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Commit fbbf4b2f authored by Laura A DeCicco's avatar Laura A DeCicco
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Latest vignette build.

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vignettes/dataRetrieval-concordance.tex
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\Sconcordance{concordance:dataRetrieval.tex:dataRetrieval.Rnw:% \Sconcordance{concordance:dataRetrieval.tex:dataRetrieval.Rnw:%
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vignettes/dataRetrieval.lof
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\select@language {american} \select@language {american}
\contentsline {figure}{\numberline {1}{\ignorespaces Temperature and discharge plot of Choptank River in 2012}}{11}{figure.caption.4} \contentsline {figure}{\numberline {1}{\ignorespaces Temperature and discharge plot of Choptank River in 2012}}{10}{figure.caption.4}
\contentsline {figure}{\numberline {2}{\ignorespaces Nitrate plot of Choptank River}}{14}{figure.caption.5} \contentsline {figure}{\numberline {2}{\ignorespaces Nitrate plot of Choptank River}}{13}{figure.caption.5}
\contentsline {figure}{\numberline {3}{\ignorespaces Default multiPlotDataOverview}}{26}{figure.caption.10} \contentsline {figure}{\numberline {3}{\ignorespaces Default multiPlotDataOverview}}{23}{figure.caption.10}
\contentsline {figure}{\numberline {4}{\ignorespaces A simple R help file\relax }}{30}{figure.caption.14} \contentsline {figure}{\numberline {4}{\ignorespaces A simple R help file\relax }}{27}{figure.caption.14}
\contentsline {figure}{\numberline {5}{\ignorespaces A simple table produced in Microsoft\textregistered \ Excel. Additional formatting will be requried, for example converting u to $\mu $ \relax }}{33}{figure.caption.15} \contentsline {figure}{\numberline {5}{\ignorespaces A simple table produced in Microsoft\textregistered \ Excel. Additional formatting will be requried, for example converting u to $\mu $ \relax }}{30}{figure.caption.15}
\contentsfinish \contentsfinish
vignettes/dataRetrieval.log
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**dataRetrieval.tex **dataRetrieval.tex
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[]|\OT1/phv/b/n/10.95 Table| | [][]\OT1/phv/m/n/10.95 Daily mean data avail-ab []|\OT1/phv/b/n/10.95 Table| | [][]\OT1/phv/m/n/10.95 Daily mean data avail-ab
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\OT1/ptm/m/n/10.95 ters. This func-tion com-bines \OT1/pcr/m/n/10.95 getSiteFil
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.95 , pro-duc-ing one dataframe
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\OT1/ptm/m/n/10.95 Finally, there is a func-tion called \OT1/pcr/m/n/10.95 merg
eReport \OT1/ptm/m/n/10.95 that will look at both the Daily and Sam-ple datafra
me,
[]
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30 3651 mg/l[] 30 3651 mg/l[]
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\select@language {american} \select@language {american}
\contentsline {table}{\numberline {1}{\ignorespaces Common USGS Parameter Codes\relax }}{5}{table.caption.1} \contentsline {table}{\numberline {1}{\ignorespaces Common USGS Parameter Codes\relax }}{4}{table.caption.1}
\contentsline {table}{\numberline {2}{\ignorespaces Commonly used USGS Stat Codes\relax }}{6}{table.caption.2} \contentsline {table}{\numberline {2}{\ignorespaces Commonly used USGS Stat Codes\relax }}{5}{table.caption.2}
\contentsline {table}{\numberline {3}{\ignorespaces Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]\relax }}{7}{table.caption.3} \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 }}{17}{table.caption.6} \contentsline {table}{\numberline {4}{\ignorespaces Daily dataframe\relax }}{16}{table.caption.6}
\contentsline {table}{\numberline {5}{\ignorespaces Sample dataframe\relax }}{19}{table.caption.8} \contentsline {table}{\numberline {5}{\ignorespaces Sample dataframe\relax }}{17}{table.caption.8}
\contentsline {table}{\numberline {6}{\ignorespaces Example data\relax }}{20}{table.caption.9} \contentsline {table}{\numberline {6}{\ignorespaces Example data\relax }}{18}{table.caption.9}
\contentsline {table}{\numberline {7}{\ignorespaces dataRetrieval functions\relax }}{28}{table.caption.12} \contentsline {table}{\numberline {7}{\ignorespaces dataRetrieval functions\relax }}{25}{table.caption.12}
\contentsline {table}{\numberline {8}{\ignorespaces dataRetrieval miscellaneous functions\relax }}{28}{table.caption.13} \contentsline {table}{\numberline {8}{\ignorespaces dataRetrieval miscellaneous functions\relax }}{25}{table.caption.13}
\contentsfinish \contentsfinish
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...@@ -72,7 +72,7 @@ ...@@ -72,7 +72,7 @@
\usepackage{csquotes} \usepackage{csquotes}
\usepackage{setspace} \usepackage{setspace}
\doublespacing % \doublespacing
\renewcommand{\topfraction}{0.85} \renewcommand{\topfraction}{0.85}
\renewcommand{\textfraction}{0.1} \renewcommand{\textfraction}{0.1}
...@@ -82,7 +82,8 @@ ...@@ -82,7 +82,8 @@
\usepackage{mathptmx}% Times Roman font \usepackage{mathptmx}% Times Roman font
\usepackage[scaled=.90]{helvet}% Helvetica, served as a model for arial \usepackage[scaled=.90]{helvet}% Helvetica, served as a model for arial
\usepackage{indentfirst} % \usepackage{indentfirst}
% \setlength\parindent{20pt}
\setlength{\parskip}{0pt} \setlength{\parskip}{0pt}
\usepackage{courier} \usepackage{courier}
...@@ -148,7 +149,7 @@ ...@@ -148,7 +149,7 @@
singlelinecheck=false singlelinecheck=false
} }
\setlength\parindent{20pt}
\textwidth=6.2in \textwidth=6.2in
\textheight=8.5in \textheight=8.5in
...@@ -266,8 +267,8 @@ Once the site-ID (siteNumber) is known, the next required input for USGS data re ...@@ -266,8 +267,8 @@ Once the site-ID (siteNumber) is known, the next required input for USGS data re
Not every station will measure all parameters. A short list of commonly measured parameters is shown in Table \ref{tab:params}. Not every station will measure all parameters. A short list of commonly measured parameters is shown in Table \ref{tab:params}.
% latex table generated in R 3.1.1 by xtable 1.7-3 package % latex table generated in R 3.1.1 by xtable 1.7-4 package
% Thu Sep 11 16:26:30 2014 % Wed Sep 17 13:24:06 2014
\begin{table}[ht] \begin{table}[ht]
\caption{Common USGS Parameter Codes} \caption{Common USGS Parameter Codes}
\label{tab:params} \label{tab:params}
...@@ -329,8 +330,8 @@ For unit values data (sensor data measured at regular time intervals such as 15 ...@@ -329,8 +330,8 @@ For unit values data (sensor data measured at regular time intervals such as 15
Some common codes are shown in Table \ref{tab:stat}. Some common codes are shown in Table \ref{tab:stat}.
% latex table generated in R 3.1.1 by xtable 1.7-3 package % latex table generated in R 3.1.1 by xtable 1.7-4 package
% Thu Sep 11 16:26:31 2014 % Wed Sep 17 13:24:07 2014
\begin{table}[ht] \begin{table}[ht]
\caption{Commonly used USGS Stat Codes} \caption{Commonly used USGS Stat Codes}
\label{tab:stat} \label{tab:stat}
...@@ -410,8 +411,8 @@ To discover what data is available for a particular USGS site, including measure ...@@ -410,8 +411,8 @@ To discover what data is available for a particular USGS site, including measure
\end{knitrout} \end{knitrout}
% latex table generated in R 3.1.1 by xtable 1.7-3 package % latex table generated in R 3.1.1 by xtable 1.7-4 package
% Thu Sep 11 16:26:32 2014 % Wed Sep 17 13:24:07 2014
\begin{table}[ht] \begin{table}[ht]
\caption{Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]} \caption{Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]}
\label{tab:gda} \label{tab:gda}
...@@ -423,7 +424,7 @@ To discover what data is available for a particular USGS site, including measure ...@@ -423,7 +424,7 @@ To discover what data is available for a particular USGS site, including measure
& Temperature, water & 1988-10-01 & 2012-05-09 & 894 & deg C \\ & 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] & 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 & 2014-09-10 & 24360 & ft$^3$/s \\ [5pt] & Stream flow, mean. daily & 1948-01-01 & 2014-09-16 & 24366 & 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 \\ [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 \\
...@@ -785,8 +786,8 @@ There are 4750 data points, and 4750 days. ...@@ -785,8 +786,8 @@ There are 4750 data points, and 4750 days.
% latex table generated in R 3.1.1 by xtable 1.7-3 package % latex table generated in R 3.1.1 by xtable 1.7-4 package
% Thu Sep 11 16:26:44 2014 % Wed Sep 17 13:24:23 2014
\begin{table}[ht] \begin{table}[ht]
\caption{Daily dataframe} \caption{Daily dataframe}
\label{tab:DailyDF1} \label{tab:DailyDF1}
...@@ -906,8 +907,8 @@ To illustrate how the dataRetrieval package handles a more complex censoring pro ...@@ -906,8 +907,8 @@ To illustrate how the dataRetrieval package handles a more complex censoring pro
% latex table generated in R 3.1.1 by xtable 1.7-3 package % latex table generated in R 3.1.1 by xtable 1.7-4 package
% Thu Sep 11 16:26:45 2014 % Wed Sep 17 13:24:25 2014
\begin{table}[ht] \begin{table}[ht]
\caption{Example data} \caption{Example data}
\label{tab:exampleComplexQW} \label{tab:exampleComplexQW}
...@@ -985,7 +986,7 @@ Finally, qUnit is a numeric argument that defines the discharge units used in th ...@@ -985,7 +986,7 @@ Finally, qUnit is a numeric argument that defines the discharge units used in th
So, if you have a file called \enquote{ChoptankRiverFlow.txt} located in a folder called \enquote{RData} on the C drive (this example is for the Windows\textregistered\ operating systems), and the file is structured as follows (tab-separated): So, if you have a file called \enquote{ChoptankRiverFlow.txt} located in a folder called \enquote{RData} on the C drive (this example is for the Windows\textregistered\ operating systems), and the file is structured as follows (tab-separated):
\singlespacing % \singlespacing
\begin{verbatim} \begin{verbatim}
date Qdaily date Qdaily
10/1/1999 107 10/1/1999 107
...@@ -996,7 +997,7 @@ date Qdaily ...@@ -996,7 +997,7 @@ date Qdaily
10/6/1999 98 10/6/1999 98
... ...
\end{verbatim} \end{verbatim}
\doublespacing % \doublespacing
The call to open this file, convert the discharge to cubic meters per second, and populate the Daily data frame would be: The call to open this file, convert the discharge to cubic meters per second, and populate the Daily data frame would be:
\begin{knitrout} \begin{knitrout}
...@@ -1019,7 +1020,6 @@ Microsoft\textregistered\ Excel files can be a bit tricky to import into R direc ...@@ -1019,7 +1020,6 @@ Microsoft\textregistered\ Excel files can be a bit tricky to import into R direc
\label{sec:SampleFile} \label{sec:SampleFile}
%------------------------------------------------------------ %------------------------------------------------------------
\doublespacing
The \texttt{getSampleDataFromFile} function will import a user-generated file and populate the Sample dataframe. The difference between sample data and discharge data is that the code requires a third column that contains a remark code, either blank or \verb@"<"@, which will tell the program that the data were \enquote{left-censored} (or, below the detection limit of the sensor). Therefore, the data must be in the form: date, remark, value. An example of a comma-delimited file is: The \texttt{getSampleDataFromFile} function will import a user-generated file and populate the Sample dataframe. The difference between sample data and discharge data is that the code requires a third column that contains a remark code, either blank or \verb@"<"@, which will tell the program that the data were \enquote{left-censored} (or, below the detection limit of the sensor). Therefore, the data must be in the form: date, remark, value. An example of a comma-delimited file is:
\singlespacing \singlespacing
...@@ -1032,7 +1032,6 @@ cdate;remarkCode;Nitrate ...@@ -1032,7 +1032,6 @@ cdate;remarkCode;Nitrate
2/3/2000,,1.54 2/3/2000,,1.54
... ...
\end{verbatim} \end{verbatim}
\doublespacing
The call to open this file, and populate the Sample dataframe is: The call to open this file, and populate the Sample dataframe is:
\begin{knitrout} \begin{knitrout}
...@@ -1059,7 +1058,8 @@ date rdp dp rpp pp rtp tp ...@@ -1059,7 +1058,8 @@ date rdp dp rpp pp rtp tp
2005-10-30 < 0.020 2005-10-30 < 0.020
... ...
\end{verbatim} \end{verbatim}
\doublespacing
\begin{knitrout} \begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt} \begin{alltt}
...@@ -1348,7 +1348,7 @@ There are a few steps that are required in order to create a table in Microsoft\ ...@@ -1348,7 +1348,7 @@ There are a few steps that are required in order to create a table in Microsoft\
5 Suspended sediment discharge 1980-10-01 5 Suspended sediment discharge 1980-10-01
End Count Units End Count Units
1 2012-05-09 529 deg C 1 2012-05-09 529 deg C
2 2014-09-10 24360 ft3/s 2 2014-09-16 24366 ft3/s
3 2012-05-09 527 uS/cm @25C 3 2012-05-09 527 uS/cm @25C
4 1991-09-30 3651 mg/l 4 1991-09-30 3651 mg/l
5 1991-09-30 3652 tons/day 5 1991-09-30 3652 tons/day
......
vignettes/dataRetrieval.toc
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...@@ -3,26 +3,26 @@ ...@@ -3,26 +3,26 @@
\contentsline {section}{\numberline {2}General USGS Web Retrievals}{4}{section.2} \contentsline {section}{\numberline {2}General USGS Web Retrievals}{4}{section.2}
\contentsline {subsection}{\numberline {2.1}Site Information}{6}{subsection.2.1} \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 {2.1.1}getSiteFileData}{6}{subsubsection.2.1.1}
\contentsline {subsubsection}{\numberline {2.1.2}getDataAvailability}{7}{subsubsection.2.1.2} \contentsline {subsubsection}{\numberline {2.1.2}getDataAvailability}{6}{subsubsection.2.1.2}
\contentsline {subsection}{\numberline {2.2}Parameter Information}{8}{subsection.2.2} \contentsline {subsection}{\numberline {2.2}Parameter Information}{7}{subsection.2.2}
\contentsline {subsection}{\numberline {2.3}Daily Values}{8}{subsection.2.3} \contentsline {subsection}{\numberline {2.3}Daily Values}{7}{subsection.2.3}
\contentsline {subsection}{\numberline {2.4}Unit Values}{12}{subsection.2.4} \contentsline {subsection}{\numberline {2.4}Unit Values}{11}{subsection.2.4}
\contentsline {subsection}{\numberline {2.5}Water Quality Values}{13}{subsection.2.5} \contentsline {subsection}{\numberline {2.5}Water Quality Values}{12}{subsection.2.5}
\contentsline {subsection}{\numberline {2.6}STORET Water Quality Retrievals}{15}{subsection.2.6} \contentsline {subsection}{\numberline {2.6}STORET Water Quality Retrievals}{14}{subsection.2.6}
\contentsline {subsection}{\numberline {2.7}URL Construction}{15}{subsection.2.7} \contentsline {subsection}{\numberline {2.7}URL Construction}{14}{subsection.2.7}
\contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{16}{section.3} \contentsline {section}{\numberline {3}Data Retrievals Structured For Use In The EGRET Package}{14}{section.3}
\contentsline {subsection}{\numberline {3.1}INFO Data}{16}{subsection.3.1} \contentsline {subsection}{\numberline {3.1}INFO Data}{15}{subsection.3.1}
\contentsline {subsection}{\numberline {3.2}Daily Data}{17}{subsection.3.2} \contentsline {subsection}{\numberline {3.2}Daily Data}{15}{subsection.3.2}
\contentsline {subsection}{\numberline {3.3}Sample Data}{18}{subsection.3.3} \contentsline {subsection}{\numberline {3.3}Sample Data}{16}{subsection.3.3}
\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{19}{subsection.3.4} \contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{17}{subsection.3.4}
\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{21}{subsection.3.5} \contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{19}{subsection.3.5}
\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{21}{subsubsection.3.5.1} \contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{19}{subsubsection.3.5.1}
\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{23}{subsubsection.3.5.2} \contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{20}{subsubsection.3.5.2}
\contentsline {subsection}{\numberline {3.6}Merge Report}{24}{subsection.3.6} \contentsline {subsection}{\numberline {3.6}Merge Report}{21}{subsection.3.6}
\contentsline {subsection}{\numberline {3.7}EGRET Plots}{25}{subsection.3.7} \contentsline {subsection}{\numberline {3.7}EGRET Plots}{22}{subsection.3.7}
\contentsline {section}{\numberline {4}Summary}{27}{section.4} \contentsline {section}{\numberline {4}Summary}{24}{section.4}
\contentsline {section}{\numberline {5}Getting Started in R}{29}{section.5} \contentsline {section}{\numberline {5}Getting Started in R}{26}{section.5}
\contentsline {subsection}{\numberline {5.1}New to R?}{29}{subsection.5.1} \contentsline {subsection}{\numberline {5.1}New to R?}{26}{subsection.5.1}
\contentsline {subsection}{\numberline {5.2}R User: Installing dataRetrieval}{31}{subsection.5.2} \contentsline {subsection}{\numberline {5.2}R User: Installing dataRetrieval}{28}{subsection.5.2}
\contentsline {section}{\numberline {6}Creating tables in Microsoft\textregistered \ software from R}{31}{section.6} \contentsline {section}{\numberline {6}Creating tables in Microsoft\textregistered \ software from R}{28}{section.6}
\contentsfinish \contentsfinish
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