diff --git a/man/getWaterML1Data.Rd b/man/getWaterML1Data.Rd
index 6735e0f697d431d63dbc41ae34bbb4e7b864dd24..b845b95aab3ae93e62c3d5ef0afa7c7044912937 100644
--- a/man/getWaterML1Data.Rd
+++ b/man/getWaterML1Data.Rd
@@ -25,5 +25,7 @@ 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)
+goundwaterExampleURL <- "http://waterservices.usgs.gov/nwis/gwlevels/?format=waterml&sites=431049071324301&startDT=2013-10-01&endDT=2014-06-30"
+groundWater <- getWaterML1Data(goundwaterExampleURL)
}
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index 19e8199efeefbbfcf32e9b38669b8ab97e04c80f..6c049207280a631800833b12426de7a62aaf9832 100644
--- a/vignettes/dataRetrieval-concordance.tex
+++ b/vignettes/dataRetrieval-concordance.tex
@@ -1,9 +1,9 @@
\Sconcordance{concordance:dataRetrieval.tex:dataRetrieval.Rnw:%
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diff --git a/vignettes/dataRetrieval.Rnw b/vignettes/dataRetrieval.Rnw
index 571507536f12d486d77dfc11c214fc24be10bc66..10862cbb57c73b20f9e0047d65c9ca00d06e2367 100644
--- a/vignettes/dataRetrieval.Rnw
+++ b/vignettes/dataRetrieval.Rnw
@@ -52,7 +52,7 @@
{\thesubsubsection}{0.5em}{}
\titlecontents{section}
-[2.3em] % adjust left margin
+[2em] % adjust left margin
{\sffamily} % font formatting
{\contentslabel{2.3em}} % section label and offset
{\hspace*{-2.3em}}
@@ -73,14 +73,14 @@
{\titlerule*[0.25pc]{.}\contentspage}
\titlecontents{table}
-[-2.3em] % adjust left margin
+[0em] % adjust left margin
{\sffamily} % font formatting
{\textbf{Table}\hspace*{2em} \contentslabel {2em}} % section label and offset
{\hspace*{4em}}
{\titlerule*[0.25pc]{.}\contentspage}
\titlecontents{figure}
-[-2.3em] % adjust left margin
+[0em] % adjust left margin
{\sffamily} % font formatting
{\textbf{Figure}\hspace*{2em} \contentslabel {2em}} % section label and offset
{\hspace*{4em}}
@@ -152,15 +152,24 @@ knit_hooks$set(inline = function(x) {
if (is.numeric(x)) round(x, 3)})
knit_hooks$set(crop = hook_pdfcrop)
-bold.colHeaders <- function(x) paste("\\multicolumn{1}{c}{\\textbf{\\textsf{", x, "}}}", sep = "")
+bold.colHeaders <- function(x) {
+ x <- gsub("\\^(\\d)","$\\^\\1$",x)
+ x <- gsub("\\%","\\\\%",x)
+ x <- gsub("\\_"," ",x)
+ returnX <- paste("\\multicolumn{1}{c}{\\textbf{\\textsf{", x, "}}}", sep = "")
+}
addSpace <- function(x) ifelse(x != "1", "[5pt]","")
@
+\noindent{\huge\textsf{\textbf{The dataRetrieval R package}}}
+\noindent\textsf{By Laura De Cicco and Robert Hirsch}
-\maketitle
+\noindent\textsf{\today}
-\newpage
+% \maketitle
+%
+% \newpage
\tableofcontents
\listoffigures
@@ -516,11 +525,13 @@ There are additional water quality data sets available from the Water Quality Da
<<label=getQWData, echo=TRUE>>=
-# specificCond <- getWQPData('WIDNR_WQX-10032762',
-# 'Specific conductance','','')
-# head(specificCond)
+specificCond <- getWQPData('WIDNR_WQX-10032762',
+ 'Specific conductance','','')
+head(specificCond)
@
+There are
+
\FloatBarrier
%------------------------------------------------------------
\subsection{URL Construction}
diff --git a/vignettes/dataRetrieval.lof b/vignettes/dataRetrieval.lof
index 582b0ff3d40294bd7c1e46f08f8794fb108430d3..874492184ba2946bce598a5d461db6b2a2510213 100644
--- a/vignettes/dataRetrieval.lof
+++ b/vignettes/dataRetrieval.lof
@@ -1,6 +1,6 @@
\select@language {american}
-\contentsline {figure}{\numberline {1}{\ignorespaces Temperature and discharge plot of Choptank River in 2012}}{12}{figure.caption.4}
-\contentsline {figure}{\numberline {2}{\ignorespaces Nitrate plot of Choptank River}}{15}{figure.caption.5}
+\contentsline {figure}{\numberline {1}{\ignorespaces Temperature and discharge plot of Choptank River in 2012}}{11}{figure.caption.4}
+\contentsline {figure}{\numberline {2}{\ignorespaces Nitrate plot of Choptank River}}{14}{figure.caption.5}
\contentsline {figure}{\numberline {3}{\ignorespaces Default multiPlotDataOverview}}{27}{figure.caption.10}
\contentsline {figure}{\numberline {4}{\ignorespaces A simple R help file\relax }}{31}{figure.caption.14}
\contentsline {figure}{\numberline {5}{\ignorespaces A simple table produced in Microsoft Excel\relax }}{34}{figure.caption.15}
diff --git a/vignettes/dataRetrieval.log b/vignettes/dataRetrieval.log
index 543b8cc6256af806c9032f4dce7aa35e4f451a5e..c73a0b0efd0f300b660533e4794ea534a534bbb1 100644
--- a/vignettes/dataRetrieval.log
+++ b/vignettes/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) 1 AUG 2014 16:04
entering extended mode
**dataRetrieval.tex
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.tex
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[][]\OT1/pcr/m/n/10.95 url_uv[] []<-[] []\OT1/pcr/b/n/10.95 constructNWISURL[][
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+Overfull \hbox (44.67563pt too wide) in paragraph at lines 1119--1119
[] \OT1/pcr/m/n/10.95 First day of the discharge record is 2000-01-01 and last
day is 2013-01-01[]
[]
-Overfull \hbox (44.67563pt too wide) in paragraph at lines 1097--1097
+Overfull \hbox (44.67563pt too wide) in paragraph at lines 1119--1119
[] \OT1/pcr/m/n/10.95 The first sample is from 2000-01-04 and the last sample i
s from 2012-12-18[]
[]
@@ -899,16 +908,16 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
[25]
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<figure/egretEx.pdf, id=374, 505.89pt x 505.89pt>
File: figure/egretEx.pdf Graphic file (type pdf)
<use figure/egretEx.pdf>
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+
+Overfull \hbox (51.24562pt too wide) in paragraph at lines 1280--1280
+[] \OT1/pcr/m/n/10.95 Sample1 <- localSample[!duplicated(localSample[c("DecYea
+r","ConcHigh")]),][]
+ []
+
+<Rhelp.png, id=403, 433.62pt x 395.22656pt>
File: Rhelp.png Graphic file (type png)
<use Rhelp.png>
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[31 <D:/LADData/RCode/dataRetrieval/vignettes/Rhelp.png>]
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+Overfull \hbox (11.82567pt too wide) in paragraph at lines 1390--1390
[]\OT1/pcr/m/n/10.95 Suspended sediment concentration (SSC) 1980-10-01 1991-09-
30 3651 mg/l[]
[]
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(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.aux)
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+Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 1434.
+Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 1434.
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b>
-Output written on dataRetrieval.pdf (34 pages, 337808 bytes).
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diff --git a/vignettes/dataRetrieval.lot b/vignettes/dataRetrieval.lot
index cc647ff2674014ecbf2d5a37029198b27cfb40d1..b3fc11f5e7f66063666043ac55440bbf7e4bceec 100644
--- a/vignettes/dataRetrieval.lot
+++ b/vignettes/dataRetrieval.lot
@@ -1,7 +1,7 @@
\select@language {american}
-\contentsline {table}{\numberline {1}{\ignorespaces Common USGS Parameter Codes\relax }}{6}{table.caption.1}
-\contentsline {table}{\numberline {2}{\ignorespaces Commonly used USGS Stat Codes\relax }}{7}{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 }}{8}{table.caption.3}
+\contentsline {table}{\numberline {1}{\ignorespaces Common USGS Parameter Codes\relax }}{5}{table.caption.1}
+\contentsline {table}{\numberline {2}{\ignorespaces Commonly used USGS Stat Codes\relax }}{6}{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 }}{7}{table.caption.3}
\contentsline {table}{\numberline {4}{\ignorespaces Daily dataframe\relax }}{18}{table.caption.6}
\contentsline {table}{\numberline {5}{\ignorespaces Sample dataframe\relax }}{20}{table.caption.8}
\contentsline {table}{\numberline {6}{\ignorespaces Example data\relax }}{21}{table.caption.9}
diff --git a/vignettes/dataRetrieval.pdf b/vignettes/dataRetrieval.pdf
index b655d7a645a9e5981325ec96fcf5d92a31e69238..51d9e77bc289b99b354da5848c59e47315242c14 100644
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diff --git a/vignettes/dataRetrieval.synctex.gz b/vignettes/dataRetrieval.synctex.gz
index b440e6bb3a914c7306db0d056b8ecd1f44fa915e..3fd107c6e1fe5d61cd822fd25ab9321893f82615 100644
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diff --git a/vignettes/dataRetrieval.tex b/vignettes/dataRetrieval.tex
index 161ba002a2f5b5a53224043b0761a770471d41ad..7904149aff074199778b139c2784dac09234ca79 100644
--- a/vignettes/dataRetrieval.tex
+++ b/vignettes/dataRetrieval.tex
@@ -101,7 +101,7 @@
{\thesubsubsection}{0.5em}{}
\titlecontents{section}
-[2.3em] % adjust left margin
+[2em] % adjust left margin
{\sffamily} % font formatting
{\contentslabel{2.3em}} % section label and offset
{\hspace*{-2.3em}}
@@ -122,14 +122,14 @@
{\titlerule*[0.25pc]{.}\contentspage}
\titlecontents{table}
-[-2.3em] % adjust left margin
+[0em] % adjust left margin
{\sffamily} % font formatting
{\textbf{Table}\hspace*{2em} \contentslabel {2em}} % section label and offset
{\hspace*{4em}}
{\titlerule*[0.25pc]{.}\contentspage}
\titlecontents{figure}
-[-2.3em] % adjust left margin
+[0em] % adjust left margin
{\sffamily} % font formatting
{\textbf{Figure}\hspace*{2em} \contentslabel {2em}} % section label and offset
{\hspace*{4em}}
@@ -191,11 +191,15 @@
+\noindent{\huge\textsf{\textbf{The dataRetrieval R package}}}
+\noindent\textsf{By Laura De Cicco and Robert Hirsch}
-\maketitle
+\noindent\textsf{\today}
-\newpage
+% \maketitle
+%
+% \newpage
\tableofcontents
\listoffigures
@@ -262,8 +266,8 @@ 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 3.1.0 by xtable 1.7-3 package
-% Tue Jul 15 09:39:32 2014
+% latex table generated in R 3.1.1 by xtable 1.7-3 package
+% Fri Aug 01 16:04:17 2014
\begin{table}[ht]
\caption{Common USGS Parameter Codes}
\label{tab:params}
@@ -325,8 +329,8 @@ For unit values data (sensor data measured at regular time intervals such as 15
Some common codes are shown in Table \ref{tab:stat}.
-% latex table generated in R 3.1.0 by xtable 1.7-3 package
-% Tue Jul 15 09:39:33 2014
+% latex table generated in R 3.1.1 by xtable 1.7-3 package
+% Fri Aug 01 16:04:18 2014
\begin{table}[ht]
\caption{Commonly used USGS Stat Codes}
\label{tab:stat}
@@ -406,8 +410,8 @@ To discover what data is available for a particular USGS site, including measure
\end{knitrout}
-% latex table generated in R 3.1.0 by xtable 1.7-3 package
-% Tue Jul 15 09:39:34 2014
+% latex table generated in R 3.1.1 by xtable 1.7-3 package
+% Fri Aug 01 16:04:19 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}
@@ -419,7 +423,7 @@ To discover what data is available for a particular USGS site, including measure
& Temperature, water & 1988-10-01 & 2012-05-09 & 894 & deg C \\
[5pt] & Temperature, water & 2010-10-01 & 2012-05-09 & 529 & deg C \\
[5pt] & Temperature, water & 2010-10-01 & 2012-05-09 & 529 & deg C \\
- [5pt] & Stream flow, mean. daily & 1948-01-01 & 2014-07-14 & 24302 & ft$^3$/s \\
+ [5pt] & Stream flow, mean. daily & 1948-01-01 & 2014-07-31 & 24319 & ft$^3$/s \\
[5pt] & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & uS/cm @25C \\
[5pt] & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & uS/cm @25C \\
[5pt] & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & uS/cm @25C \\
@@ -692,13 +696,31 @@ There are additional water quality data sets available from the Water Quality Da
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlcom{# specificCond <- getWQPData('WIDNR_WQX-10032762',}
-\hlcom{# 'Specific conductance','','')}
-\hlcom{# head(specificCond)}
+\hlstd{specificCond} \hlkwb{<-} \hlkwd{getWQPData}\hlstd{(}\hlstr{'WIDNR_WQX-10032762'}\hlstd{,}
+ \hlstr{'Specific conductance'}\hlstd{,}\hlstr{''}\hlstd{,}\hlstr{''}\hlstd{)}
+\hlkwd{head}\hlstd{(specificCond)}
\end{alltt}
+\begin{verbatim}
+ dateTime qualifier.Specific conductance
+1 2011-02-14
+2 2011-02-17
+3 2011-03-03
+4 2011-03-10
+5 2011-03-29
+6 2011-04-07
+ value.Specific conductance
+1 1360
+2 1930
+3 1240
+4 1480
+5 1130
+6 1200
+\end{verbatim}
\end{kframe}
\end{knitrout}
+There are
+
\FloatBarrier
%------------------------------------------------------------
\subsection{URL Construction}
@@ -773,8 +795,8 @@ There are 4750 data points, and 4750 days.
-% latex table generated in R 3.1.0 by xtable 1.7-3 package
-% Tue Jul 15 09:39:42 2014
+% latex table generated in R 3.1.1 by xtable 1.7-3 package
+% Fri Aug 01 16:04:33 2014
\begin{table}[ht]
\caption{Daily dataframe}
\label{tab:DailyDF1}
@@ -894,8 +916,8 @@ To illustrate how the dataRetrieval package handles a more complex censoring pro
-% latex table generated in R 3.1.0 by xtable 1.7-3 package
-% Tue Jul 15 09:39:43 2014
+% latex table generated in R 3.1.1 by xtable 1.7-3 package
+% Fri Aug 01 16:04:34 2014
\begin{table}[ht]
\caption{Example data}
\label{tab:exampleComplexQW}
@@ -1249,11 +1271,10 @@ To see the raw code for a particular code, type the name of the function, withou
\hlstd{removeDuplicates}
\end{alltt}
\begin{verbatim}
-function (localSample = Sample)
-{
- Sample1 <- localSample[!duplicated(localSample[c("DecYear",
- "ConcHigh")]), ]
- return(Sample1)
+function(localSample=Sample) {
+ Sample1 <- localSample[!duplicated(localSample[c("DecYear","ConcHigh")]),]
+
+ return(Sample1)
}
<environment: namespace:dataRetrieval>
\end{verbatim}
@@ -1337,7 +1358,7 @@ 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 2014-07-14 24302 ft3/s
+2 2014-07-31 24319 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 7109b28de4d8a7d2e2565bfdb7812c404d83f893..f99df5d8d664fb002e519459edeea6301a817f8b 100644
--- a/vignettes/dataRetrieval.toc
+++ b/vignettes/dataRetrieval.toc
@@ -1,19 +1,19 @@
\select@language {american}
-\contentsline {section}{\numberline {1}Introduction to dataRetrieval}{4}{section.1}
-\contentsline {section}{\numberline {2}General USGS Web Retrievals}{5}{section.2}
-\contentsline {subsection}{\numberline {2.1}Site Information}{7}{subsection.2.1}
-\contentsline {subsubsection}{\numberline {2.1.1}getSiteFileData}{7}{subsubsection.2.1.1}
-\contentsline {subsubsection}{\numberline {2.1.2}getDataAvailability}{8}{subsubsection.2.1.2}
-\contentsline {subsection}{\numberline {2.2}Parameter Information}{9}{subsection.2.2}
-\contentsline {subsection}{\numberline {2.3}Daily Values}{9}{subsection.2.3}
-\contentsline {subsection}{\numberline {2.4}Unit Values}{13}{subsection.2.4}
-\contentsline {subsection}{\numberline {2.5}Water Quality Values}{14}{subsection.2.5}
-\contentsline {subsection}{\numberline {2.6}STORET Water Quality Retrievals}{16}{subsection.2.6}
-\contentsline {subsection}{\numberline {2.7}URL Construction}{16}{subsection.2.7}
-\contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{17}{section.3}
+\contentsline {section}{\numberline {1}Introduction to dataRetrieval}{3}{section.1}
+\contentsline {section}{\numberline {2}General USGS Web Retrievals}{4}{section.2}
+\contentsline {subsection}{\numberline {2.1}Site Information}{6}{subsection.2.1}
+\contentsline {subsubsection}{\numberline {2.1.1}getSiteFileData}{6}{subsubsection.2.1.1}
+\contentsline {subsubsection}{\numberline {2.1.2}getDataAvailability}{7}{subsubsection.2.1.2}
+\contentsline {subsection}{\numberline {2.2}Parameter Information}{8}{subsection.2.2}
+\contentsline {subsection}{\numberline {2.3}Daily Values}{8}{subsection.2.3}
+\contentsline {subsection}{\numberline {2.4}Unit Values}{12}{subsection.2.4}
+\contentsline {subsection}{\numberline {2.5}Water Quality Values}{13}{subsection.2.5}
+\contentsline {subsection}{\numberline {2.6}STORET Water Quality Retrievals}{15}{subsection.2.6}
+\contentsline {subsection}{\numberline {2.7}URL Construction}{15}{subsection.2.7}
+\contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{16}{section.3}
\contentsline {subsection}{\numberline {3.1}INFO Data}{17}{subsection.3.1}
\contentsline {subsection}{\numberline {3.2}Daily Data}{17}{subsection.3.2}
-\contentsline {subsection}{\numberline {3.3}Sample Data}{19}{subsection.3.3}
+\contentsline {subsection}{\numberline {3.3}Sample Data}{18}{subsection.3.3}
\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{20}{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}
diff --git a/vignettes/figure/egretEx.pdf b/vignettes/figure/egretEx.pdf
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diff --git a/vignettes/figure/getQWtemperaturePlot.pdf b/vignettes/figure/getQWtemperaturePlot.pdf
index a61cf799470a0b907fa21b3ad5a4273a04b53a7e..a436b0514b04e8a83abdbe0342d1323b7a62d49f 100644
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