diff --git a/DESCRIPTION b/DESCRIPTION
index 0d43ad3392dcc7b7f06926de997be2bff60847ae..cfeac6c5670a1a02758c293e2f07e1232f481b02 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -20,7 +20,6 @@ Collate:
'getSiteFileData.r'
'getDataFromFile.r'
'getParameterInfo.r'
- 'getPreLoadedData.r'
'checkStartEndDate.r'
'dateFormatCheck.r'
'formatCheckDate.r'
@@ -36,10 +35,8 @@ Collate:
'populateParameterINFO.r'
'removeDuplicates.r'
'getDVData.r'
- 'getPreLoadedDailyData.r'
'getDailyDataFromFile.r'
'getSampleData.r'
- 'getPreLoadedSampleData.r'
'getSampleDataFromFile.r'
'getMetaData.r'
'mergeReport.r'
diff --git a/NAMESPACE b/NAMESPACE
index cfa3034906a489e8501b0b57268d954fae68b2f6..ad346ed18573994ad4461bb6b628b92988d356d0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -12,9 +12,6 @@ export(getDataAvailability)
export(getDataFromFile)
export(getMetaData)
export(getParameterInfo)
-export(getPreLoadedDailyData)
-export(getPreLoadedData)
-export(getPreLoadedSampleData)
export(getQWData)
export(getQWDataFromFile)
export(getRDB1Data)
diff --git a/R/getPreLoadedDailyData.r b/R/getPreLoadedDailyData.r
deleted file mode 100644
index 11df232210e3ba5b2697107bba3452a4fe6b9801..0000000000000000000000000000000000000000
--- a/R/getPreLoadedDailyData.r
+++ /dev/null
@@ -1,22 +0,0 @@
-#' Import Preloaded Daily Data for WRTDS use
-#'
-#' This function is intended to convert daily data that is already loaded into the R enviornment to the WRTDS daily data frame.
-#'
-#' @param loadedData dataframe that is already loaded in R session
-#' @param qUnit number 1 is cubic feet per second, 2 is cubic meters per second, 3 is 10^3 cubic feet per second, and 4 is 10^3 cubic meters per second
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords data import WRTDS
-#' @export
-#' @return Daily dataframe
-#' @examples
-#' Daily <- getPreLoadedDailyData(ChoptankRiverFlow, interactive=FALSE)
-getPreLoadedDailyData <- function (loadedData,qUnit=1,interactive=TRUE){
- data <- getPreLoadedData(loadedData)
- convertQ<-c(35.314667,1)
- qConvert<-convertQ[qUnit]
- if (interactive){
- if(qUnit==1) cat("\n the input discharge are assumed to be in cubic feet per second\nif they are in cubic meters per second, then the call to getPreLoadedDailyData should specify qUnit=2\n")
- }
- localDaily <- populateDaily(data,qConvert, interactive=interactive)
- return(localDaily)
-}
diff --git a/R/getPreLoadedData.r b/R/getPreLoadedData.r
deleted file mode 100644
index 3dcdbe298dc8545c91f430579be2d9fcf1a8a87e..0000000000000000000000000000000000000000
--- a/R/getPreLoadedData.r
+++ /dev/null
@@ -1,31 +0,0 @@
-#' Convert Preloaded Flow Data
-#'
-#' Imports data from data already pre-loaded into the R workspace. Specifically used to import water flow data for use in the WRTDS package.
-#' For WRTDS usage, the first column is expected to be dates, the second column measured values.
-#' The third column is optional, it contains any remark codes.
-#'
-#' @param rawData dataframe data already loaded into R workspace
-#' @keywords data import
-#' @return retval dataframe with dateTime, value, and code columns
-#' @export
-#' @examples
-#' ChoptankRiverFlow <- ChoptankRiverFlow
-#' rawData <- getPreLoadedData(ChoptankRiverFlow)
-#' rawDataSample <- getPreLoadedData(ChoptankRiverNitrate)
-getPreLoadedData <- function (rawData){
- retval <- as.data.frame(rawData, stringsAsFactors=FALSE)
- if(ncol(retval) == 2){
- names(retval) <- c('dateTime', 'value')
- } else if (ncol(retval) == 3){
- names(retval) <- c('dateTime', 'code', 'value')
- }
- retval$dateTime <- as.character(retval$dateTime)
- if(dateFormatCheck(retval$dateTime)){
- retval$dateTime <- as.Date(retval$dateTime)
- } else {
- retval$dateTime <- as.Date(retval$dateTime,format="%m/%d/%Y")
- }
-
- retval$value <- as.numeric(retval$value)
- return (retval)
-}
diff --git a/R/getPreLoadedSampleData.r b/R/getPreLoadedSampleData.r
deleted file mode 100644
index 2862993ab1cbf2f6e317cb4c9535b570660b2cd9..0000000000000000000000000000000000000000
--- a/R/getPreLoadedSampleData.r
+++ /dev/null
@@ -1,17 +0,0 @@
-#' Import Preloaded Sample Data for WRTDS use
-#'
-#' This function is intended to convert sample data that is already loaded into the R enviornment to the WRTDS daily data frame.
-#'
-#' @param loadedData dataframe that is already loaded in R session
-#' @param interactive logical Option for interactive mode. If true, there is user interaction for error handling and data checks.
-#' @keywords data import WRTDS
-#' @export
-#' @return Sample dataframe
-#' @examples
-#' Sample <- getPreLoadedSampleData(ChoptankRiverNitrate, interactive=FALSE)
-getPreLoadedSampleData <- function (loadedData,interactive=TRUE){
-
- compressedData <- compressData(loadedData,interactive=interactive)
- Sample <- populateSampleColumns(compressedData)
- return(Sample)
-}
diff --git a/man/getPreLoadedDailyData.Rd b/man/getPreLoadedDailyData.Rd
deleted file mode 100644
index 8be9941cee8a1e22b9c42a2f1e1783955a01990b..0000000000000000000000000000000000000000
--- a/man/getPreLoadedDailyData.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-\name{getPreLoadedDailyData}
-\alias{getPreLoadedDailyData}
-\title{Import Preloaded Daily Data for WRTDS use}
-\usage{
- getPreLoadedDailyData(loadedData, qUnit = 1,
- interactive = TRUE)
-}
-\arguments{
- \item{loadedData}{dataframe that is already loaded in R
- session}
-
- \item{qUnit}{number 1 is cubic feet per second, 2 is
- cubic meters per second, 3 is 10^3 cubic feet per second,
- and 4 is 10^3 cubic meters per second}
-
- \item{interactive}{logical Option for interactive mode.
- If true, there is user interaction for error handling and
- data checks.}
-}
-\value{
- Daily dataframe
-}
-\description{
- This function is intended to convert daily data that is
- already loaded into the R enviornment to the WRTDS daily
- data frame.
-}
-\examples{
-Daily <- getPreLoadedDailyData(ChoptankRiverFlow, interactive=FALSE)
-}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-
diff --git a/man/getPreLoadedData.Rd b/man/getPreLoadedData.Rd
deleted file mode 100644
index 8aefe64af90936bf7ab631ee19de8d33baa2fdec..0000000000000000000000000000000000000000
--- a/man/getPreLoadedData.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-\name{getPreLoadedData}
-\alias{getPreLoadedData}
-\title{Convert Preloaded Flow Data}
-\usage{
- getPreLoadedData(rawData)
-}
-\arguments{
- \item{rawData}{dataframe data already loaded into R
- workspace}
-}
-\value{
- retval dataframe with dateTime, value, and code columns
-}
-\description{
- Imports data from data already pre-loaded into the R
- workspace. Specifically used to import water flow data
- for use in the WRTDS package. For WRTDS usage, the first
- column is expected to be dates, the second column
- measured values. The third column is optional, it
- contains any remark codes.
-}
-\examples{
-ChoptankRiverFlow <- ChoptankRiverFlow
-rawData <- getPreLoadedData(ChoptankRiverFlow)
-rawDataSample <- getPreLoadedData(ChoptankRiverNitrate)
-}
-\keyword{data}
-\keyword{import}
-
diff --git a/man/getPreLoadedSampleData.Rd b/man/getPreLoadedSampleData.Rd
deleted file mode 100644
index 1e8834a400df76773c56f0d66f2f281f4bffabf2..0000000000000000000000000000000000000000
--- a/man/getPreLoadedSampleData.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-\name{getPreLoadedSampleData}
-\alias{getPreLoadedSampleData}
-\title{Import Preloaded Sample Data for WRTDS use}
-\usage{
- getPreLoadedSampleData(loadedData, interactive = TRUE)
-}
-\arguments{
- \item{loadedData}{dataframe that is already loaded in R
- session}
-
- \item{interactive}{logical Option for interactive mode.
- If true, there is user interaction for error handling and
- data checks.}
-}
-\value{
- Sample dataframe
-}
-\description{
- This function is intended to convert sample data that is
- already loaded into the R enviornment to the WRTDS daily
- data frame.
-}
-\examples{
-Sample <- getPreLoadedSampleData(ChoptankRiverNitrate, interactive=FALSE)
-}
-\keyword{WRTDS}
-\keyword{data}
-\keyword{import}
-
diff --git a/man/getSampleData.Rd b/man/getSampleData.Rd
index aa83390b01f2f112a4441e86fe4491d60803de99..03563421128d0064c62f7f0f5666acfec800454d 100644
--- a/man/getSampleData.Rd
+++ b/man/getSampleData.Rd
@@ -27,8 +27,9 @@
}
\description{
Imports data from NWIS web service. This function gets
- the data from here: \url{http://qwwebservices.usgs.gov/}
- A list of parameter codes can be found here:
+ 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}
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index 9c4b7d7c852ad58e193f20fa190ef5178afa4338..4e0d91d301a16c0d0b2a53fc95bfe3c5efe616cf 100644
--- a/vignettes/dataRetrieval-concordance.tex
+++ b/vignettes/dataRetrieval-concordance.tex
@@ -1,9 +1,9 @@
\Sconcordance{concordance:dataRetrieval.tex:dataRetrieval.Rnw:%
1 49 1 50 0 1 6 11 1 1 5 46 1 113 0 7 1 42 0 21 1 10 %
-0 16 1 9 0 21 1 5 0 6 1 8 0 14 1 42 0 17 1 3 0 15 1 6 %
-0 16 1 10 0 5 1 8 0 20 1 3 0 18 1 1 0 21 1 9 0 20 1 4 %
-0 4 1 18 0 29 1 6 0 10 1 10 0 14 1 21 0 19 1 5 0 19 1 %
-5 0 17 1 8 0 14 1 15 0 16 1 5 0 9 1 5 0 62 1 6 0 14 1 %
-17 0 36 1 5 0 24 1 5 0 20 1 37 0 13 1 10 0 22 1 5 0 5 %
-1 13 0 5 1 5 0 11 1 5 0 7 1 5 0 16 1 51 0 15 1 49 0 7 %
-1 32 0 24 1 18 0 8 1 5 0 56 1}
+0 16 1 9 0 21 1 5 0 6 1 8 0 14 1 42 0 17 1 4 0 15 1 6 %
+0 16 1 10 0 5 1 8 0 20 1 4 0 18 1 3 0 21 1 10 0 20 1 %
+4 0 4 1 18 0 29 1 8 0 10 1 10 0 14 1 21 0 19 1 5 0 19 %
+1 5 0 17 1 8 0 14 1 15 0 16 1 5 0 9 1 5 0 62 1 6 0 11 %
+1 1 4 36 1 5 0 24 1 5 0 20 1 38 0 13 1 10 0 79 1 5 0 %
+5 1 13 0 5 1 5 0 11 1 5 0 7 1 5 0 16 1 51 0 15 1 49 0 %
+7 1 32 0 24 1 19 0 8 1 5 0 56 1}
diff --git a/vignettes/dataRetrieval.Rnw b/vignettes/dataRetrieval.Rnw
index a5f0489a095d67ab7e4dac61b4aff024ad1666c0..7e5ab3318dde9a3a50b62ddfbb2ec421a5700d4b 100644
--- a/vignettes/dataRetrieval.Rnw
+++ b/vignettes/dataRetrieval.Rnw
@@ -557,7 +557,8 @@ For every sample, the EGRET package requires a pair of numbers to define an inte
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 is therefore:
<<thirdExample,echo=FALSE>>=
-getPreLoadedSampleData(DF)
+ compressedData <- compressData(DF)
+ Sample <- populateSampleColumns(compressedData)
@
@@ -654,7 +655,64 @@ library(EGRET)
multiPlotDataOverview()
@
+
\clearpage
+
+%------------------------------------------------------------
+\section{Summary}
+%------------------------------------------------------------
+
+The following table summarizes the data retrieval functions:
+
+\begin{table}[!ht]
+\begin{minipage}{\linewidth}
+\begin{center}
+\caption{dataRetrieval functions}
+\begin{tabular}{lll}
+ \hline
+Data Type & Function Name & Description \\
+ \hline
+ Daily (raw) & retrieveNWISData & Raw USGS daily data \\
+ Daily & getDVData & USGS daily values \\
+ Daily & getDailyDataFromFile & User generated daily data \\
+ Sample (raw) & retrieveNWISqwData & Raw USGS water quality data \\
+ Sample (raw) & getRawQWData & Raw Water Quality Data Portal data \\
+ Sample (raw) & getQWDataFromFile & Raw user generated water quality data \\
+ Sample (processed) & getQWData & USGS Water Quality Portal data \\
+ Sample (processed) & getWQPData & General Water Quality Portal\\
+ Sample & getSampleData & USGS water quality data\\
+ Sample & getSTORETSampleData & STORET Water Quality Data Portal data \\
+ Sample & getSampleDataFromFile & User generated sample data \\
+ Unit (raw) & retrieveUnitNWISData & Raw USGS instantaneous data \\
+ Information & getMetaData & USGS station and parameter code information \\
+ Information & getParameterInfo & USGS parameter code information \\
+ Information & getSiteFileData & USGS station information \\
+ Information & getDataAvailability & Data available at USGS stations \\
+ \hline
+\end{tabular}
+\end{center}
+\end{minipage}
+\end{table}
+
+\begin{table}[!ht]
+\begin{minipage}{\linewidth}
+\begin{center}
+\caption{dataRetrieval functions 2}
+\begin{tabular}{l p{4cm} p{4cm}}
+ \hline
+Data Type & EGRET Functions & Other Retrieval Functions \\
+ \hline
+ Daily Data & getDVData \par getDailyDataFromFile & retrieveNWISData \\
+ Water Quality Sample Data & getSampleData \par getSTORETSampleData \par getSampleDataFromFile \par & retrieveNWISqwData \par getRawQWData \par getQWDataFromFile \par getQWData \par getWQPData\\
+ Unit Data& & retrieveUnitNWISData \\
+ Meta Data & getMetaData & getParameterInfo \par getSiteFileData \par getDataAvailability \\
+ \hline
+\end{tabular}
+\end{center}
+\end{minipage}
+\end{table}
+
+
\appendix
%------------------------------------------------------------
diff --git a/vignettes/dataRetrieval.log b/vignettes/dataRetrieval.log
index 6a240d1a982e9677f9d9e9f686f81ef0f98b546e..4acb9c778fa3c2977883cd63ef49e1a647ef02bb 100644
--- a/vignettes/dataRetrieval.log
+++ b/vignettes/dataRetrieval.log
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9) (preloaded format=pdflatex 2012.1.6) 13 SEP 2013 16:58
+This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9) (preloaded format=pdflatex 2012.1.6) 28 OCT 2013 16:27
entering extended mode
**dataRetrieval.tex
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.tex
@@ -698,90 +698,94 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
[10]
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[]\OT1/ptm/m/n/10.95 Parameter in-for-ma-tion is ob-tained from []$\OT1/pcr/m/n
/10.95 http : / / nwis . waterdata . usgs . gov / nwis / pmcodes/$[]
[]
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+ Default added (so using `tbp') on input line 623.
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+<figure/getNWIStemperaturePlot.pdf, id=236, 505.89pt x 505.89pt>
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\OT1/ptm/m/n/10.95 There are ad-di-tional data sets avail-able on the Wa-ter Qu
al-ity Data Por-tal ([]$\OT1/pcr/m/n/10.95 http : / / www . waterqualitydata .$
[]
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[][]\OT1/pcr/m/n/10.95 url_uv[] []<-[] []\OT1/pcr/b/n/10.95 constructNWISURL[][
]\OT1/pcr/m/n/10.95 (siteNumber,[][]"00060"[][],startDate,endDate,[][]\TS1/pcr/
m/n/10.95 '\OT1/pcr/m/n/10.95 uv\TS1/pcr/m/n/10.95 '[][]\OT1/pcr/m/n/10.95 )[][
@@ -792,21 +796,17 @@ m/n/10.95 '\OT1/pcr/m/n/10.95 uv\TS1/pcr/m/n/10.95 '[][]\OT1/pcr/m/n/10.95 )[][
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[] \OT1/pcr/m/n/10.95 First day of the discharge record is 2000-01-01 and last
day is 2013-01-01[]
[]
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+Overfull \hbox (44.67563pt too wide) in paragraph at lines 1091--1091
[] \OT1/pcr/m/n/10.95 The first sample is from 2000-01-04 and the last sample i
s from 2012-12-18[]
[]
@@ -853,146 +855,150 @@ s from 2012-12-18[]
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[]\OT1/pcr/m/n/10.95 Suspended sediment concentration (SSC) 1980-10-01 1991-09-
30 3651 mg/l[]
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[]\OT1/ptm/m/n/10.95 Hirsch, R. M., Moyer, D. L. and Arch-field, S. A. (2010),
Weighted Re-gres-sions on
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n to Chesa-peake Bay River
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\OT1/ptm/m/n/10.95 In-puts. JAWRA Jour-nal of the Amer-i-can Wa-ter Re-sources
As-so-ci-a-tion, 46: 857-880.
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\OT1/ptm/m/n/10.95 doi: 10.1111/j.1752-1688.2010.00482.x []$\OT1/pcr/m/n/10.95
http : / / onlinelibrary . wiley . com / doi /$
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diff --git a/vignettes/dataRetrieval.pdf b/vignettes/dataRetrieval.pdf
index 12dbd481c0db79e2de797ca002821f25c4a58030..53bb4ac34aeb114a9960c7c3ab88d14834993f6e 100644
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diff --git a/vignettes/dataRetrieval.tex b/vignettes/dataRetrieval.tex
index ece61138119d7c905aeb890cdafd135c8fde485d..709a75ac99d19439dc6ca258bdc5abd5daede792 100644
--- a/vignettes/dataRetrieval.tex
+++ b/vignettes/dataRetrieval.tex
@@ -330,8 +330,8 @@ Once the site-ID is known, the next required input for USGS data retrievals is t
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 3.0.1 by xtable 1.7-1 package
-% Fri Sep 13 16:57:38 2013
+% latex table generated in R 3.0.2 by xtable 1.7-1 package
+% Mon Oct 28 16:27:10 2013
\begin{table}[ht]
\centering
\begin{tabular}{rll}
@@ -356,8 +356,8 @@ For real-time data, the parameter code and site ID will suffice. For most varia
\url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
Some common stat codes are shown in Table \ref{tab:stat}.
-% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Fri Sep 13 16:57:38 2013
+% latex table generated in R 3.0.2 by xtable 1.7-1 package
+% Mon Oct 28 16:27:10 2013
\begin{table}[ht]
\centering
\begin{tabular}{rll}
@@ -484,6 +484,7 @@ It is also possible to only request parameter information for a subset of variab
\hlcom{# This pulls out just the daily data:}
\hlstd{ChoptankDailyData} \hlkwb{<-} \hlkwd{subset}\hlstd{(ChoptankAvailableData,}
\hlstr{"dv"} \hlopt{==} \hlstd{service)}
+
\hlcom{# This pulls out the mean:}
\hlstd{ChoptankDailyData} \hlkwb{<-} \hlkwd{subset}\hlstd{(ChoptankDailyData,}
\hlstr{"00003"} \hlopt{==} \hlstd{statCd)}
@@ -492,8 +493,8 @@ It is also possible to only request parameter information for a subset of variab
\end{knitrout}
-% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Fri Sep 13 16:57:40 2013
+% latex table generated in R 3.0.2 by xtable 1.7-1 package
+% Mon Oct 28 16:27:11 2013
\begin{table}[ht]
\centering
\begin{tabular}{rlllll}
@@ -501,7 +502,7 @@ It is also possible to only request parameter information for a subset of variab
& shortName & Start & End & Count & Units \\
\hline
1 & Temperature, water & 2010-10-01 & 2012-05-09 & 529 & deg C \\
- 2 & Stream flow, mean. daily & 1948-01-01 & 2013-09-12 & 23997 & ft3/s \\
+ 2 & Stream flow, mean. daily & 1948-01-01 & 2013-10-27 & 24042 & ft3/s \\
3 & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & uS/cm @25C \\
4 & Suspended sediment concentration (SSC) & 1980-10-01 & 1991-09-30 & 3651 & mg/l \\
5 & Suspended sediment discharge & 1980-10-01 & 1991-09-30 & 3652 & tons/day \\
@@ -568,6 +569,7 @@ The dates (start and end) need to be in the format \texttt{"}YYYY-MM-DD\texttt{"
\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00060"} \hlcom{# Discharge (cfs)}
\hlstd{startDate} \hlkwb{<-} \hlstr{""} \hlcom{# Will request earliest date}
\hlstd{endDate} \hlkwb{<-} \hlstr{""} \hlcom{# Will request latest date}
+
\hlstd{discharge} \hlkwb{<-} \hlkwd{retrieveNWISData}\hlstd{(siteNumber,}
\hlstd{parameterCd, startDate, endDate)}
\end{alltt}
@@ -586,8 +588,10 @@ Another example that doesn't use the defaults would be a request for mean and ma
\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{retrieveNWISData}\hlstd{(siteNumber, parameterCd,}
\hlstd{startDate, endDate,} \hlkwc{StatCd}\hlstd{=statCd)}
+
\hlstd{temperatureAndFlow} \hlkwb{<-} \hlkwd{renameColumns}\hlstd{(temperatureAndFlow)}
\end{alltt}
\end{kframe}
@@ -602,13 +606,14 @@ An example of plotting the above data (Figure \ref{fig:getNWIStemperaturePlot}):
\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{))}
+
\hlkwd{with}\hlstd{(temperatureAndFlow,} \hlkwd{plot}\hlstd{(}
- \hlstd{datetime, Temperature_water_01,}
+ \hlstd{datetime, Temperature_water_degrees_Celsius_Max_01,}
\hlkwc{xlab}\hlstd{=}\hlstr{"Date"}\hlstd{,}\hlkwc{ylab}\hlstd{=}\hlstr{"Temperature [C]"}
\hlstd{))}
\hlkwd{par}\hlstd{(}\hlkwc{new}\hlstd{=}\hlnum{TRUE}\hlstd{)}
\hlkwd{with}\hlstd{(temperatureAndFlow,} \hlkwd{plot}\hlstd{(}
- \hlstd{datetime, Stream_flow_mean_daily,}
+ \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{)}
@@ -691,8 +696,10 @@ To get USGS water quality data from water samples collected at the streamgage (a
\hlstd{parameterCd} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"00618"}\hlstd{,}\hlstr{"71851"}\hlstd{)}
\hlstd{startDate} \hlkwb{<-} \hlstr{"1979-10-11"}
\hlstd{endDate} \hlkwb{<-} \hlstr{"2012-12-18"}
+
\hlstd{dissolvedNitrate} \hlkwb{<-} \hlkwd{getRawQWData}\hlstd{(siteNumber, parameterCd,}
\hlstd{startDate, endDate)}
+
\hlstd{dissolvedNitrateSimple} \hlkwb{<-} \hlkwd{getQWData}\hlstd{(siteNumber, parameterCd,}
\hlstd{startDate, endDate)}
\hlkwd{names}\hlstd{(dissolvedNitrateSimple)}
@@ -835,8 +842,8 @@ There are 4750 data points, and 4750 days.
Details of the Daily dataframe are listed below:
-% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Fri Sep 13 16:57:53 2013
+% latex table generated in R 3.0.2 by xtable 1.7-1 package
+% Mon Oct 28 16:27:21 2013
\begin{table}[ht]
\centering
\begin{tabular}{rllll}
@@ -944,8 +951,8 @@ As an example to understand how the dataRetrieval package handles a more complex
\begin{center}
-% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Fri Sep 13 16:57:54 2013
+% latex table generated in R 3.0.2 by xtable 1.7-1 package
+% Mon Oct 28 16:27:22 2013
\begin{table}[ht]
\centering
\begin{tabular}{rllrlrlr}
@@ -974,26 +981,7 @@ For every sample, the EGRET package requires a pair of numbers to define an inte
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 is therefore:
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{verbatim}
- Date ConcLow ConcHigh Uncen ConcAve Julian Month
-1 2003-02-15 0.520 0.520 1 0.520 55927 2
-2 2003-06-30 0.310 0.310 1 0.310 56062 6
-3 2004-09-15 0.205 0.205 1 0.205 56505 9
-4 2005-01-30 0.430 0.430 1 0.430 56642 1
-5 2005-05-30 0.050 0.050 1 0.050 56762 5
-6 2005-10-30 0.020 0.020 1 0.020 56915 10
- Day DecYear MonthSeq SinDY CosDY
-1 46 2003 1838 0.70407 0.7101
-2 182 2003 1842 0.02575 -0.9997
-3 259 2005 1857 -0.96251 -0.2712
-4 30 2005 1861 0.48506 0.8745
-5 151 2005 1865 0.52943 -0.8484
-6 304 2006 1870 -0.87861 0.4775
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
+
\FloatBarrier
@@ -1081,6 +1069,7 @@ Finally, there is a function called mergeReport that will look at both the Daily
\hlstd{parameterCd} \hlkwb{<-} \hlstr{"00631"} \hlcom{# Nitrate}
\hlstd{startDate} \hlkwb{<-} \hlstr{"2000-01-01"}
\hlstd{endDate} \hlkwb{<-} \hlstr{"2013-01-01"}
+
\hlstd{Daily} \hlkwb{<-} \hlkwd{getDVData}\hlstd{(siteNumber,} \hlstr{"00060"}\hlstd{, startDate, endDate)}
\end{alltt}
\begin{verbatim}
@@ -1094,10 +1083,10 @@ There are 4750 data points, and 4750 days.
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 220 samples
+ 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 1.3 2.4
+ 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}
@@ -1146,7 +1135,64 @@ As has been mentioned, the data is specifically formatted to be used with the EG
\end{knitrout}
+
\clearpage
+
+%------------------------------------------------------------
+\section{Summary}
+%------------------------------------------------------------
+
+The following table summarizes the data retrieval functions:
+
+\begin{table}[!ht]
+\begin{minipage}{\linewidth}
+\begin{center}
+\caption{dataRetrieval functions}
+\begin{tabular}{lll}
+ \hline
+Data Type & Function Name & Description \\
+ \hline
+ Daily (raw) & retrieveNWISData & Raw USGS daily data \\
+ Daily & getDVData & USGS daily values \\
+ Daily & getDailyDataFromFile & User generated daily data \\
+ Sample (raw) & retrieveNWISqwData & Raw USGS water quality data \\
+ Sample (raw) & getRawQWData & Raw Water Quality Data Portal data \\
+ Sample (raw) & getQWDataFromFile & Raw user generated water quality data \\
+ Sample (processed) & getQWData & USGS Water Quality Portal data \\
+ Sample (processed) & getWQPData & General Water Quality Portal\\
+ Sample & getSampleData & USGS water quality data\\
+ Sample & getSTORETSampleData & STORET Water Quality Data Portal data \\
+ Sample & getSampleDataFromFile & User generated sample data \\
+ Unit (raw) & retrieveUnitNWISData & Raw USGS instantaneous data \\
+ Information & getMetaData & USGS station and parameter code information \\
+ Information & getParameterInfo & USGS parameter code information \\
+ Information & getSiteFileData & USGS station information \\
+ Information & getDataAvailability & Data available at USGS stations \\
+ \hline
+\end{tabular}
+\end{center}
+\end{minipage}
+\end{table}
+
+\begin{table}[!ht]
+\begin{minipage}{\linewidth}
+\begin{center}
+\caption{dataRetrieval functions 2}
+\begin{tabular}{l p{4cm} p{4cm}}
+ \hline
+Data Type & EGRET Functions & Other Retrieval Functions \\
+ \hline
+ Daily Data & getDVData \par getDailyDataFromFile & retrieveNWISData \\
+ Water Quality Sample Data & getSampleData \par getSTORETSampleData \par getSampleDataFromFile \par & retrieveNWISqwData \par getRawQWData \par getQWDataFromFile \par getQWData \par getWQPData\\
+ Unit Data& & retrieveUnitNWISData \\
+ Meta Data & getMetaData & getParameterInfo \par getSiteFileData \par getDataAvailability \\
+ \hline
+\end{tabular}
+\end{center}
+\end{minipage}
+\end{table}
+
+
\appendix
%------------------------------------------------------------
@@ -1239,8 +1285,8 @@ After installing the package, you need to open the library each time you re-star
\label{sec:appendix2INFO}
%------------------------------------------------------------
-% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Fri Sep 13 16:57:57 2013
+% latex table generated in R 3.0.2 by xtable 1.7-1 package
+% Mon Oct 28 16:27:25 2013
\begin{table}[ht]
\centering
\begin{tabular}{rl}
@@ -1305,8 +1351,8 @@ After installing the package, you need to open the library each time you re-star
There are 62 columns returned from the water quality portal.
-% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Fri Sep 13 16:57:57 2013
+% latex table generated in R 3.0.2 by xtable 1.7-1 package
+% Mon Oct 28 16:27:25 2013
\begin{table}[ht]
\centering
\begin{tabular}{rl}
@@ -1362,8 +1408,8 @@ There are 62 columns returned from the water quality portal.
\FloatBarrier
-% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Fri Sep 13 16:57:57 2013
+% latex table generated in R 3.0.2 by xtable 1.7-1 package
+% Mon Oct 28 16:27:25 2013
\begin{table}[ht]
\centering
\begin{tabular}{rl}
@@ -1413,6 +1459,7 @@ There are a few steps that are required in order to create a table in a Microsof
\hlstd{availableData} \hlkwb{<-} \hlkwd{getDataAvailability}\hlstd{(siteNumber)}
\hlstd{dailyData} \hlkwb{<-} \hlstd{availableData[}\hlstr{"dv"} \hlopt{==} \hlstd{availableData}\hlopt{$}\hlstd{service,]}
\hlstd{dailyData} \hlkwb{<-} \hlstd{dailyData[}\hlstr{"00003"} \hlopt{==} \hlstd{dailyData}\hlopt{$}\hlstd{statCd,]}
+
\hlstd{tableData} \hlkwb{<-} \hlkwd{with}\hlstd{(dailyData,}
\hlkwd{data.frame}\hlstd{(}
\hlkwc{shortName}\hlstd{=srsname,}
@@ -1432,7 +1479,7 @@ There are a few steps that are required in order to create a table in a Microsof
5 Suspended sediment discharge 1980-10-01
End Count Units
1 2012-05-09 529 deg C
-2 2013-09-12 23997 ft3/s
+2 2013-10-27 24042 ft3/s
3 2012-05-09 527 uS/cm @25C
4 1991-09-30 3651 mg/l
5 1991-09-30 3652 tons/day
diff --git a/vignettes/dataRetrieval.toc b/vignettes/dataRetrieval.toc
index ef8524f7f3c3e26edbfe9f68d70bbfddc825a03f..274fbcf6fdcc0aafb85ad13d8d2de65bdab11c45 100644
--- a/vignettes/dataRetrieval.toc
+++ b/vignettes/dataRetrieval.toc
@@ -5,26 +5,27 @@
\contentsline {subsection}{\numberline {2.2}Site Information}{9}{subsection.2.2}
\contentsline {subsubsection}{\numberline {2.2.1}getSiteFileData}{9}{subsubsection.2.2.1}
\contentsline {subsubsection}{\numberline {2.2.2}getDataAvailability}{9}{subsubsection.2.2.2}
-\contentsline {subsection}{\numberline {2.3}Parameter Information}{11}{subsection.2.3}
-\contentsline {subsection}{\numberline {2.4}Daily Values}{11}{subsection.2.4}
-\contentsline {subsection}{\numberline {2.5}Unit Values}{14}{subsection.2.5}
-\contentsline {subsection}{\numberline {2.6}Water Quality Values}{15}{subsection.2.6}
-\contentsline {subsection}{\numberline {2.7}STORET Water Quality Retrievals}{17}{subsection.2.7}
-\contentsline {subsection}{\numberline {2.8}URL Construction}{17}{subsection.2.8}
-\contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{18}{section.3}
-\contentsline {subsection}{\numberline {3.1}INFO Data}{18}{subsection.3.1}
-\contentsline {subsection}{\numberline {3.2}Daily Data}{18}{subsection.3.2}
-\contentsline {subsection}{\numberline {3.3}Sample Data}{19}{subsection.3.3}
-\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{21}{subsection.3.4}
-\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{22}{subsection.3.5}
-\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{22}{subsubsection.3.5.1}
-\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{23}{subsubsection.3.5.2}
-\contentsline {subsection}{\numberline {3.6}Merge Report}{24}{subsection.3.6}
-\contentsline {subsection}{\numberline {3.7}EGRET Plots}{25}{subsection.3.7}
-\contentsline {section}{\numberline {A}Getting Started in R}{27}{appendix.A}
-\contentsline {subsection}{\numberline {A.1}New to R?}{27}{subsection.A.1}
-\contentsline {subsection}{\numberline {A.2}R User: Installing dataRetrieval}{27}{subsection.A.2}
-\contentsline {section}{\numberline {B}Columns Names}{28}{appendix.B}
-\contentsline {subsection}{\numberline {B.1}INFO dataframe}{28}{subsection.B.1}
-\contentsline {subsection}{\numberline {B.2}Water Quality Portal}{30}{subsection.B.2}
-\contentsline {section}{\numberline {C}Creating tables in Microsoft from R}{33}{appendix.C}
+\contentsline {subsection}{\numberline {2.3}Parameter Information}{12}{subsection.2.3}
+\contentsline {subsection}{\numberline {2.4}Daily Values}{12}{subsection.2.4}
+\contentsline {subsection}{\numberline {2.5}Unit Values}{15}{subsection.2.5}
+\contentsline {subsection}{\numberline {2.6}Water Quality Values}{16}{subsection.2.6}
+\contentsline {subsection}{\numberline {2.7}STORET Water Quality Retrievals}{18}{subsection.2.7}
+\contentsline {subsection}{\numberline {2.8}URL Construction}{18}{subsection.2.8}
+\contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{19}{section.3}
+\contentsline {subsection}{\numberline {3.1}INFO Data}{19}{subsection.3.1}
+\contentsline {subsection}{\numberline {3.2}Daily Data}{19}{subsection.3.2}
+\contentsline {subsection}{\numberline {3.3}Sample Data}{20}{subsection.3.3}
+\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{22}{subsection.3.4}
+\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{23}{subsection.3.5}
+\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{23}{subsubsection.3.5.1}
+\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{24}{subsubsection.3.5.2}
+\contentsline {subsection}{\numberline {3.6}Merge Report}{25}{subsection.3.6}
+\contentsline {subsection}{\numberline {3.7}EGRET Plots}{26}{subsection.3.7}
+\contentsline {section}{\numberline {4}Summary}{28}{section.4}
+\contentsline {section}{\numberline {A}Getting Started in R}{28}{appendix.A}
+\contentsline {subsection}{\numberline {A.1}New to R?}{29}{subsection.A.1}
+\contentsline {subsection}{\numberline {A.2}R User: Installing dataRetrieval}{29}{subsection.A.2}
+\contentsline {section}{\numberline {B}Columns Names}{30}{appendix.B}
+\contentsline {subsection}{\numberline {B.1}INFO dataframe}{30}{subsection.B.1}
+\contentsline {subsection}{\numberline {B.2}Water Quality Portal}{32}{subsection.B.2}
+\contentsline {section}{\numberline {C}Creating tables in Microsoft from R}{35}{appendix.C}
diff --git a/vignettes/figure/egretEx.pdf b/vignettes/figure/egretEx.pdf
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