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Commit e4e62045 authored by Laura A DeCicco's avatar Laura A DeCicco
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1 merge request!2Updating naming convention + other minor changes.
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man/getWaterML1Data.Rd
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......@@ -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)
}
vignettes/dataRetrieval-concordance.tex
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\Sconcordance{concordance:dataRetrieval.tex:dataRetrieval.Rnw:%
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1 20 0 44 1 4 0 32 1 4 0 21 1 4 0 21 1 37 0 13 1 9 0 %
95 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 55 1}
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0 24 1 3 0 23 1 3 0 6 1 7 0 18 1 3 0 25 1 1 0 17 1 9 %
0 6 1 7 0 21 1 8 0 16 1 2 0 11 1 23 0 21 1 9 0 20 1 3 %
0 6 1 17 0 27 1 6 0 11 1 9 0 15 1 20 0 21 1 4 0 21 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 32 1 4 0 21 1 4 0 21 1 37 0 13 1 %
9 0 95 1 4 0 9 1 12 0 13 1 4 0 14 1 4 0 5 1 4 0 23 1 %
18 0 8 1 4 0 55 1}
vignettes/dataRetrieval.Rnw
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......@@ -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}
......
vignettes/dataRetrieval.lof
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\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}
......
vignettes/dataRetrieval.log
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**dataRetrieval.tex
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.tex
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[]|\OT1/phv/b/n/10.95 Table| | [][]\OT1/phv/m/n/10.95 Daily mean data avail-ab
ile at the Chop-tank River near Greens-boro, MD. [Some columns
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[]\OT1/ptm/m/n/10.95 To ob-tain all of the avail-able in-for-ma-tion con-cern-i
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[][]\OT1/pcr/m/n/10.95 url_uv[] []<-[] []\OT1/pcr/b/n/10.95 constructNWISURL[][
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[] \OT1/pcr/m/n/10.95 First day of the discharge record is 2000-01-01 and last
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[] \OT1/pcr/m/n/10.95 The first sample is from 2000-01-04 and the last sample i
s from 2012-12-18[]
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[] \OT1/pcr/m/n/10.95 Sample1 <- localSample[!duplicated(localSample[c("DecYea
r","ConcHigh")]),][]
[]
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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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\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}
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{\thesubsubsection}{0.5em}{}
\titlecontents{section}
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{\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}.
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\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}
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% 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.
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\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
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% 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
......
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\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}
......
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