diff --git a/inst/doc/Rplots.pdf b/inst/doc/Rplots.pdf
index 46b2f1617b19364ed5cff6642d145a08bb58f5ab..06e77e86c0e6d801b89584514681073a0d00fa04 100644
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diff --git a/inst/doc/dataRetrieval-concordance.tex b/inst/doc/dataRetrieval-concordance.tex
index 81fc932fc119d7fde40b573d155b6eb0eaad427e..dec73fe01f2498d39fc4f0a7e4390dac694e528d 100644
--- a/inst/doc/dataRetrieval-concordance.tex
+++ b/inst/doc/dataRetrieval-concordance.tex
@@ -2,10 +2,10 @@
1 84 1 1 8 1 1 1 10 16 0 1 2 5 1 1 10 15 0 1 2 13 1 1 2 1 0 1 2 1 0 1 1 %
3 0 1 2 2 1 1 2 7 0 1 2 7 1 1 3 2 0 1 1 12 0 1 2 5 1 1 4 3 0 1 3 1 0 1 %
3 7 0 1 3 4 0 1 2 2 1 1 8 7 0 1 4 1 0 1 2 21 0 1 2 7 1 1 3 2 0 2 1 7 0 %
-1 2 1 1 1 2 7 0 1 2 9 1 1 3 2 0 2 1 1 2 3 0 1 2 1 1 1 2 10 0 1 2 4 1 1 %
-2 1 0 3 1 1 3 4 0 1 2 4 1 1 6 4 0 1 1 1 4 3 0 3 1 3 0 1 2 3 1 1 -5 1 9 %
-14 1 1 2 1 0 1 1 1 2 1 0 1 3 5 0 2 2 10 0 1 2 3 1 1 5 4 0 1 1 3 0 1 2 3 %
-1 1 -5 1 9 12 1 1 4 2 0 2 1 1 3 1 0 1 3 1 0 1 1 7 0 1 2 1 1 1 6 5 0 1 1 %
+1 2 1 1 1 2 7 0 1 2 9 1 1 4 2 0 2 1 1 2 3 0 1 2 4 1 1 3 1 0 3 1 1 3 5 0 %
+1 3 4 1 1 2 1 0 1 4 3 0 1 1 1 4 3 0 3 1 3 0 1 2 3 1 1 -5 1 9 14 1 1 2 1 %
+0 1 1 1 2 1 0 1 3 5 0 2 2 10 0 1 2 3 1 1 2 1 0 1 4 3 0 1 1 4 0 1 3 3 1 %
+1 -6 1 10 12 1 1 4 2 0 2 1 1 3 1 0 1 3 1 0 1 1 7 0 1 2 1 1 1 6 5 0 1 1 %
3 0 1 2 2 1 1 -4 1 8 11 1 1 3 2 0 1 1 12 0 1 2 8 1 1 3 2 0 5 1 3 0 1 2 %
13 1 1 2 1 0 1 1 3 0 1 2 8 1 1 2 1 0 2 1 1 3 5 0 1 2 2 1 1 11 18 0 1 2 %
9 1 1 3 5 0 1 2 2 1 1 12 24 0 1 2 11 1 1 14 12 0 1 2 9 1 1 2 17 0 1 3 %
diff --git a/inst/doc/dataRetrieval-fig1.pdf b/inst/doc/dataRetrieval-fig1.pdf
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diff --git a/inst/doc/dataRetrieval-fig2.pdf b/inst/doc/dataRetrieval-fig2.pdf
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diff --git a/inst/doc/dataRetrieval-fig3.pdf b/inst/doc/dataRetrieval-fig3.pdf
index 33c0f4820e24139ee94b744e2ca213a92047f9c7..13609b4ad33d666daab44857d10aca9ab600f2d5 100644
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diff --git a/inst/doc/dataRetrieval-figegretEx.pdf b/inst/doc/dataRetrieval-figegretEx.pdf
index a3a2c62753ff3d9d87c6aaefda19fc7d528414e2..eabd34090461d3ee4db8bff18c5ba52555cae604 100644
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diff --git a/inst/doc/dataRetrieval.Rnw b/inst/doc/dataRetrieval.Rnw
index c0db6f453f3b1500b26b33c06361bae42bd4b2d6..fdc171bbd9f8f8cf6e53b565308afc1ec0cc38b6 100644
--- a/inst/doc/dataRetrieval.Rnw
+++ b/inst/doc/dataRetrieval.Rnw
@@ -226,7 +226,8 @@ To obtain historic daily records of USGS data, use the retrieveNWISData function
The dates (start and end) need to be in the format \texttt{"}YYYY-MM-DD\texttt{"} (note: the user does need to include the quotes). Setting the start date to \texttt{"}\texttt{"} will indicate to the program to ask for the earliest date, setting the end date to \texttt{"}\texttt{"} will ask for the latest available date.
-<<label=getNWISDaily, echo=TRUE>>=
+<<label=getNWISDaily, echo=TRUE, eval=FALSE>>=
+
# Continuing with our Choptank River example
parameterCd <- "00060" # Discharge (cfs)
startDate <- "" # Will request earliest date
@@ -235,16 +236,12 @@ endDate <- "" # Will request latest date
discharge <- retrieveNWISData(siteNumber, parameterCd, startDate, endDate)
@
-A dataframe is returned that looks like the following:
-<<dischargeData, echo=FALSE>>=
-head(discharge)
-@
-
The variable datetime is automatically imported as a Date. 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://waterdata.usgs.gov/usa/nwis/help?codes_help}
Another example that doesn't use the defaults would be a request for mean and maximum daily temperature and discharge in early 2012:
<<label=getNWIStemperature, echo=TRUE>>=
+
parameterCd <- c("00010","00060") # Temperature and discharge
statCd <- c("00001","00003") # Mean and maximum
startDate <- "2012-01-01"
@@ -252,6 +249,7 @@ endDate <- "2012-06-30"
temperatureAndFlow <- retrieveNWISData(siteNumber, parameterCd,
startDate, endDate, StatCd=statCd,interactive=FALSE)
+
@
Daily data is pulled from \url{http://waterservices.usgs.gov/rest/DV-Test-Tool.html}.
@@ -259,14 +257,14 @@ Daily data is pulled from \url{http://waterservices.usgs.gov/rest/DV-Test-Tool.h
An example of plotting the above data (Figure \ref{fig:TD}):
<<label=getNWIStemperaturePlot, echo=TRUE>>=
-
+colnames <- names(temperatureAndFlow)
with(temperatureAndFlow, plot(
- datetime, X01_00010_00003,
+ get(colnames[3]), get(colnames[6]),
xlab="Date",ylab="Temperature [C]"
))
par(new=TRUE)
with(temperatureAndFlow, plot(
- datetime, X02_00060_00003,
+ get(colnames[3]), get(colnames[8]),
col="red",type="l",xaxt="n",yaxt="n",xlab="",ylab="",axes=FALSE
))
axis(4,col="red",col.axis="red")
@@ -297,9 +295,9 @@ Any data that are collected at regular time intervals (such as 15-minute or hour
<<label=getNWISUnit, echo=TRUE>>=
parameterCd <- "00060" # Discharge (cfs)
-startDate <- "2013-03-12"
+startDate <- "2012-05-12"
# or use (yesterday): startDate <- as.character(Sys.Date()-1)
-endDate <- "2013-03-13"
+endDate <- "2012-05-13"
# or use (today): endDate <- as.character(Sys.Date())
dischargeToday <- retrieveUnitNWISData(siteNumber, parameterCd,
startDate, endDate)
@@ -313,11 +311,13 @@ Note that time now becomes important, so the variable datetime is a POSIXct, and
A simple plotting example is shown in Figure \ref{fig:RT}:
<<label=getNWISUnit, echo=TRUE>>=
+colnames <- names(dischargeToday)
with(dischargeToday, plot(
- datetime, X02_00060,
+ get(colnames[3]), get(colnames[4]),
ylab="Discharge [cfs]",xlab=""
))
title(ChoptankInfo$station.nm)
+
@
\newpage
@@ -327,7 +327,7 @@ title(ChoptankInfo$station.nm)
<<getNWISUnit>>
@
\end{center}
-\caption{Real-time discharge plot of Choptank River from March 12-13, 2013.}
+\caption{Real-time discharge plot of Choptank River from May 12-13, 2012.}
\label{fig:RT}
\end{figure}
diff --git a/inst/doc/dataRetrieval.log b/inst/doc/dataRetrieval.log
index a4b2780545799820219fa7e5976ab9b5be06cdbe..b7d83422ac3be2c326cf83ca27312ad3448b0d5e 100644
--- a/inst/doc/dataRetrieval.log
+++ b/inst/doc/dataRetrieval.log
@@ -1,4 +1,4 @@
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+This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9) (preloaded format=pdflatex 2012.1.6) 28 MAR 2013 14:05
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diff --git a/inst/doc/dataRetrieval.pdf b/inst/doc/dataRetrieval.pdf
index 5d41513c50afcea16bcf4de8d83e7184a8928316..2e7205efc29d66ab8b775b770400b32c4066f6f6 100644
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diff --git a/inst/doc/dataRetrieval.synctex.gz b/inst/doc/dataRetrieval.synctex.gz
index ab345af9a38503e21930525b5b235c96add42dfe..7caadbef7b28a24e6ee263d38c3a4920feaaf1f4 100644
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diff --git a/inst/doc/dataRetrieval.tex b/inst/doc/dataRetrieval.tex
index e5d8210b5ab16b3b4bfc3ad5ebf9aedafc71c0e4..c47b3e55dddaf4cf31a6b8cfb8b88429e063e692 100644
--- a/inst/doc/dataRetrieval.tex
+++ b/inst/doc/dataRetrieval.tex
@@ -86,7 +86,7 @@ Not every station will measure all parameters. A short list of commonly measured
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 14 17:51:22 2013
+% Thu Mar 28 14:04:21 2013
\begin{table}[!ht]
\centering
\caption{Common USGS Parameter Codes}
@@ -109,7 +109,7 @@ For real-time data, the parameter code and site ID will suffice. For most varia
Some common stat codes are shown in Table \ref{tab:stat}.
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 14 17:51:22 2013
+% Thu Mar 28 14:04:21 2013
\begin{table}[!ht]
\centering
\caption{Commonly found USGS Stat Codes}
@@ -176,7 +176,7 @@ To find out the available data at a particular USGS site, including measured par
2 00010 00001 1988-10-01 2012-06-24 940 dv
3 00010 00002 2010-10-01 2012-06-24 575 dv
4 00010 00003 2010-10-01 2012-06-24 575 dv
-5 00060 00003 1948-01-01 2013-03-13 23814 dv
+5 00060 00003 1948-01-01 2013-03-27 23828 dv
6 00095 00001 2010-10-01 2012-06-24 551 dv
7 00095 00002 2010-10-01 2012-06-24 551 dv
\end{Soutput}
@@ -224,7 +224,7 @@ The daily data at the Choptank River site can be displayed in a \LaTeX table usi
caption.placement="top",include.rownames=FALSE)
\end{Sinput}
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 14 17:51:27 2013
+% Thu Mar 28 14:04:26 2013
\begin{table}[ht]
\centering
\caption{Daily mean data availabile at the Choptank River}
@@ -234,7 +234,7 @@ The daily data at the Choptank River site can be displayed in a \LaTeX table usi
shortName & Start & End & Count & Units \\
\hline
Temperature, water & 2010-10-01 & 2012-06-24 & 575 & deg C \\
- Stream flow, mean. daily & 1948-01-01 & 2013-03-13 & 23814 & cfs \\
+ Stream flow, mean. daily & 1948-01-01 & 2013-03-27 & 23828 & cfs \\
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 \\
@@ -291,19 +291,6 @@ The dates (start and end) need to be in the format \texttt{"}YYYY-MM-DD\texttt{"
\end{Sinput}
\end{Schunk}
-A dataframe is returned that looks like the following:
-\begin{Schunk}
-\begin{Soutput}
- agency_cd site_no datetime X02_00060_00003 X02_00060_00003_cd
-1 USGS 01491000 1948-01-01 190 A
-2 USGS 01491000 1948-01-02 900 A
-3 USGS 01491000 1948-01-03 480 A
-4 USGS 01491000 1948-01-04 210 A
-5 USGS 01491000 1948-01-05 210 A
-6 USGS 01491000 1948-01-06 220 A
-\end{Soutput}
-\end{Schunk}
-
The variable datetime is automatically imported as a Date. 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://waterdata.usgs.gov/usa/nwis/help?codes_help}
@@ -316,6 +303,7 @@ Another example that doesn't use the defaults would be a request for mean and ma
> endDate <- "2012-06-30"
> temperatureAndFlow <- retrieveNWISData(siteNumber, parameterCd,
startDate, endDate, StatCd=statCd,interactive=FALSE)
+>
\end{Sinput}
\end{Schunk}
@@ -325,13 +313,14 @@ An example of plotting the above data (Figure \ref{fig:TD}):
\begin{Schunk}
\begin{Sinput}
+> colnames <- names(temperatureAndFlow)
> with(temperatureAndFlow, plot(
- datetime, X01_00010_00003,
+ get(colnames[3]), get(colnames[6]),
xlab="Date",ylab="Temperature [C]"
))
> par(new=TRUE)
> with(temperatureAndFlow, plot(
- datetime, X02_00060_00003,
+ get(colnames[3]), get(colnames[8]),
col="red",type="l",xaxt="n",yaxt="n",xlab="",ylab="",axes=FALSE
))
> axis(4,col="red",col.axis="red")
@@ -362,9 +351,9 @@ Any data that are collected at regular time intervals (such as 15-minute or hour
\begin{Schunk}
\begin{Sinput}
> parameterCd <- "00060" # Discharge (cfs)
-> startDate <- "2013-03-12"
+> startDate <- "2012-05-12"
> # or use (yesterday): startDate <- as.character(Sys.Date()-1)
-> endDate <- "2013-03-13"
+> endDate <- "2012-05-13"
> # or use (today): endDate <- as.character(Sys.Date())
> dischargeToday <- retrieveUnitNWISData(siteNumber, parameterCd,
startDate, endDate)
@@ -373,13 +362,13 @@ Any data that are collected at regular time intervals (such as 15-minute or hour
Which produces the following dataframe:
\begin{Schunk}
\begin{Soutput}
- agency_cd site_no datetime tz_cd X02_00060 X02_00060_cd
-1 USGS 01491000 2013-03-12 00:00:00 EST 190 P
-2 USGS 01491000 2013-03-12 00:15:00 EST 187 P
-3 USGS 01491000 2013-03-12 00:30:00 EST 187 P
-4 USGS 01491000 2013-03-12 00:45:00 EST 187 P
-5 USGS 01491000 2013-03-12 01:00:00 EST 192 P
-6 USGS 01491000 2013-03-12 01:15:00 EST 184 P
+ agency site dateTime X02_00060_00011 X02_00060_00011_cd
+1 USGS 01491000 2012-05-12 00:00:00 83 A
+2 USGS 01491000 2012-05-12 00:15:00 83 A
+3 USGS 01491000 2012-05-12 00:30:00 83 A
+4 USGS 01491000 2012-05-12 00:45:00 83 A
+5 USGS 01491000 2012-05-12 01:00:00 85 A
+6 USGS 01491000 2012-05-12 01:15:00 83 A
\end{Soutput}
\end{Schunk}
@@ -388,11 +377,13 @@ Note that time now becomes important, so the variable datetime is a POSIXct, and
A simple plotting example is shown in Figure \ref{fig:RT}:
\begin{Schunk}
\begin{Sinput}
+> colnames <- names(dischargeToday)
> with(dischargeToday, plot(
- datetime, X02_00060,
+ get(colnames[3]), get(colnames[4]),
ylab="Discharge [cfs]",xlab=""
))
> title(ChoptankInfo$station.nm)
+>
\end{Sinput}
\end{Schunk}
\newpage
@@ -401,7 +392,7 @@ A simple plotting example is shown in Figure \ref{fig:RT}:
\begin{center}
\includegraphics{dataRetrieval-fig2}
\end{center}
-\caption{Real-time discharge plot of Choptank River from March 12-13, 2013.}
+\caption{Real-time discharge plot of Choptank River from May 12-13, 2012.}
\label{fig:RT}
\end{figure}
@@ -426,8 +417,8 @@ To get USGS water quality data from water samples collected at the streamgage (a
> names(dissolvedNitrateSimple)
\end{Sinput}
\begin{Soutput}
-[1] "dateTime" "qualifier.71851" "value.71851" "qualifier.00618"
-[5] "value.00618"
+[1] "dateTime" "qualifier.00618" "value.00618" "qualifier.71851"
+[5] "value.71851"
\end{Soutput}
\end{Schunk}
Note that in this dataframe, datetime is imported as Dates (no times are included), and the qualifier is either blank or \texttt{"}\verb@<@\texttt{"} signifying a censored value. A plotting example is shown in Figure \ref{fig:nitrate}.
@@ -537,7 +528,7 @@ The function to obtain the daily values (discharge in this case) is getDVData.
Details of the Daily dataframe are listed below:
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 14 17:51:38 2013
+% Thu Mar 28 14:04:42 2013
\begin{tabular}{llll}
\hline
ColumnName & Type & Description & Units \\
@@ -575,7 +566,7 @@ The function to obtain sample data from the water quality portal is getSampleDat
Details of the Sample dataframe are listed below:
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 14 17:51:40 2013
+% Thu Mar 28 14:04:43 2013
\begin{table}[!ht]
\centering
\caption{Sample dataframe}
@@ -612,7 +603,7 @@ As an example to understand how the dataRetrieval package handles a more complex
\begin{center}
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 14 17:51:40 2013
+% Thu Mar 28 14:04:43 2013
\begin{tabular}{llrlrlr}
\hline
cdate & rdp & dp & rpp & pp & rtp & tp \\
@@ -750,13 +741,13 @@ Finally, there is a function called mergeReport that will look at both the Daily
4 1979-12-05 1.40 1.40 1 1.40 47454 12 339 1979.925 1560
5 1979-12-21 1.20 1.20 1 1.20 47470 12 355 1979.969 1560
6 1980-01-24 0.84 0.84 1 0.84 47504 1 24 1980.064 1561
- SinDY CosDY Q LogQ
-1 0.4699767 -0.8826788 3.256437 1.180634
-2 -0.9927882 -0.1198812 3.398022 1.223193
-3 -0.9295235 0.3687629 3.199804 1.163089
-4 -0.4547551 0.8906165 2.973269 1.089662
-5 -0.1961425 0.9805754 2.944952 1.080093
-6 0.3925740 0.9197204 10.901986 2.388945
+ SinDY CosDY Q LogQ
+1 0.4699767 -0.8826788 3.341388 1.206386
+2 -0.9927882 -0.1198812 4.275844 1.452981
+3 -0.9295235 0.3687629 2.944952 1.080093
+4 -0.4547551 0.8906165 3.086536 1.127050
+5 -0.1961425 0.9805754 3.058219 1.117833
+6 0.3925740 0.9197204 9.089708 2.207143
\end{Soutput}
\end{Schunk}
@@ -875,7 +866,7 @@ To then open the library, simply type:
%------------------------------------------------------------
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 14 17:51:44 2013
+% Thu Mar 28 14:04:54 2013
\begin{tabular}{l}
\hline
\hline
@@ -933,7 +924,7 @@ agency.cd \\
There are 62 columns returned from the water quality portal.
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 14 17:51:44 2013
+% Thu Mar 28 14:04:54 2013
\begin{tabular}{l}
\hline
\hline
@@ -982,7 +973,7 @@ OrganizationIdentifier \\
\FloatBarrier
% latex table generated in R 2.15.3 by xtable 1.7-1 package
-% Thu Mar 14 17:51:44 2013
+% Thu Mar 28 14:04:54 2013
\begin{tabular}{l}
\hline
\hline
diff --git a/inst/doc/dataRetrieval.toc b/inst/doc/dataRetrieval.toc
index 4892dc38088891f3a7330a81f4516c16aeb11499..f05553d7aa44793f0a9945381c7f4fe909a895f7 100644
--- a/inst/doc/dataRetrieval.toc
+++ b/inst/doc/dataRetrieval.toc
@@ -7,25 +7,25 @@
\contentsline {subsubsection}{\numberline {2.2.2}getDataAvailability}{5}{subsubsection.2.2.2}
\contentsline {subsection}{\numberline {2.3}Parameter Information}{6}{subsection.2.3}
\contentsline {subsection}{\numberline {2.4}Daily Values}{7}{subsection.2.4}
-\contentsline {subsection}{\numberline {2.5}Unit Values}{9}{subsection.2.5}
-\contentsline {subsection}{\numberline {2.6}Water Quality Values}{11}{subsection.2.6}
-\contentsline {subsection}{\numberline {2.7}STORET Water Quality Retrievals}{12}{subsection.2.7}
-\contentsline {subsection}{\numberline {2.8}URL Construction}{13}{subsection.2.8}
-\contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{13}{section.3}
-\contentsline {subsection}{\numberline {3.1}INFO Data}{14}{subsection.3.1}
-\contentsline {subsection}{\numberline {3.2}Daily Data}{14}{subsection.3.2}
-\contentsline {subsection}{\numberline {3.3}Sample Data}{15}{subsection.3.3}
-\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{16}{subsection.3.4}
-\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{17}{subsection.3.5}
-\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{17}{subsubsection.3.5.1}
-\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{18}{subsubsection.3.5.2}
-\contentsline {subsection}{\numberline {3.6}Merge Report}{19}{subsection.3.6}
-\contentsline {subsection}{\numberline {3.7}EGRET Plots}{20}{subsection.3.7}
-\contentsline {section}{\numberline {A}Getting Started in R}{22}{appendix.A}
-\contentsline {subsection}{\numberline {A.1}New to R?}{22}{subsection.A.1}
-\contentsline {subsection}{\numberline {A.2}R User: Installing dataRetrieval}{22}{subsection.A.2}
-\contentsline {subsection}{\numberline {A.3}R Developers: Installing dataRetrieval from gitHub}{23}{subsection.A.3}
-\contentsline {section}{\numberline {B}Columns Names}{25}{appendix.B}
-\contentsline {subsection}{\numberline {B.1}INFO dataframe}{25}{subsection.B.1}
-\contentsline {subsection}{\numberline {B.2}Water Quality Portal}{26}{subsection.B.2}
-\contentsline {section}{\numberline {C}Creating tables in Microsoft from R}{28}{appendix.C}
+\contentsline {subsection}{\numberline {2.5}Unit Values}{8}{subsection.2.5}
+\contentsline {subsection}{\numberline {2.6}Water Quality Values}{10}{subsection.2.6}
+\contentsline {subsection}{\numberline {2.7}STORET Water Quality Retrievals}{11}{subsection.2.7}
+\contentsline {subsection}{\numberline {2.8}URL Construction}{12}{subsection.2.8}
+\contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{12}{section.3}
+\contentsline {subsection}{\numberline {3.1}INFO Data}{13}{subsection.3.1}
+\contentsline {subsection}{\numberline {3.2}Daily Data}{13}{subsection.3.2}
+\contentsline {subsection}{\numberline {3.3}Sample Data}{14}{subsection.3.3}
+\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{15}{subsection.3.4}
+\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{16}{subsection.3.5}
+\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{16}{subsubsection.3.5.1}
+\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{17}{subsubsection.3.5.2}
+\contentsline {subsection}{\numberline {3.6}Merge Report}{18}{subsection.3.6}
+\contentsline {subsection}{\numberline {3.7}EGRET Plots}{19}{subsection.3.7}
+\contentsline {section}{\numberline {A}Getting Started in R}{21}{appendix.A}
+\contentsline {subsection}{\numberline {A.1}New to R?}{21}{subsection.A.1}
+\contentsline {subsection}{\numberline {A.2}R User: Installing dataRetrieval}{21}{subsection.A.2}
+\contentsline {subsection}{\numberline {A.3}R Developers: Installing dataRetrieval from gitHub}{22}{subsection.A.3}
+\contentsline {section}{\numberline {B}Columns Names}{24}{appendix.B}
+\contentsline {subsection}{\numberline {B.1}INFO dataframe}{24}{subsection.B.1}
+\contentsline {subsection}{\numberline {B.2}Water Quality Portal}{25}{subsection.B.2}
+\contentsline {section}{\numberline {C}Creating tables in Microsoft from R}{27}{appendix.C}
diff --git a/man/checkStartEndDate.Rd b/man/checkStartEndDate.Rd
index aa1aa87150fb5d96f1f4f053fd04972bebad9d9e..892f64cca9c0ad84ad4ad691484ae396ed210d2e 100644
--- a/man/checkStartEndDate.Rd
+++ b/man/checkStartEndDate.Rd
@@ -26,6 +26,6 @@ startDate <- '1985-01-01'
endDate <- '1990-01-01'
checkStartEndDate(startDate, endDate, interactive = FALSE)
}
-\keyword{flow}
\keyword{WRTDS}
+\keyword{flow}
diff --git a/man/compressData.Rd b/man/compressData.Rd
index 17d40a4d71f6d04dd298450d5fc90f0746fd515e..92d9134d44d9369c41a427c163d614c96601a8d5 100644
--- a/man/compressData.Rd
+++ b/man/compressData.Rd
@@ -36,6 +36,6 @@ value3 <- c(3,4,5)
dataInput <- data.frame(dateTime, comment1, value1, comment2, value2, comment3, value3, stringsAsFactors=FALSE)
compressData(dataInput, interactive=FALSE)
}
-\keyword{flow}
\keyword{WRTDS}
+\keyword{flow}
diff --git a/man/constructNWISURL.Rd b/man/constructNWISURL.Rd
index 7a4a78ff1b56100e2e5b56229dd29487617f6ee0..1cd8ce4840245552bab6a76276140032fffe20b8 100644
--- a/man/constructNWISURL.Rd
+++ b/man/constructNWISURL.Rd
@@ -3,7 +3,8 @@
\title{Construct NWIS url for data retrieval}
\usage{
constructNWISURL(siteNumber, parameterCd, startDate,
- endDate, service, statCd = "00003")
+ endDate, service, statCd = "00003",
+ interactive = FALSE)
}
\arguments{
\item{siteNumber}{string or vector of strings USGS site
@@ -26,6 +27,10 @@
values are "dv" (daily values), "uv" (unit/instantaneous
values), "qw" (water quality data), and "wqp" (water
quality portal, which can include STORET).}
+
+ \item{interactive}{logical Option for interactive mode.
+ If true, there is user interaction for error handling and
+ data checks.}
}
\value{
url string
@@ -50,9 +55,9 @@ url_qw_single <- constructNWISURL(siteNumber,"34220",startDate,endDate,'qwdata')
url_qw <- constructNWISURL(siteNumber,c('34247','30234','32104','34220'),startDate,endDate,'qwdata')
url_wqp <- constructNWISURL(siteNumber,"34220",startDate,endDate,'wqp')
}
+\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
-\keyword{USGS}
\keyword{web}
diff --git a/man/dataOverview.Rd b/man/dataOverview.Rd
index c99da9b50f9d0142972deef2188cd549ca498cfd..6fe56a3ac2930bf546840bcbdb75fea354dadd3f 100644
--- a/man/dataOverview.Rd
+++ b/man/dataOverview.Rd
@@ -21,8 +21,8 @@ dataOverview(localDaily = exDaily, localSample = exSample)
\seealso{
\code{\link{mergeReport}}
}
-\keyword{data}
-\keyword{import}
\keyword{USGS}
\keyword{WRTDS}
+\keyword{data}
+\keyword{import}
diff --git a/man/dateFormatCheck.Rd b/man/dateFormatCheck.Rd
index 99532817221093d2a64e3ce0e6ac8e3e3aabd07b..dd75fee619a69001adad54bba538e9d5980ee496 100644
--- a/man/dateFormatCheck.Rd
+++ b/man/dateFormatCheck.Rd
@@ -18,6 +18,6 @@
date <- '1985-01-01'
dateFormatCheck(date)
}
-\keyword{flow}
\keyword{WRTDS}
+\keyword{flow}
diff --git a/man/formatCheckDate.Rd b/man/formatCheckDate.Rd
index 0bf8637101b5ac2a8f016bcc8faccdc3edac4dfe..64c54b65061785ecf5741d3f1c4eac8c9ac3af0d 100644
--- a/man/formatCheckDate.Rd
+++ b/man/formatCheckDate.Rd
@@ -27,6 +27,6 @@ Date <- '1985-01-01'
dateString <- 'StartDate'
formatCheckDate(Date, dateString, interactive = FALSE)
}
-\keyword{flow}
\keyword{WRTDS}
+\keyword{flow}
diff --git a/man/formatCheckParameterCd.Rd b/man/formatCheckParameterCd.Rd
index 086bea0aa058edc05bb1775bf7025433c33b96ee..d1574546ed4940e46494b4c4bbd46bacce0da90e 100644
--- a/man/formatCheckParameterCd.Rd
+++ b/man/formatCheckParameterCd.Rd
@@ -23,6 +23,6 @@
pCode <- '01234'
formatCheckParameterCd(pCode, interactive = FALSE)
}
-\keyword{flow}
\keyword{WRTDS}
+\keyword{flow}
diff --git a/man/formatCheckSiteNumber.Rd b/man/formatCheckSiteNumber.Rd
index 60a912a66d584e466306e309483b57e7a1f38d54..5d8b42cd9e9cb3a8d96bdf4d70ac01ec0fbe8a03 100644
--- a/man/formatCheckSiteNumber.Rd
+++ b/man/formatCheckSiteNumber.Rd
@@ -22,6 +22,6 @@
site<- '01234567'
formatCheckSiteNumber(site, interactive = FALSE)
}
-\keyword{flow}
\keyword{WRTDS}
+\keyword{flow}
diff --git a/man/getDVData.Rd b/man/getDVData.Rd
index 00c4faca602080dadd5471d104db558a7dfccfa8..7dc0a25d34cf307103f25a063e3a4f770f2910c2 100644
--- a/man/getDVData.Rd
+++ b/man/getDVData.Rd
@@ -46,8 +46,8 @@ Daily <- getDVData('01594440','00060', '1985-01-01', '1985-03-31', interactive=F
\code{\link{retrieveNWISData}},
\code{\link{populateDaily}}
}
-\keyword{data}
-\keyword{import}
\keyword{USGS}
\keyword{WRTDS}
+\keyword{data}
+\keyword{import}
diff --git a/man/getDailyDataFromFile.Rd b/man/getDailyDataFromFile.Rd
index 95f1ece41ac37dce3485e090992a4e76fbc70cc5..2c8ded37b9a18f130b42c18ecc9f4d3787a3c696 100644
--- a/man/getDailyDataFromFile.Rd
+++ b/man/getDailyDataFromFile.Rd
@@ -40,9 +40,9 @@ filePath <- '~/RData/' # Sample format
fileName <- 'ChoptankRiverFlow.txt'
\dontrun{getDailyDataFromFile(filePath,fileName,separator="\\t")}
}
+\keyword{USGS}
+\keyword{WRTDS}
\keyword{data}
\keyword{file}
\keyword{import}
-\keyword{USGS}
-\keyword{WRTDS}
diff --git a/man/getDataAvailability.Rd b/man/getDataAvailability.Rd
index fd9d46033e9e1e6165f538fcf14a54ab1c79bf69..06dbf8e02217726e0d4a9cc9e24f837a4ac1eb38 100644
--- a/man/getDataAvailability.Rd
+++ b/man/getDataAvailability.Rd
@@ -31,9 +31,9 @@
# These examples require an internet connection to run
availableData <- getDataAvailability('05114000',interactive=FALSE)
}
+\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
-\keyword{USGS}
\keyword{web}
diff --git a/man/getMetaData.Rd b/man/getMetaData.Rd
index 77a11bcff1f726b0ecde6225df4d5f1b3b21a8fe..fb57f7d818c177f9756645238dada84569867e04 100644
--- a/man/getMetaData.Rd
+++ b/man/getMetaData.Rd
@@ -39,10 +39,10 @@
# Automatically gets information about site 05114000 and temperature, no interaction with user
INFO <- getMetaData('05114000','00010',interactive=FALSE)
}
+\keyword{USGS}
+\keyword{WRTDS}
\keyword{data}
\keyword{import}
\keyword{service}
-\keyword{USGS}
\keyword{web}
-\keyword{WRTDS}
diff --git a/man/getMultipleParameterNames.Rd b/man/getMultipleParameterNames.Rd
index 3177e1b6c5b0b27172ec344fff2391cee52d5489..dc266131310a138046da77d2b30e5bf2c1c45482 100644
--- a/man/getMultipleParameterNames.Rd
+++ b/man/getMultipleParameterNames.Rd
@@ -28,9 +28,9 @@
# These examples require an internet connection to run
availableData <- getMultipleParameterNames(c("00060", "00065", "00010"),interactive=FALSE)
}
+\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
-\keyword{USGS}
\keyword{web}
diff --git a/man/getParameterInfo.Rd b/man/getParameterInfo.Rd
index 6344c8980314b462fbeb13a1be1a227e0e06a434..fb9df67602ba06d11c33ae51c97619337e355980 100644
--- a/man/getParameterInfo.Rd
+++ b/man/getParameterInfo.Rd
@@ -28,9 +28,9 @@
paramINFO <- getParameterInfo('01075')
paramINFO2 <- getParameterInfo('00931',interactive=FALSE)
}
+\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
-\keyword{USGS}
\keyword{web}
diff --git a/man/getPreLoadedDailyData.Rd b/man/getPreLoadedDailyData.Rd
index a39fbbe6d2b72f71d83137208ac0c65157e98722..8be9941cee8a1e22b9c42a2f1e1783955a01990b 100644
--- a/man/getPreLoadedDailyData.Rd
+++ b/man/getPreLoadedDailyData.Rd
@@ -28,7 +28,7 @@
\examples{
Daily <- getPreLoadedDailyData(ChoptankRiverFlow, interactive=FALSE)
}
+\keyword{WRTDS}
\keyword{data}
\keyword{import}
-\keyword{WRTDS}
diff --git a/man/getPreLoadedSampleData.Rd b/man/getPreLoadedSampleData.Rd
index 50708517441fb2c28f93936156fd4fd6c024f9c7..1e8834a400df76773c56f0d66f2f281f4bffabf2 100644
--- a/man/getPreLoadedSampleData.Rd
+++ b/man/getPreLoadedSampleData.Rd
@@ -23,7 +23,7 @@
\examples{
Sample <- getPreLoadedSampleData(ChoptankRiverNitrate, interactive=FALSE)
}
+\keyword{WRTDS}
\keyword{data}
\keyword{import}
-\keyword{WRTDS}
diff --git a/man/getQWData.Rd b/man/getQWData.Rd
index f38d6a2322478fb8c29957201f772fe36d05034b..8348de8d5e2cd018928e1498e8d0ce37842488d7 100644
--- a/man/getQWData.Rd
+++ b/man/getQWData.Rd
@@ -46,9 +46,9 @@ rawProcessedSample <- getQWData('01594440','01075', '1985-01-01', '1985-03-31')
rawProcessedSampleAll <- getQWData('05114000','', '1985-01-01', '1985-03-31')
rawProcessedSampleSelect <- getQWData('05114000','00915;00931', '1985-01-01', '1985-04-30', interactive=FALSE)
}
+\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
-\keyword{USGS}
\keyword{web}
diff --git a/man/getRawQWData.Rd b/man/getRawQWData.Rd
index a77fc37ffda4adb1e1bc2c75b3a3a5b26ab57a98..738023e62faec1f5e19e3f7973eb04b875e5d7d0 100644
--- a/man/getRawQWData.Rd
+++ b/man/getRawQWData.Rd
@@ -45,9 +45,9 @@ rawSample <- getRawQWData('01594440','01075', '1985-01-01', '1985-03-31')
rawSampleAll <- getRawQWData('05114000','', '1985-01-01', '1985-03-31')
rawSampleSelect <- getRawQWData('05114000',c('00915','00931'), '1985-01-01', '1985-04-30', interactive=FALSE)
}
+\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
-\keyword{USGS}
\keyword{web}
diff --git a/man/getSampleData.Rd b/man/getSampleData.Rd
index 782b13c6c3bf602196a178982319a1be56c4f766..f8fc6db8dd5b2a7f164977fe2e1c287b8eefcb84 100644
--- a/man/getSampleData.Rd
+++ b/man/getSampleData.Rd
@@ -46,8 +46,8 @@ Sample_Select <- getSampleData('05114000','00915;00931', '', '', interactive=FAL
\code{\link{compressData}},
\code{\link{populateSampleColumns}}
}
-\keyword{data}
-\keyword{import}
\keyword{USGS}
\keyword{WRTDS}
+\keyword{data}
+\keyword{import}
diff --git a/man/getSampleDataFromFile.Rd b/man/getSampleDataFromFile.Rd
index 34a0e31df6f8ab4745627cbc5afc3f4ea08c175f..f295b54c36bbffe76ecd4934edde2f67b6531f51 100644
--- a/man/getSampleDataFromFile.Rd
+++ b/man/getSampleDataFromFile.Rd
@@ -35,9 +35,9 @@ filePath <- '~/RData/' # Sample format
fileName <- 'ChoptankRiverNitrate.csv'
#Sample <- getSampleDataFromFile(filePath,fileName, separator=";",interactive=FALSE)
}
+\keyword{USGS}
+\keyword{WRTDS}
\keyword{data}
\keyword{file}
\keyword{import}
-\keyword{USGS}
-\keyword{WRTDS}
diff --git a/man/getSiteFileData.Rd b/man/getSiteFileData.Rd
index 53291b62e542ee7599124ff7866c16c95ed96e9a..37a7d14a54aa31799bcb74be2ebf6e8137323eac 100644
--- a/man/getSiteFileData.Rd
+++ b/man/getSiteFileData.Rd
@@ -24,9 +24,9 @@
# These examples require an internet connection to run
siteINFO <- getSiteFileData('05114000',interactive=FALSE)
}
+\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
-\keyword{USGS}
\keyword{web}
diff --git a/man/getWQPData.Rd b/man/getWQPData.Rd
index 3f5c8e143044f445ad8c2d9c19f888cfaba54b7e..a3b275d477aa664bc684d798eb3b33d64ddcf9f5 100644
--- a/man/getWQPData.Rd
+++ b/man/getWQPData.Rd
@@ -43,9 +43,9 @@
getWQPData('USGS-01594440','Chloride', '', '')
getWQPData('WIDNR_WQX-10032762','Specific conductance', '', '')
}
+\keyword{WQP}
\keyword{data}
\keyword{import}
\keyword{service}
\keyword{web}
-\keyword{WQP}
diff --git a/man/getWaterML1Data.Rd b/man/getWaterML1Data.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..c8cc08e7b825ada8063f05c23dac753d8e697e95
--- /dev/null
+++ b/man/getWaterML1Data.Rd
@@ -0,0 +1,33 @@
+\name{getWaterML1Data}
+\alias{getWaterML1Data}
+\title{Function to return data from the NWISWeb WaterML1.1 daily values service}
+\usage{
+ getWaterML1Data(obs_url)
+}
+\arguments{
+ \item{obs_url}{string containing the url for the
+ retrieval}
+}
+\value{
+ Daily a data frame containing columns 'Date' and
+ 'Discharge'
+}
+\description{
+ This function accepts a url parameter that already
+ contains the desired NWIS site, parameter code,
+ statistic, startdate and enddate. It returns a data frame
+ containing "Date" and "Discharge"
+}
+\examples{
+url <- "http://waterservices.usgs.gov/nwis/dv/?format=waterml,1.1&sites="
+sites <- "02177000"
+startDate <- "2012-09-01"
+endDate <- "2012-10-01"
+offering <- '00003'
+property <- '00060'
+obs_url <- constructNWISURL(sites,property,startDate,endDate,'dv')
+data <- getWaterML1Data(obs_url)
+urlMulti <- constructNWISURL("04085427",c("00060","00010"),startDate,endDate,'dv',statCd=c("00003","00001"))
+multiData <- getWaterML1Data(urlMulti)
+}
+
diff --git a/man/mergeReport.Rd b/man/mergeReport.Rd
index 800f34ba5ab6684f1af1975045caad09cf96f825..5efff9d3878cddc49ca7a82527a2ece4d08a4f52 100644
--- a/man/mergeReport.Rd
+++ b/man/mergeReport.Rd
@@ -33,8 +33,8 @@ Sample <- mergeReport(interactive=FALSE)
\code{\link{getDVData}},
\code{\link{populateSampleColumns}}
}
-\keyword{data}
-\keyword{import}
\keyword{USGS}
\keyword{WRTDS}
+\keyword{data}
+\keyword{import}
diff --git a/man/padVariable.Rd b/man/padVariable.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..cf3aee545f2616faa1b17dcc20135c43ea3b97f8
--- /dev/null
+++ b/man/padVariable.Rd
@@ -0,0 +1,28 @@
+\name{padVariable}
+\alias{padVariable}
+\title{Pad string with leading zeros}
+\usage{
+ padVariable(x, padTo)
+}
+\arguments{
+ \item{x}{string}
+
+ \item{padTo}{number Final desired length of the string}
+}
+\value{
+ x string returned with leading zeros
+}
+\description{
+ Function to pad a string with leading zeros. Useful for
+ parameter codes and USGS site IDs.
+}
+\examples{
+pCode <- '10'
+correctPCode <- padVariable(pCode,5)
+}
+\keyword{USGS}
+\keyword{data}
+\keyword{import}
+\keyword{service}
+\keyword{web}
+
diff --git a/man/populateDaily.Rd b/man/populateDaily.Rd
index e59aafb215c75061b4ac028d2c5a414956f109af..5722f563c0cd546c3c1cb92f01026ffb4690c6a3 100644
--- a/man/populateDaily.Rd
+++ b/man/populateDaily.Rd
@@ -33,6 +33,6 @@ Daily <- populateDaily(dataInput, 2, interactive=FALSE)
\author{
Robert M. Hirsch \email{rhirsch@usgs.gov}
}
-\keyword{flow}
\keyword{WRTDS}
+\keyword{flow}
diff --git a/man/processQWData.Rd b/man/processQWData.Rd
index d5cc07572769a86d41ddf0ae9eb1f8082b06b5f6..660c8bb571bcef093ad463a30d4d779727da1c13 100644
--- a/man/processQWData.Rd
+++ b/man/processQWData.Rd
@@ -25,9 +25,9 @@
rawSample <- getRawQWData('01594440','01075', '1985-01-01', '1985-03-31')
rawSampleSelect <- processQWData(rawSample)
}
+\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
-\keyword{USGS}
\keyword{web}
diff --git a/man/retrieveNWISData.Rd b/man/retrieveNWISData.Rd
index f973bd8b29a7e78e912f8c8a7ef32008d0eb5654..7260b72e5252aafdab9eac5fd5ce3a0541710d5d 100644
--- a/man/retrieveNWISData.Rd
+++ b/man/retrieveNWISData.Rd
@@ -47,9 +47,9 @@ rawDailyQ <- retrieveNWISData(siteNumber,pCode, startDate, endDate)
rawDailyTemperature <- retrieveNWISData(siteNumber,'00010', startDate, endDate, StatCd='00001',interactive=FALSE)
rawDailyQAndTempMeanMax <- retrieveNWISData(siteNumber,c('00010','00060'), startDate, endDate, StatCd=c('00001','00003'), interactive=FALSE)
}
+\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
-\keyword{USGS}
\keyword{web}
diff --git a/man/retrieveNWISqwData.Rd b/man/retrieveNWISqwData.Rd
index 4e5a169e402d4b4af02344a248be66f16508e587..254045c748b2520c03b207a717b6a2034639f995 100644
--- a/man/retrieveNWISqwData.Rd
+++ b/man/retrieveNWISqwData.Rd
@@ -44,9 +44,9 @@ data$dateTime <- as.Date(data$dateTime)
compressedData <- compressData(data, interactive=interactive)
Sample <- populateSampleColumns(compressedData)
}
+\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
-\keyword{USGS}
\keyword{web}
diff --git a/man/retrieveUnitNWISData.Rd b/man/retrieveUnitNWISData.Rd
index 5228b6abf6422ca473a5b364761c62350c086d65..4622f8dd8136872c8f58ed1f8cd1eafa15ae7f9b 100644
--- a/man/retrieveUnitNWISData.Rd
+++ b/man/retrieveUnitNWISData.Rd
@@ -42,9 +42,9 @@ EndDate <- as.character(Sys.Date())
# These examples require an internet connection to run
rawData <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate,interactive=FALSE)
}
+\keyword{USGS}
\keyword{data}
\keyword{import}
\keyword{service}
-\keyword{USGS}
\keyword{web}