorbox{shadecolor}{##1}\hskip-\fboxsep
+ % There is no \\@totalrightmargin, so:
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+ \MakeFramed {\advance\hsize-\width
+ \@totalleftmargin\z@ \linewidth\hsize
+ \@setminipage}}%
+ {\par\unskip\endMakeFramed%
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+\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX
+
+\usepackage{alltt}
+
+\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
+
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+
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+ {\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}}}
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+\begin{document}
+
+
+
+\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}
+
+
+
+
+\noindent{\huge\textsf{\textbf{The dataRetrieval R package}}}
+
+\noindent\textsf{By Laura De Cicco and Robert Hirsch}
+
+\noindent\textsf{\today}
+
+% \maketitle
+%
+% \newpage
+
+\tableofcontents
+\listoffigures
+\listoftables
+
+\newpage
+
+%------------------------------------------------------------
+\section{Introduction to dataRetrieval}
+%------------------------------------------------------------
+The dataRetrieval package was created to simplify the process of loading hydrologic data into the R environment. It has been specifically designed to work seamlessly with the EGRET R package: Exploration and Graphics for RivEr Trends. See: \url{https://github.com/USGS-R/EGRET/wiki} for information on EGRET. EGRET is designed to provide analysis of water quality data sets using the Weighted Regressions on Time, Discharge and Season (WRTDS) method as well as analysis of discharge trends using robust time-series smoothing techniques. Both of these capabilities provide both tabular and graphical analyses of long-term data sets.
+
+
+The dataRetrieval package is designed to retrieve many of the major data types of 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:
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{library}\hlstd{(dataRetrieval)}
+\hlcom{# Choptank River near Greensboro, MD}
+\hlstd{siteNumber} \hlkwb{<-} \hlstr{"01491000"}
+\hlstd{ChoptankInfo} \hlkwb{<-} \hlkwd{getNWISSiteInfo}\hlstd{(siteNumber)}
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"}
+
+\hlcom{#Raw daily data:}
+\hlstd{rawDailyData} \hlkwb{<-} \hlkwd{retrieveNWISdvData}\hlstd{(siteNumber,parameterCd,}
+ \hlstr{"1980-01-01"}\hlstd{,}\hlstr{"2010-01-01"}\hlstd{)}
+\hlcom{# Data compiled for EGRET analysis}
+\hlstd{Daily} \hlkwb{<-} \hlkwd{getNWISDaily}\hlstd{(siteNumber,parameterCd,}
+ \hlstr{"1980-01-01"}\hlstd{,}\hlstr{"2010-01-01"}\hlstd{)}
+
+\hlcom{# Sample data Nitrate:}
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00618"}
+\hlstd{Sample} \hlkwb{<-} \hlkwd{getNWISSample}\hlstd{(siteNumber,parameterCd,}
+ \hlstr{"1980-01-01"}\hlstd{,}\hlstr{"2010-01-01"}\hlstd{)}
+
+\hlcom{# Metadata on site and nitrate:}
+\hlstd{INFO} \hlkwb{<-} \hlkwd{getMetaData}\hlstd{(siteNumber,parameterCd)}
+
+\hlcom{# Merge discharge and nitrate data to one dataframe:}
+\hlstd{Sample} \hlkwb{<-} \hlkwd{mergeReport}\hlstd{()}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+%------------------------------------------------------------
+\section{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}.
+
+
+% latex table generated in R 3.1.1 by xtable 1.7-4 package
+% Mon Sep 22 14:18:32 2014
+\begin{table}[ht]
+\caption{Common USGS Parameter Codes}
+\label{tab:params}
+{\footnotesize
+\begin{tabular}{rll}
+ \hline
+ & \multicolumn{1}{c}{\textbf{\textsf{pCode}}} & \multicolumn{1}{c}{\textbf{\textsf{shortName}}} \\
+ \hline
+ & 00060 & Discharge [ft$^3$/s] \\
+ [5pt] & 00065 & Gage height [ft] \\
+ [5pt] & 00010 & Temperature [C] \\
+ [5pt] & 00045 & Precipitation [in] \\
+ [5pt] & 00400 & pH \\
+ \hline
+\end{tabular}
+}
+\end{table}
+
+
+A complete list (as of September 25, 2013) is available as data attached to the package. It is accessed by the following:
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{library}\hlstd{(dataRetrieval)}
+\hlstd{parameterCdFile} \hlkwb{<-} \hlstd{parameterCdFile}
+\hlkwd{names}\hlstd{(parameterCdFile)}
+\end{alltt}
+\begin{verbatim}
+[1] "parameter_cd" "parameter_group_nm"
+[3] "parameter_nm" "casrn"
+[5] "srsname" "parameter_units"
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+
+For unit values data (sensor data measured at regular time intervals such as 15 minutes or hourly), knowing the parameter code and siteNumber is enough to make a request for data. For most variables that are measured on a continuous basis, the USGS also stores the historical data as daily values. These daily values are statistical summaries of the continuous data, e.g. maximum, minimum, mean, or median. The different statistics are specified by a 5-digit statistics code. A complete list of statistic codes can be found here:
+
+\url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
+
+Some common codes are shown in Table \ref{tab:stat}.
+
+% latex table generated in R 3.1.1 by xtable 1.7-4 package
+% Mon Sep 22 14:18:33 2014
+\begin{table}[ht]
+\caption{Commonly used USGS Stat Codes}
+\label{tab:stat}
+{\footnotesize
+\begin{tabular}{rll}
+ \hline
+ & \multicolumn{1}{c}{\textbf{\textsf{StatCode}}} & \multicolumn{1}{c}{\textbf{\textsf{shortName}}} \\
+ \hline
+ & 00001 & Maximum \\
+ [5pt] & 00002 & Minimum \\
+ [5pt] & 00003 & Mean \\
+ [5pt] & 00008 & Median \\
+ \hline
+\end{tabular}
+}
+\end{table}
+
+
+Examples for using these siteNumber's, parameter codes, and stat codes will be presented in subsequent sections.
+
+\FloatBarrier
+
+%------------------------------------------------------------
+\subsection{Site Information}
+\label{sec:usgsSite}
+%------------------------------------------------------------
+
+%------------------------------------------------------------
+\subsubsection{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.
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{siteNumbers} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"01491000"}\hlstd{,}\hlstr{"01645000"}\hlstd{)}
+\hlstd{siteINFO} \hlkwb{<-} \hlkwd{getNWISSiteInfo}\hlstd{(siteNumbers)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+A specific example piece of information can be retrieved, in this case a station name, as follows:
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{siteINFO}\hlopt{$}\hlstd{station.nm}
+\end{alltt}
+\begin{verbatim}
+[1] "CHOPTANK RIVER NEAR GREENSBORO, MD"
+[2] "SENECA CREEK AT DAWSONVILLE, MD"
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+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.
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# Continuing from the previous example:}
+\hlcom{# This pulls out just the daily data:}
+
+\hlstd{dailyDataAvailable} \hlkwb{<-} \hlkwd{getNWISDataAvailability}\hlstd{(siteNumbers,}
+ \hlkwc{type}\hlstd{=}\hlstr{"dv"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+% latex table generated in R 3.1.1 by xtable 1.7-4 package
+% Mon Sep 22 14:18:34 2014
+\begin{table}[ht]
+\caption{Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]}
+\label{tab:gda}
+{\footnotesize
+\begin{tabular}{rlllllll}
+ \hline
+ & \multicolumn{1}{c}{\textbf{\textsf{siteNumber}}} & \multicolumn{1}{c}{\textbf{\textsf{srsname}}} & \multicolumn{1}{c}{\textbf{\textsf{startDate}}} & \multicolumn{1}{c}{\textbf{\textsf{endDate}}} & \multicolumn{1}{c}{\textbf{\textsf{count}}} & \multicolumn{1}{c}{\textbf{\textsf{units}}} & \multicolumn{1}{c}{\textbf{\textsf{statCd}}} \\
+ \hline
+ & 01491000 & Temperature, water & 1988-10-01 & 2012-05-09 & 894 & deg C & 00001 \\
+ [5pt] & 01491000 & Temperature, water & 2010-10-01 & 2012-05-09 & 529 & deg C & 00002 \\
+ [5pt] & 01491000 & Temperature, water & 2010-10-01 & 2012-05-09 & 529 & deg C & 00003 \\
+ [5pt] & 01491000 & Stream flow, mean. daily & 1948-01-01 & 2014-09-21 & 24371 & ft$^3$/s & 00003 \\
+ [5pt] & 01645000 & Stream flow, mean. daily & 1930-09-26 & 2014-09-21 & 30675 & ft$^3$/s & 00003 \\
+ [5pt] & 01491000 & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & $\mu$S/cm @25C & 00003 \\
+ [5pt] & 01491000 & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & $\mu$S/cm @25C & 00001 \\
+ [5pt] & 01491000 & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & $\mu$S/cm @25C & 00002 \\
+ [5pt] & 01491000 & Suspended sediment concentration (SSC) & 1980-10-01 & 1991-09-30 & 3651 & mg/l & 00003 \\
+ [5pt] & 01491000 & Suspended sediment discharge & 1980-10-01 & 1991-09-30 & 3652 & tons/day & 00003 \\
+ \hline
+\end{tabular}
+}
+\end{table}
+
+
+See Section \ref{app:createWordTable} for instructions on converting an R dataframe to a table in Microsoft\textregistered\ software Excel or Word to display a data availability table similar to Table \ref{tab:gda}. Excel, Microsoft, PowerPoint, Windows, and Word are registered trademarks of Microsoft Corporation in the United States and other countries.
+
+\FloatBarrier
+
+%------------------------------------------------------------
+\subsection{Parameter Information}
+\label{sec:usgsParams}
+%------------------------------------------------------------
+To obtain all of the available information concerning a measured parameter (or multiple parameters), use the \texttt{getNWISPcodeInfo} function:
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# Using defaults:}
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00618"}
+\hlstd{parameterINFO} \hlkwb{<-} \hlkwd{getNWISPcodeInfo}\hlstd{(parameterCd)}
+\hlkwd{colnames}\hlstd{(parameterINFO)}
+\end{alltt}
+\begin{verbatim}
+[1] "parameter_cd" "parameter_group_nm"
+[3] "parameter_nm" "casrn"
+[5] "srsname" "parameter_units"
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+A specific example piece of information, in this case parameter name, can be obtained as follows:
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{parameterINFO}\hlopt{$}\hlstd{parameter_nm}
+\end{alltt}
+\begin{verbatim}
+[1] "Nitrate, water, filtered, milligrams per liter as nitrogen"
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+Parameter information can obtained from \url{http://nwis.waterdata.usgs.gov/usa/nwis/pmcodes}
+\FloatBarrier
+%------------------------------------------------------------
+\subsection{Daily Values}
+\label{sec:usgsDaily}
+%------------------------------------------------------------
+To obtain daily records of USGS data, use the \texttt{retrieveNWISdvData} function. The arguments for this function are siteNumber, parameterCd, startDate, endDate, statCd, and a logical (TRUE/FALSE) interactive. There are 2 default arguments: statCd (defaults to \texttt{"}00003\texttt{"}), and interactive (defaults to TRUE). If you want to use the default values, you do not need to list them in the function call. By setting the \texttt{"}interactive\texttt{"} option to FALSE, the operation of the function will advance automatically. It might make more sense to run large batch collections with the interactive option set to FALSE.
+
+The dates (start and end) must be in the format \texttt{"}YYYY-MM-DD\texttt{"} (note: the user must include the quotes). Setting the start date to \texttt{"}\texttt{"} (no space) will prompt the program to ask for the earliest date, and setting the end date to \texttt{"}\texttt{"} (no space) will prompt for the latest available date.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# Continuing with our Choptank River example}
+\hlstd{siteNumber} \hlkwb{<-} \hlstr{"01491000"}
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"} \hlcom{# Discharge}
+\hlstd{startDate} \hlkwb{<-} \hlstr{""} \hlcom{# Will request earliest date}
+\hlstd{endDate} \hlkwb{<-} \hlstr{""} \hlcom{# Will request latest date}
+
+\hlstd{discharge} \hlkwb{<-} \hlkwd{retrieveNWISdvData}\hlstd{(siteNumber,}
+ \hlstd{parameterCd, startDate, endDate)}
+\hlkwd{names}\hlstd{(discharge)}
+\end{alltt}
+\begin{verbatim}
+[1] "agency_cd" "site_no"
+[3] "datetime" "X02_00060_00003"
+[5] "X02_00060_00003_cd"
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+The column \texttt{"}datetime\texttt{"} in the returned dataframe is automatically imported as a variable of class \texttt{"}Date\texttt{"} in R. Each requested parameter has a value and remark code column. The names of these columns depend on the requested parameter and stat code combinations. USGS remark codes are often \texttt{"}A\texttt{"} (approved for publication) or \texttt{"}P\texttt{"} (provisional data subject to revision). A more complete list of remark codes can be found here:
+\url{http://nwis.waterdata.usgs.gov/usa/nwis/pmcodes}
+
+Another example that doesn't use the defaults would be a request for mean and maximum daily temperature and discharge in early 2012:
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{parameterCd} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00010"}\hlstd{,}\hlstr{"00060"}\hlstd{)} \hlcom{# Temperature and discharge}
+\hlstd{statCd} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00001"}\hlstd{,}\hlstr{"00003"}\hlstd{)} \hlcom{# Mean and maximum}
+\hlstd{startDate} \hlkwb{<-} \hlstr{"2012-01-01"}
+\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-05-01"}
+
+\hlstd{temperatureAndFlow} \hlkwb{<-} \hlkwd{retrieveNWISdvData}\hlstd{(siteNumber, parameterCd,}
+ \hlstd{startDate, endDate,} \hlkwc{statCd}\hlstd{=statCd)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+Daily data is pulled from \url{http://waterservices.usgs.gov/rest/DV-Test-Tool.html}.
+
+The column names can be automatically adjusted based on the parameter and statistic codes using the \texttt{renameColumns} function. This is not necessary, but may be useful when analyzing the data.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{names}\hlstd{(temperatureAndFlow)}
+\end{alltt}
+\begin{verbatim}
+[1] "agency_cd" "site_no"
+[3] "datetime" "X01_00010_00001"
+[5] "X01_00010_00001_cd" "X01_00010_00003"
+[7] "X01_00010_00003_cd" "X02_00060_00003"
+[9] "X02_00060_00003_cd"
+\end{verbatim}
+\begin{alltt}
+\hlstd{temperatureAndFlow} \hlkwb{<-} \hlkwd{renameColumns}\hlstd{(temperatureAndFlow)}
+\hlkwd{names}\hlstd{(temperatureAndFlow)}
+\end{alltt}
+\begin{verbatim}
+[1] "agency_cd"
+[2] "site_no"
+[3] "datetime"
+[4] "Temperature_water_degrees_Celsius_Max_01"
+[5] "Temperature_water_degrees_Celsius_Max_01_cd"
+[6] "Temperature_water_degrees_Celsius_01"
+[7] "Temperature_water_degrees_Celsius_01_cd"
+[8] "Discharge_cubic_feet_per_second"
+[9] "Discharge_cubic_feet_per_second_cd"
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+An example of plotting the above data (Figure \ref{fig:getNWIStemperaturePlot}):
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{par}\hlstd{(}\hlkwc{mar}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{5}\hlstd{,}\hlnum{5}\hlstd{,}\hlnum{5}\hlstd{,}\hlnum{5}\hlstd{))} \hlcom{#sets the size of the plot window}
+
+\hlkwd{with}\hlstd{(temperatureAndFlow,} \hlkwd{plot}\hlstd{(}
+ \hlstd{datetime, Temperature_water_degrees_Celsius_Max_01,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Date"}\hlstd{,}\hlkwc{ylab}\hlstd{=}\hlstr{"Max Temperature [C]"}
+ \hlstd{))}
+\hlkwd{par}\hlstd{(}\hlkwc{new}\hlstd{=}\hlnum{TRUE}\hlstd{)}
+\hlkwd{with}\hlstd{(temperatureAndFlow,} \hlkwd{plot}\hlstd{(}
+ \hlstd{datetime, Discharge_cubic_feet_per_second,}
+ \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,}\hlkwc{type}\hlstd{=}\hlstr{"l"}\hlstd{,}\hlkwc{xaxt}\hlstd{=}\hlstr{"n"}\hlstd{,}\hlkwc{yaxt}\hlstd{=}\hlstr{"n"}\hlstd{,}\hlkwc{xlab}\hlstd{=}\hlstr{""}\hlstd{,}\hlkwc{ylab}\hlstd{=}\hlstr{""}\hlstd{,}\hlkwc{axes}\hlstd{=}\hlnum{FALSE}
+ \hlstd{))}
+\hlkwd{axis}\hlstd{(}\hlnum{4}\hlstd{,}\hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,}\hlkwc{col.axis}\hlstd{=}\hlstr{"red"}\hlstd{)}
+\hlkwd{mtext}\hlstd{(}\hlkwd{expression}\hlstd{(}\hlkwd{paste}\hlstd{(}\hlstr{"Mean Discharge [ft"}\hlopt{^}\hlstr{"3"}\hlstd{,}\hlstr{"/s]"}\hlstd{,}
+ \hlkwc{sep}\hlstd{=}\hlstr{""}\hlstd{)),}\hlkwc{side}\hlstd{=}\hlnum{4}\hlstd{,}\hlkwc{line}\hlstd{=}\hlnum{3}\hlstd{,}\hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}
+\hlkwd{title}\hlstd{(}\hlkwd{paste}\hlstd{(siteINFO}\hlopt{$}\hlstd{station.nm[}\hlnum{1}\hlstd{],}\hlstr{"2012"}\hlstd{,}\hlkwc{sep}\hlstd{=}\hlstr{" "}\hlstd{))}
+\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"Max Temperature"}\hlstd{,} \hlstr{"Mean Discharge"}\hlstd{),}
+ \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"black"}\hlstd{,}\hlstr{"red"}\hlstd{),}\hlkwc{lty}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{NA}\hlstd{,}\hlnum{1}\hlstd{),}\hlkwc{pch}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{NA}\hlstd{))}
+\end{alltt}
+\end{kframe}\begin{figure}[]
+
+\includegraphics[width=1\linewidth,height=1\linewidth]{figure/getNWIStemperaturePlot} \caption[Temperature and discharge plot of Choptank River in 2012]{Temperature and discharge plot of Choptank River in 2012.\label{fig:getNWIStemperaturePlot}}
+\end{figure}
+
+
+\end{knitrout}
+
+
+There are occasions where NWIS values are not reported as numbers, instead there might be text describing a certain event such as \enquote{Ice.} Any value that cannot be converted to a number will be reported as NA in this package (not including remark code columns).
+
+\FloatBarrier
+
+%------------------------------------------------------------
+\subsection{Unit Values}
+\label{sec:usgsRT}
+%------------------------------------------------------------
+Any data collected at regular time intervals (such as 15-minute or hourly) are known as \enquote{unit values.} Many of these are delivered on a real time basis and very recent data (even less than an hour old in many cases) are available through the function \texttt{retrieveNWISunitData}. Some of these unit values are available for many years, and some are only available for a recent time period such as 120 days. Here is an example of a retrieval of such data.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"} \hlcom{# Discharge}
+\hlstd{startDate} \hlkwb{<-} \hlstr{"2012-05-12"}
+\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-05-13"}
+\hlstd{dischargeToday} \hlkwb{<-} \hlkwd{retrieveNWISunitData}\hlstd{(siteNumber, parameterCd,}
+ \hlstd{startDate, endDate)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+The retrieval produces the following dataframe:
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{verbatim}
+ agency_cd site_no datetime tz_cd
+1 USGS 01491000 2012-05-12 00:00:00 EST
+2 USGS 01491000 2012-05-12 00:15:00 EST
+3 USGS 01491000 2012-05-12 00:30:00 EST
+4 USGS 01491000 2012-05-12 00:45:00 EST
+5 USGS 01491000 2012-05-12 01:00:00 EST
+6 USGS 01491000 2012-05-12 01:15:00 EST
+ X02_00060_00011 X02_00060_00011_cd
+1 83 A
+2 83 A
+3 83 A
+4 83 A
+5 85 A
+6 83 A
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+Note that time now becomes important, so the variable datetime is a POSIXct, and the time zone is included in a separate column. Data are retrieved from \url{http://waterservices.usgs.gov/rest/IV-Test-Tool.html}. There are occasions where NWIS values are not reported as numbers, instead a common example is \enquote{Ice.} Any value that cannot be converted to a number will be reported as NA in this package.
+
+\newpage
+
+
+\FloatBarrier
+
+%------------------------------------------------------------
+\subsection{Water Quality Values}
+\label{sec:usgsWQP}
+%------------------------------------------------------------
+To get USGS water quality data from water samples collected at the streamgage or other monitoring site (as distinct from unit values collected through some type of automatic monitor) we can use the function \texttt{retrieveNWISqwData}, with the input arguments: siteNumber, parameterCd, startDate, endDate, and interactive (similar to \texttt{retrieveNWISunitData} and \texttt{retrieveNWISdvData}). Additionally, the argument \texttt{"}expanded\texttt{"} is a logical input that allows the user to choose between a simple return of datetimes/qualifier/values (expanded=FALSE), or a more complete and verbose output (expanded=TRUE). Expaned = TRUE includes such columns as remark codes, value qualifying text, and detection level.
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# Dissolved Nitrate parameter codes:}
+\hlstd{parameterCd} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00618"}\hlstd{,}\hlstr{"71851"}\hlstd{)}
+\hlstd{startDate} \hlkwb{<-} \hlstr{"1985-10-01"}
+\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-09-30"}
+
+\hlstd{dissolvedNitrate} \hlkwb{<-} \hlkwd{retrieveNWISqwData}\hlstd{(siteNumber, parameterCd,}
+ \hlstd{startDate, endDate,} \hlkwc{expanded}\hlstd{=}\hlnum{TRUE}\hlstd{)}
+\hlkwd{names}\hlstd{(dissolvedNitrate)}
+\end{alltt}
+\begin{verbatim}
+ [1] "dateTime" "site"
+ [3] "dateTimeEnd" "remark_cd_00618"
+ [5] "result_va_00618" "val_qual_tx_00618"
+ [7] "meth_cd_00618" "dqi_cd_00618"
+ [9] "rpt_lev_va_00618" "rpt_lev_cd_00618"
+[11] "remark_cd_71851" "result_va_71851"
+[13] "val_qual_tx_71851" "meth_cd_71851"
+[15] "dqi_cd_71851" "rpt_lev_va_71851"
+[17] "rpt_lev_cd_71851"
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{with}\hlstd{(dissolvedNitrate,} \hlkwd{plot}\hlstd{(}
+ \hlstd{dateTime, result_va_00618,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Date"}\hlstd{,}\hlkwc{ylab} \hlstd{=} \hlkwd{paste}\hlstd{(parameterINFO}\hlopt{$}\hlstd{srsname,}
+ \hlstr{"["}\hlstd{,parameterINFO}\hlopt{$}\hlstd{parameter_units,}\hlstr{"]"}\hlstd{)}
+ \hlstd{))}
+\hlkwd{title}\hlstd{(siteINFO}\hlopt{$}\hlstd{station.nm[}\hlnum{1}\hlstd{])}
+\end{alltt}
+\end{kframe}\begin{figure}[]
+
+\includegraphics[width=\maxwidth]{figure/getQWtemperaturePlot} \caption[Nitrate, water, filtered, milligrams per liter as nitrogen at CHOPTANK RIVER NEAR GREENSBORO, MD]{Nitrate, water, filtered, milligrams per liter as nitrogen at CHOPTANK RIVER NEAR GREENSBORO, MD\label{fig:getQWtemperaturePlot}}
+\end{figure}
+
+
+\end{knitrout}
+
+\FloatBarrier
+
+%------------------------------------------------------------
+\subsection{URL Construction}
+\label{sec:usgsURL}
+%------------------------------------------------------------
+There may be times when you might be interested in seeing the URL (Web address) that was used to obtain the raw data. The \texttt{constructNWISURL} function returns the URL. In addition to input variables that have been described, there is a new argument \texttt{"}service\texttt{"}. The service argument can be \texttt{"}dv\texttt{"} (daily values), \texttt{"}uv\texttt{"} (unit values), \texttt{"}qw\texttt{"} (NWIS water quality values), or \texttt{"}wqp\texttt{"} (general Water Quality Portal values).
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# Dissolved Nitrate parameter codes:}
+\hlstd{pCode} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00618"}\hlstd{,}\hlstr{"71851"}\hlstd{)}
+\hlstd{startDate} \hlkwb{<-} \hlstr{"1964-06-11"}
+\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-12-18"}
+\hlstd{url_qw} \hlkwb{<-} \hlkwd{constructNWISURL}\hlstd{(siteNumber,pCode,startDate,endDate,}\hlstr{'qw'}\hlstd{)}
+\hlstd{url_dv} \hlkwb{<-} \hlkwd{constructNWISURL}\hlstd{(siteNumber,}\hlstr{"00060"}\hlstd{,startDate,endDate,}
+ \hlstr{'dv'}\hlstd{,}\hlkwc{statCd}\hlstd{=}\hlstr{"00003"}\hlstd{)}
+\hlstd{url_uv} \hlkwb{<-} \hlkwd{constructNWISURL}\hlstd{(siteNumber,}\hlstr{"00060"}\hlstd{,startDate,endDate,}\hlstr{'uv'}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+
+%------------------------------------------------------------
+\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 (data from EPA), NWIS database (data from USGS), STEWARDS database (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{retrieveWQPqwData} function can take either a USGS parameter code, or a more general cahracteristic name in the parameterCd input argument. The Water Quality Data Portal includes data discovery tools and information on characteristic names. The following example retrieves specific conductance from a DNR site in Wisconsin.
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{specificCond} \hlkwb{<-} \hlkwd{retrieveWQPqwData}\hlstd{(}\hlstr{'WIDNR_WQX-10032762'}\hlstd{,}
+ \hlstr{'Specific conductance'}\hlstd{,}\hlstr{'2011-05-01'}\hlstd{,}\hlstr{'2011-09-30'}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+\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:
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{sites} \hlkwb{<-} \hlkwd{getNWISSites}\hlstd{(}\hlkwc{bBox}\hlstd{=}\hlstr{"-83.0,36.5,-81.0,38.5"}\hlstd{,}
+ \hlkwc{parameterCd}\hlstd{=}\hlstr{"00010,00060"}\hlstd{,}
+ \hlkwc{hasDataTypeCd}\hlstd{=}\hlstr{"dv"}\hlstd{)}
+
+\hlkwd{names}\hlstd{(sites)}
+\end{alltt}
+\begin{verbatim}
+ [1] "agency_cd" "site_no"
+ [3] "station_nm" "site_tp_cd"
+ [5] "dec_lat_va" "dec_long_va"
+ [7] "coord_acy_cd" "dec_coord_datum_cd"
+ [9] "alt_va" "alt_acy_va"
+[11] "alt_datum_cd" "huc_cd"
+\end{verbatim}
+\begin{alltt}
+\hlkwd{nrow}\hlstd{(sites)}
+\end{alltt}
+\begin{verbatim}
+[1] 205
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+
+%------------------------------------------------------------
+\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:
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dischargeWI} \hlkwb{<-} \hlkwd{getNWISData}\hlstd{(}\hlkwc{stateCd}\hlstd{=}\hlstr{"WI"}\hlstd{,}
+ \hlkwc{parameterCd}\hlstd{=}\hlstr{"00060"}\hlstd{,}
+ \hlkwc{drainAreaMin}\hlstd{=}\hlstr{"50"}\hlstd{,}
+ \hlkwc{statCd}\hlstd{=}\hlstr{"00003"}\hlstd{)}
+\hlkwd{names}\hlstd{(dischargeWI)}
+\end{alltt}
+\begin{verbatim}
+[1] "agency_cd" "site_no"
+[3] "datetime" "X01_00060_00003"
+[5] "X01_00060_00003_cd"
+\end{verbatim}
+\begin{alltt}
+\hlkwd{nrow}\hlstd{(dischargeWI)}
+\end{alltt}
+\begin{verbatim}
+[1] 282
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+%------------------------------------------------------------
+\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}.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{sitesNJ} \hlkwb{<-} \hlkwd{getWQPSites}\hlstd{(}\hlkwc{statecode}\hlstd{=}\hlstr{"US:34"}\hlstd{,}
+ \hlkwc{characteristicName}\hlstd{=}\hlstr{"Chloride"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+%------------------------------------------------------------
+\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:
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dataPH} \hlkwb{<-} \hlkwd{getWQPData}\hlstd{(}\hlkwc{statecode}\hlstd{=}\hlstr{"US:55"}\hlstd{,}
+ \hlkwc{characteristicName}\hlstd{=}\hlstr{"pH"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+
+\FloatBarrier
+
+%------------------------------------------------------------
+\section{Data Retrievals Structured For Use In The EGRET Package}
+\label{sec:EGRETdfs}
+%------------------------------------------------------------
+Rather than using the raw data as retrieved by the Web, the dataRetrieval package also includes functions that return the data in a structure that has been designed to work with the EGRET R package (\url{https://github.com/USGS-R/EGRET/wiki}). In general, these dataframes may be much more \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{getMetaData} function obtains metadata, or data about the streamgage and measured parameters. This function combines \texttt{getNWISSiteInfo} and \texttt{getNWISPcodeInfo}, producing one dataframe called INFO.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00618"}
+\hlstd{INFO} \hlkwb{<-}\hlkwd{getMetaData}\hlstd{(siteNumber,parameterCd,} \hlkwc{interactive}\hlstd{=}\hlnum{FALSE}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+\FloatBarrier
+
+%------------------------------------------------------------
+\subsection{Daily Data}
+\label{Dailysubsection}
+%------------------------------------------------------------
+The \texttt{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.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{siteNumber} \hlkwb{<-} \hlstr{"01491000"}
+\hlstd{startDate} \hlkwb{<-} \hlstr{"2000-01-01"}
+\hlstd{endDate} \hlkwb{<-} \hlstr{"2013-01-01"}
+\hlcom{# This call will get NWIS (ft3/s) data , and convert it to m3/s:}
+\hlstd{Daily} \hlkwb{<-} \hlkwd{getNWISDaily}\hlstd{(siteNumber,} \hlstr{"00060"}\hlstd{, startDate, endDate)}
+\end{alltt}
+\begin{verbatim}
+There are 4750 data points, and 4750 days.
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+
+
+% latex table generated in R 3.1.1 by xtable 1.7-4 package
+% Mon Sep 22 14:18:43 2014
+\begin{table}[ht]
+\caption{Daily dataframe}
+\label{tab:DailyDF1}
+{\footnotesize
+\begin{tabular}{rllll}
+ \hline
+ & \multicolumn{1}{c}{\textbf{\textsf{ColumnName}}} & \multicolumn{1}{c}{\textbf{\textsf{Type}}} & \multicolumn{1}{c}{\textbf{\textsf{Description}}} & \multicolumn{1}{c}{\textbf{\textsf{Units}}} \\
+ \hline
+ & Date & Date & Date & date \\
+ [5pt] & Q & number & Discharge in m$^3$/s & m$^3$/s \\
+ [5pt] & Julian & number & Number of days since January 1, 1850 & days \\
+ [5pt] & Month & integer & Month of the year [1-12] & months \\
+ [5pt] & Day & integer & Day of the year [1-366] & days \\
+ [5pt] & DecYear & number & Decimal year & years \\
+ [5pt] & MonthSeq & integer & Number of months since January 1, 1850 & months \\
+ [5pt] & Qualifier & string & Qualifying code & character \\
+ [5pt] & i & integer & Index of days, starting with 1 & days \\
+ [5pt] & LogQ & number & Natural logarithm of Q & numeric \\
+ [5pt] & Q7 & number & 7 day running average of Q & m$^3$/s \\
+ [5pt] & Q30 & number & 30 day running average of Q & m$^3$/s \\
+ \hline
+\end{tabular}
+}
+\end{table}
+
+
+
+If discharge values are negative or zero, the code will set all of these values to zero and then add a small constant to all of the daily discharge values. This constant is 0.001 times the mean discharge. The code will also report on the number of zero and negative values and the size of the constant. Use EGRET analysis only if the number of zero values is a very small fraction of the total days in the record (say less than 0.1\% of the days), and there are no negative discharge values. Columns Q7 and Q30 are the 7 and 30 day running averages for the 7 or 30 days ending on this specific date. Table \ref{tab:DailyDF1} lists details of the Daily data frame.
+
+Notice that the \enquote{Day of the year} column can span from 1 to 366. The 366 accounts for leap years. Every day has a consistent day of the year. This means, February 28\textsuperscript{th} is always the 59\textsuperscript{th} day of the year, Feb. 29\textsuperscript{th} is always the 60\textsuperscript{th} day of the year, and March 1\textsuperscript{st} is always the 61\textsuperscript{st} day of the year whether or not it is a leap year.
+
+\FloatBarrier
+
+%------------------------------------------------------------
+\subsection{Sample Data}
+\label{Samplesubsection}
+%------------------------------------------------------------
+The \texttt{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{retrieveWQPqwData} or \texttt{getWQPData} as described in the previous section.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00618"}
+\hlstd{Sample} \hlkwb{<-}\hlkwd{getNWISSample}\hlstd{(siteNumber,parameterCd,}
+ \hlstd{startDate, endDate)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+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.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{site} \hlkwb{<-} \hlstr{'WIDNR_WQX-10032762'}
+\hlstd{characteristicName} \hlkwb{<-} \hlstr{'Specific conductance'}
+\hlstd{Sample} \hlkwb{<-}\hlkwd{getWQPSample}\hlstd{(site,characteristicName,}
+ \hlstd{startDate, endDate)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+\pagebreak
+
+
+\begin{table}
+{\footnotesize
+ \begin{threeparttable}[b]
+ \caption{Sample dataframe}
+ \label{tab:SampleDataframe}
+ \begin{tabular}{llll}
+ \hline
+\multicolumn{1}{c}{\textbf{\textsf{ColumnName}}} &
+\multicolumn{1}{c}{\textbf{\textsf{Type}}} &
+\multicolumn{1}{c}{\textbf{\textsf{Description}}} &
+\multicolumn{1}{c}{\textbf{\textsf{Units}}} \\
+ \hline
+ Date & Date & Date & date \\
+ [5pt]ConcLow & number & Lower limit of concentration & mg/L \\
+ [5pt]ConcHigh & number & Upper limit of concentration & mg/L \\
+ [5pt]Uncen & integer & Uncensored data (1=true, 0=false) & integer \\
+ [5pt]ConcAve & number & Average of ConcLow and ConcHigh & mg/L \\
+ [5pt]Julian & number & Number of days since January 1, 1850 & days \\
+ [5pt]Month & integer & Month of the year [1-12] & months \\
+ [5pt]Day & integer & Day of the year [1-366] & days \\
+ [5pt]DecYear & number & Decimal year & years \\
+ [5pt]MonthSeq & integer & Number of months since January 1, 1850 & months \\
+ [5pt]SinDY & number & Sine of DecYear & numeric \\
+ [5pt]CosDY & number & Cosine of DecYear & numeric \\
+ [5pt]Q \tnote{1} & number & Discharge & m\textsuperscript{3}/s \\
+ [5pt]LogQ \tnote{1} & number & Natural logarithm of discharge & numeric \\
+ \hline
+\end{tabular}
+
+ \begin{tablenotes}
+ \item[1] Discharge columns are populated from data in the Daily dataframe after calling the \texttt{mergeReport} function.
+ \end{tablenotes}
+ \end{threeparttable}
+}
+\end{table}
+
+Notice that the \enquote{Day of the year} column can span from 1 to 366. The 366 accounts for leap years. Every day has a consistent day of the year. This means, February 28\textsuperscript{th} is always the 59\textsuperscript{th} day of the year, Feb. 29\textsuperscript{th} is always the 60\textsuperscript{th} day of the year, and March 1\textsuperscript{st} is always the 61\textsuperscript{st} day of the year whether or not it is a leap year.
+
+Section \ref{sec:cenValues} is about summing multiple constituents, including how interval censoring is used. Since the Sample data frame is structured to only contain one constituent, when more than one parameter codes are requested, the \texttt{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}.
+
+
+
+% latex table generated in R 3.1.1 by xtable 1.7-4 package
+% Mon Sep 22 14:18:44 2014
+\begin{table}[ht]
+\caption{Example data}
+\label{tab:exampleComplexQW}
+{\footnotesize
+\begin{tabular}{rllrlrlr}
+ \hline
+ & \multicolumn{1}{c}{\textbf{\textsf{cdate}}} & \multicolumn{1}{c}{\textbf{\textsf{rdp}}} & \multicolumn{1}{c}{\textbf{\textsf{dp}}} & \multicolumn{1}{c}{\textbf{\textsf{rpp}}} & \multicolumn{1}{c}{\textbf{\textsf{pp}}} & \multicolumn{1}{c}{\textbf{\textsf{rtp}}} & \multicolumn{1}{c}{\textbf{\textsf{tp}}} \\
+ \hline
+ & 2003-02-15 & & 0.020 & & 0.500 & & \\
+ [5pt] & 2003-06-30 & $<$ & 0.010 & & 0.300 & & \\
+ [5pt] & 2004-09-15 & $<$ & 0.005 & $<$ & 0.200 & & \\
+ [5pt] & 2005-01-30 & & & & & & 0.430 \\
+ [5pt] & 2005-05-30 & & & & & $<$ & 0.050 \\
+ [5pt] & 2005-10-30 & & & & & $<$ & 0.020 \\
+ \hline
+\end{tabular}
+}
+\end{table}
+
+
+The dataRetrieval package will \enquote{add up} all the values in a given row to form the total for that sample when using the Sample dataframe. Thus, you only want to enter data that should be added together. If you want a dataframe with multiple constituents that are not summed, do not use getNWISSample, getWQPSample, or getUserSample. The raw data functions: \texttt{getWQPData}, \texttt{retrieveNWISqwData}, \texttt{retrieveWQPqwData}, \texttt{getWQPData} will not sum constituents, but leave them in their individual columns.
+
+For example, we might know the value for dp on 5/30/2005, but we don't want to put it in the table because under the rules of this data set, we are not supposed to add it in to the values in 2005.
+
+For every sample, the EGRET package requires a pair of numbers to define an interval in which the true value lies (ConcLow and ConcHigh). In a simple uncensored case (the reported value is above the detection limit), ConcLow equals ConcHigh and the interval collapses down to a single point. In a simple censored case, the value might be reported as \verb@<@0.2, then ConcLow=NA and ConcHigh=0.2. We use NA instead of 0 as a way to elegantly handle future logarithm calculations.
+
+For the more complex example case, let us say dp is reported as \verb@<@0.01 and pp is reported as 0.3. We know that the total must be at least 0.3 and could be as much as 0.31. Therefore, ConcLow=0.3 and ConcHigh=0.31. Another case would be if dp is reported as \verb@<@0.005 and pp is reported \verb@<@0.2. We know in this case that the true value could be as low as zero, but could be as high as 0.205. Therefore, in this case, ConcLow=NA and ConcHigh=0.205. The Sample dataframe for the example data would be:
+
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+ \hlstd{Sample}
+\end{alltt}
+\begin{verbatim}
+ Date ConcLow ConcHigh Uncen ConcAve Julian Month
+1 2003-02-15 0.52 0.520 1 0.5200 55927 2
+2 2003-06-30 0.30 0.310 0 0.3050 56062 6
+3 2004-09-15 NA 0.205 0 0.1025 56505 9
+4 2005-01-30 0.43 0.430 1 0.4300 56642 1
+5 2005-05-30 NA 0.050 0 0.0250 56762 5
+6 2005-10-30 NA 0.020 0 0.0100 56915 10
+ Day DecYear MonthSeq SinDY CosDY
+1 46 2003 1838 0.70253 0.7117
+2 182 2003 1842 0.03872 -0.9993
+3 259 2005 1857 -0.96134 -0.2754
+4 30 2005 1861 0.48251 0.8759
+5 151 2005 1865 0.54163 -0.8406
+6 304 2006 1870 -0.88205 0.4712
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+Section \ref{sec:userFiles} discusses inputting user-generated files. The functions \texttt{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:
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{fileName} \hlkwb{<-} \hlstr{"ChoptankRiverFlow.txt"}
+\hlstd{filePath} \hlkwb{<-} \hlstr{"C:/RData/"}
+\hlstd{Daily} \hlkwb{<-}\hlkwd{getFileDaily}\hlstd{(filePath,fileName,}
+ \hlkwc{separator}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+Microsoft\textregistered\ Excel files can be a bit tricky to import into R directly. The simplest way to get Excel data into R is to open the Excel file in Excel, then save it as a .csv file (comma-separated values).
+
+\FloatBarrier
+
+%------------------------------------------------------------
+\subsubsection{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:
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{fileName} \hlkwb{<-} \hlstr{"ChoptankRiverNitrate.csv"}
+\hlstd{filePath} \hlkwb{<-} \hlstr{"C:/RData/"}
+\hlstd{Sample} \hlkwb{<-}\hlkwd{getUserSample}\hlstd{(filePath,fileName,}
+ \hlkwc{separator}\hlstd{=}\hlstr{","}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+When multiple constituents are to be summed, the format can be date, remark\_A, value\_A, remark\_b, value\_b, etc... A tab-separated example might look like the file below, where the columns are date, remark dissolved phosphate (rdp), dissolved phosphate (dp), remark particulate phosphorus (rpp), particulate phosphorus (pp), remark total phosphate (rtp), and total phosphate (tp):
+
+\singlespacing
+\begin{verbatim}
+date rdp dp rpp pp rtp tp
+2003-02-15 0.020 0.500
+2003-06-30 < 0.010 0.300
+2004-09-15 < 0.005 < 0.200
+2005-01-30 0.430
+2005-05-30 < 0.050
+2005-10-30 < 0.020
+...
+\end{verbatim}
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{fileName} \hlkwb{<-} \hlstr{"ChoptankPhosphorus.txt"}
+\hlstd{filePath} \hlkwb{<-} \hlstr{"C:/RData/"}
+\hlstd{Sample} \hlkwb{<-}\hlkwd{getUserSample}\hlstd{(filePath,fileName,}
+ \hlkwc{separator}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+\FloatBarrier
+
+%------------------------------------------------------------
+\subsection{Merge Report}
+%------------------------------------------------------------
+Finally, there is a function called \texttt{mergeReport} that will look at both the Daily and Sample dataframe, and populate Q and LogQ columns into the Sample dataframe. The default arguments are Daily and Sample, however if you want to use other similarly structured dataframes, you can specify localDaily or localSample. Once \texttt{mergeReport} has been run, the Sample dataframe will be augmented with the daily discharges for all the days with samples. None of the water quality functions in EGRET will work without first having run the \texttt{mergeReport} function.
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{siteNumber} \hlkwb{<-} \hlstr{"01491000"}
+\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00631"} \hlcom{# Nitrate}
+\hlstd{startDate} \hlkwb{<-} \hlstr{"2000-01-01"}
+\hlstd{endDate} \hlkwb{<-} \hlstr{"2013-01-01"}
+
+\hlstd{Daily} \hlkwb{<-} \hlkwd{getNWISDaily}\hlstd{(siteNumber,} \hlstr{"00060"}\hlstd{, startDate, endDate)}
+\end{alltt}
+\begin{verbatim}
+There are 4750 data points, and 4750 days.
+\end{verbatim}
+\begin{alltt}
+\hlstd{Sample} \hlkwb{<-} \hlkwd{getNWISSample}\hlstd{(siteNumber,parameterCd, startDate, endDate)}
+\hlstd{Sample} \hlkwb{<-} \hlkwd{mergeReport}\hlstd{()}
+\end{alltt}
+\begin{verbatim}
+
+ Discharge Record is 4750 days long, which is 13 years
+ First day of the discharge record is 2000-01-01 and last day is 2013-01-01
+ The water quality record has 222 samples
+ The first sample is from 2000-01-04 and the last sample is from 2012-12-18
+ Discharge: Minimum, mean and maximum 0.00991 4.55 246
+ Concentration: Minimum, mean and maximum 0.2 1.2 2.4
+ Percentage of the sample values that are censored is 0 %
+\end{verbatim}
+\begin{alltt}
+\hlkwd{head}\hlstd{(Sample)}
+\end{alltt}
+\begin{verbatim}
+ Date Q LogQ ConcLow ConcHigh Uncen ConcAve
+1 2000-01-04 2.747 1.0104 1.59 1.59 1 1.59
+2 2000-02-03 3.936 1.3702 1.54 1.54 1 1.54
+3 2000-02-15 10.845 2.3837 1.37 1.37 1 1.37
+4 2000-02-19 15.518 2.7420 1.24 1.24 1 1.24
+5 2000-03-23 56.917 4.0416 0.52 0.52 1 0.52
+6 2000-06-05 1.812 0.5946 1.11 1.11 1 1.11
+ Julian Month Day DecYear MonthSeq SinDY CosDY
+1 54789 1 4 2000 1801 0.05576 0.9984
+2 54819 2 34 2000 1802 0.54031 0.8415
+3 54831 2 46 2000 1802 0.70101 0.7132
+4 54835 2 50 2000 1802 0.74829 0.6634
+5 54868 3 83 2000 1803 0.98742 0.1581
+6 54942 6 157 2000 1806 0.44325 -0.8964
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+\FloatBarrier
+
+%------------------------------------------------------------
+\subsection{EGRET Plots}
+%------------------------------------------------------------
+The Daily, Sample, and INFO dataframes (described in Secs. \ref{INFOsubsection} - \ref{Samplesubsection}) are specifically formatted to be used with the EGRET package. The EGRET package has powerful modeling capabilities that use WRTDS, but EGRET also has graphing and tabular tools for exploring the data without using the WRTDS algorithm. See the EGRET vignette, user guide, and/or wiki (\url{https://github.com/USGS-R/EGRET/wiki}) for detailed information. Figure \ref{fig:egretEx} shows one of the plotting functions that can be used directly from the dataRetrieval dataframes.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# Continuing Choptank example from the previous sections}
+\hlkwd{library}\hlstd{(EGRET)}
+\hlkwd{multiPlotDataOverview}\hlstd{()}
+\end{alltt}
+\end{kframe}\begin{figure}[]
+
+\includegraphics[width=\maxwidth]{figure/egretEx} \caption[Default \texttt{multiPlotDataOverview}]{Default \texttt{multiPlotDataOverview}\label{fig:egretEx}}
+\end{figure}
+
+
+\end{knitrout}
+
+\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{retrieveNWISdvData} & Raw USGS daily data \\
+ [5pt]Daily\tnote{1} & \texttt{getNWISDaily} & USGS daily values \\
+ [5pt]Daily\tnote{1} & \texttt{getUserDaily} & User generated daily data \\
+ [5pt]Sample & \texttt{retrieveNWISqwData} & Raw USGS water quality data \\
+ [5pt]Sample & \texttt{retrieveWQPqwData} & Raw Water Quality Data Portal data \\
+ [5pt]Sample & \texttt{getWQPData} & General Water Quality Portal\\
+ [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{retrieveNWISunitData} & Raw USGS instantaneous data \\
+ [5pt]Information\tnote{1} & \texttt{getMetaData} & USGS station and parameter code information \\
+ [5pt]Information & \texttt{getNWISPcodeInfo} & USGS parameter code information \\
+ [5pt]Information & \texttt{getNWISSiteInfo} & USGS station information \\
+ [5pt]Information & \texttt{getNWISDataAvailability} & Data available at USGS stations \\
+ \hline
+\end{tabular}
+
+ \begin{tablenotes}
+ \item[1] Indicates that the function creates a data frame suitable for use in EGRET software
+ \end{tablenotes}
+ \end{threeparttable}
+}
+\end{table}
+
+
+\begin{table}[!ht]
+\begin{minipage}{\linewidth}
+{\footnotesize
+\caption{dataRetrieval functions organization}
+\label{tab:dataRetrievalOrg}
+\hspace*{-1.5cm}
+\begin{tabular}{|c|cccc|}
+
+\multicolumn{1}{c}{\textbf{\textsf{Source}}} &
+\multicolumn{1}{c}{\textbf{\textsf{Site Query}}} &
+\multicolumn{1}{c}{\textbf{\textsf{Meta Data}}} &
+\multicolumn{1}{c}{\textbf{\textsf{Raw Data}}} &
+\multicolumn{1}{c}{\textbf{\textsf{EGRET Data}}} \\ [0pt]
+\hline
+\textbf{NWIS:} & \texttt{getNWISSites} & & \texttt{getNWISData} & \\
+\textit{Daily} & & \texttt{getNWISSiteInfo} & \texttt{retrieveNWISdvData} & \texttt{getNWISDaily} \\
+\textit{Unit/Instantaneous} & \texttt{getNWISDataAvailability} & \texttt{getNWISPcodeInfo} & \texttt{retrieveNWISunitData} & \\
+\textit{Groundwater} & & \texttt{getNWISInfo} & & \\
+\textit{Water Quality} & & & \texttt{retrieveNWISqwDAta} & \texttt{getNWISSample}\\
+\hline
+\textbf{Water Quality Portal:} & \texttt{getWQPSites} & \texttt{getWQPInfo} & \texttt{retrieveWQPqwData} & \texttt{getWQPSample} \\
+\textit{USGS} & & & \texttt{getWQPData} & \\
+\textit{EPA} & & & & \\
+\textit{USDA} & & & & \\
+\hline
+\textbf{User-supplied files:} & & & & \\
+\textit{Daily} & & & & \texttt{getUserDaily}\\
+\textit{Sample} & & & & \texttt{getUserSample}\\
+\textit{Site Information} & & \texttt{getUserInfo} & & \\
+
+ \hline
+\end{tabular}
+\hspace*{-1.5cm}
+}
+\end{minipage}
+\end{table}
+
+
+
+\begin{table}[!ht]
+\begin{minipage}{\linewidth}
+{\footnotesize
+\caption{dataRetrieval function organization}
+\label{tab:dataRetrievalMisc}
+\begin{tabular}{ll}
+ \hline
+\multicolumn{1}{c}{\textbf{\textsf{Function Name}}} &
+\multicolumn{1}{c}{\textbf{\textsf{Description}}} \\ [0pt]
+ \hline
+ \texttt{compressData} & Converts value/qualifier into ConcLow, ConcHigh, Uncen\\
+ [5pt]\texttt{getRDB1Data} & Retrieves and converts RDB data to dataframe\\
+ [5pt]\texttt{getWaterML1Data} & Retrieves and converts WaterML1 data to dataframe\\
+ [5pt]\texttt{getWaterML2Data} & Retrieves and converts WaterML2 data to dataframe\\
+ [5pt]\texttt{mergeReport} & Merges flow data from the daily record into the sample record\\
+ [5pt]\texttt{populateDateColumns} & Generates Julian, Month, Day, DecYear, and MonthSeq columns\\
+ [5pt]\texttt{removeDuplicates} & Removes duplicated rows\\
+ [5pt]\texttt{renameColumns} & Renames columns from raw data retrievals\\
+ \hline
+\end{tabular}
+}
+\end{minipage}
+\end{table}
+
+\FloatBarrier
+\clearpage
+
+
+%------------------------------------------------------------
+\section{Getting Started in R}
+\label{sec:appendix1}
+%------------------------------------------------------------
+This section describes the options for downloading and installing the dataRetrieval package.
+
+%------------------------------------------------------------
+\subsection{New to R?}
+%------------------------------------------------------------
+If you are new to R, you will need to first install the latest version of R, which can be found here: \url{http://www.r-project.org/}.
+
+At any time, you can get information about any function in R by typing a question mark before the functions name. This will open a file (in RStudio, in the Help window) that describes the function, the required arguments, and provides working examples.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlopt{?}\hlstd{removeDuplicates}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+This will open a help file similar to Figure \ref{fig:help}.
+
+\FloatBarrier
+
+To see the raw code for a particular code, type the name of the function, without parentheses.:
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{removeDuplicates}
+\end{alltt}
+\begin{verbatim}
+function (localSample = Sample)
+{
+ Sample1 <- localSample[!duplicated(localSample[c("DecYear",
+ "ConcHigh")]), ]
+ return(Sample1)
+}
+<environment: namespace:dataRetrieval>
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+
+\begin{figure}[ht!]
+\centering
+ \resizebox{0.95\textwidth}{!}{\includegraphics{Rhelp.png}}
+\caption{A simple R help file}
+\label{fig:help}
+\end{figure}
+
+Additionally, many R packages have vignette files attached (such as this paper). To view the vignette:
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{vignette}\hlstd{(dataRetrieval)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+\FloatBarrier
+\clearpage
+%------------------------------------------------------------
+\subsection{R User: Installing dataRetrieval}
+%------------------------------------------------------------
+The following command installs dataRetrieval and subsequent required packages:
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{install.packages}\hlstd{(}\hlstr{"dataRetrieval"}\hlstd{,}
+\hlkwc{repos}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"http://usgs-r.github.com"}\hlstd{,}\hlstr{"http://cran.us.r-project.org"}\hlstd{),}
+\hlkwc{dependencies}\hlstd{=}\hlnum{TRUE}\hlstd{,}
+\hlkwc{type}\hlstd{=}\hlstr{"both"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+After installing the package, you need to open the library each time you re-start R. This is done with the simple command:
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{library}\hlstd{(dataRetrieval)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+%------------------------------------------------------------
+\section{Creating tables in Microsoft\textregistered\ software from R}
+\label{app:createWordTable}
+%------------------------------------------------------------
+There are a few steps that are required in order to create a table in Microsoft\textregistered\ software (Excel, Word, PowerPoint, etc.) from an R dataframe. There are certainly a variety of good methods, one of which is detailed here. The example we will step through here will be to create a table in Microsoft Excel based on the dataframe tableData:
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{availableData} \hlkwb{<-} \hlkwd{getNWISDataAvailability}\hlstd{(siteNumber)}
+\hlstd{dailyData} \hlkwb{<-} \hlstd{availableData[}\hlstr{"dv"} \hlopt{==} \hlstd{availableData}\hlopt{$}\hlstd{service,]}
+\hlstd{dailyData} \hlkwb{<-} \hlstd{dailyData[}\hlstr{"00003"} \hlopt{==} \hlstd{dailyData}\hlopt{$}\hlstd{statCd,]}
+
+\hlstd{tableData} \hlkwb{<-} \hlkwd{with}\hlstd{(dailyData,}
+ \hlkwd{data.frame}\hlstd{(}
+ \hlkwc{shortName}\hlstd{=srsname,}
+ \hlkwc{Start}\hlstd{=startDate,}
+ \hlkwc{End}\hlstd{=endDate,}
+ \hlkwc{Count}\hlstd{=count,}
+ \hlkwc{Units}\hlstd{=parameter_units)}
+ \hlstd{)}
+\hlstd{tableData}
+\end{alltt}
+\begin{verbatim}
+ shortName Start
+1 Temperature, water 2010-10-01
+2 Stream flow, mean. daily 1948-01-01
+3 Specific conductance 2010-10-01
+4 Suspended sediment concentration (SSC) 1980-10-01
+5 Suspended sediment discharge 1980-10-01
+ End Count Units
+1 2012-05-09 529 deg C
+2 2014-09-21 24371 ft3/s
+3 2012-05-09 527 uS/cm @25C
+4 1991-09-30 3651 mg/l
+5 1991-09-30 3652 tons/day
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+First, save the dataframe as a tab delimited file (you don't want to use comma delimited because there are commas in some of the data elements):
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{write.table}\hlstd{(tableData,} \hlkwc{file}\hlstd{=}\hlstr{"tableData.tsv"}\hlstd{,}\hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{,}
+ \hlkwc{row.names} \hlstd{=} \hlnum{FALSE}\hlstd{,}\hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+This will save a file in your working directory called tableData.tsv. You can see your working directory by typing getwd() in the R console. Opening the file in a general-purpose text editor, you should see the following:
+
+\begin{verbatim}
+shortName Start End Count Units
+Temperature, water 2010-10-01 2012-06-24 575 deg C
+Stream flow, mean. daily 1948-01-01 2013-03-13 23814 ft3/s
+Specific conductance 2010-10-01 2012-06-24 551 uS/cm @25C
+Suspended sediment concentration (SSC) 1980-10-01 1991-09-30 3651 mg/l
+Suspended sediment discharge 1980-10-01 1991-09-30 3652 tons/day
+\end{verbatim}
+
+Next, follow the steps below to open this file in Excel:
+\begin{enumerate}
+\item Open Excel
+\item Click on the File tab
+\item Click on the Open option
+\item Navigate to the working directory (as shown in the results of \texttt{getwd()})
+\item Next to the File name text box, change the dropdown type to All Files (*.*)
+\item Double click tableData.tsv
+\item A text import wizard will open up, in the first window, choose the Delimited radio button if it is not automatically picked, then click on Next.
+\item In the second window, click on the Tab delimiter if it is not automatically checked, then click Finished.
+\item Use the many formatting tools within Excel to customize the table
+\end{enumerate}
+
+From Excel, it is simple to copy and paste the tables in other Microsoft\textregistered\ software. An example using one of the default Excel table formats is here.
+
+\begin{figure}[ht!]
+\centering
+ \resizebox{0.9\textwidth}{!}{\includegraphics{table1.png}}
+\caption{A simple table produced in Microsoft\textregistered\ Excel. Additional formatting will be requried, for example converting u to $\mu$ }
+\label{overflow}
+\end{figure}
+
+\clearpage
+
+%-------------------------------------
+\section{Disclaimer}
+%------------------------------------
+This information is preliminary and is subject to revision. It is being provided to meet the need for timely best science. The information is provided on the condition that neither the U.S. Geological Survey nor the U.S. Government may be held liable for any damages resulting from the authorized or unauthorized use of the information.
+
+
+\end{document}
diff --git a/vignettes/dataRetrieval.toc b/vignettes/dataRetrieval.toc
new file mode 100644
index 0000000000000000000000000000000000000000..babd748f27bf8b876eb8e6499fd44285de2a18fe
--- /dev/null
+++ b/vignettes/dataRetrieval.toc
@@ -0,0 +1,34 @@
+\select@language {american}
+\contentsline {section}{\numberline {1}Introduction to dataRetrieval}{3}{section.1}
+\contentsline {section}{\numberline {2}USGS Web Retrievals}{4}{section.2}
+\contentsline {subsection}{\numberline {2.1}Site Information}{5}{subsection.2.1}
+\contentsline {subsubsection}{\numberline {2.1.1}getNWISSiteInfo}{5}{subsubsection.2.1.1}
+\contentsline {subsubsection}{\numberline {2.1.2}getNWISDataAvailability}{6}{subsubsection.2.1.2}
+\contentsline {subsection}{\numberline {2.2}Parameter Information}{6}{subsection.2.2}
+\contentsline {subsection}{\numberline {2.3}Daily Values}{7}{subsection.2.3}
+\contentsline {subsection}{\numberline {2.4}Unit Values}{10}{subsection.2.4}
+\contentsline {subsection}{\numberline {2.5}Water Quality Values}{11}{subsection.2.5}
+\contentsline {subsection}{\numberline {2.6}URL Construction}{13}{subsection.2.6}
+\contentsline {section}{\numberline {3}Water Quality Portal Web Retrievals}{13}{section.3}
+\contentsline {section}{\numberline {4}Generalized Retrievals}{13}{section.4}
+\contentsline {subsubsection}{\numberline {4.0.1}NWIS sites}{13}{subsubsection.4.0.1}
+\contentsline {subsubsection}{\numberline {4.0.2}NWIS data}{14}{subsubsection.4.0.2}
+\contentsline {subsubsection}{\numberline {4.0.3}Water Quality Portal sites}{15}{subsubsection.4.0.3}
+\contentsline {subsubsection}{\numberline {4.0.4}Water Quality Portal data}{15}{subsubsection.4.0.4}
+\contentsline {section}{\numberline {5}Data Retrievals Structured For Use In The EGRET Package}{15}{section.5}
+\contentsline {subsection}{\numberline {5.1}INFO Data}{16}{subsection.5.1}
+\contentsline {subsection}{\numberline {5.2}Daily Data}{16}{subsection.5.2}
+\contentsline {subsection}{\numberline {5.3}Sample Data}{17}{subsection.5.3}
+\contentsline {subsection}{\numberline {5.4}Censored Values: Summation Explanation}{18}{subsection.5.4}
+\contentsline {subsection}{\numberline {5.5}User-Generated Data Files}{20}{subsection.5.5}
+\contentsline {subsubsection}{\numberline {5.5.1}getUserDaily}{20}{subsubsection.5.5.1}
+\contentsline {subsubsection}{\numberline {5.5.2}getUserSample}{21}{subsubsection.5.5.2}
+\contentsline {subsection}{\numberline {5.6}Merge Report}{22}{subsection.5.6}
+\contentsline {subsection}{\numberline {5.7}EGRET Plots}{23}{subsection.5.7}
+\contentsline {section}{\numberline {6}Summary}{25}{section.6}
+\contentsline {section}{\numberline {7}Getting Started in R}{28}{section.7}
+\contentsline {subsection}{\numberline {7.1}New to R?}{28}{subsection.7.1}
+\contentsline {subsection}{\numberline {7.2}R User: Installing dataRetrieval}{30}{subsection.7.2}
+\contentsline {section}{\numberline {8}Creating tables in Microsoft\textregistered \ software from R}{30}{section.8}
+\contentsline {section}{\numberline {9}Disclaimer}{33}{section.9}
+\contentsfinish
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