USGSstyle.Rnw

%\VignetteIndexEntry{Introduction to the EGRET package}
%\VignetteEngine{knitr::knitr}
%\VignetteDepends{}
%\VignetteSuggests{xtable, dataRetrieval,extrafont}
%\VignetteImports{methods,survival, fields}
%\VignettePackage{EGRET}

\documentclass[a4paper,11pt]{article}

\usepackage{amsmath}
\usepackage{times}
\usepackage{hyperref}
\usepackage[numbers, round]{natbib}
\usepackage[american]{babel}
\usepackage{authblk}
\usepackage{subfig}
\usepackage{placeins}
\usepackage{footnote}
\usepackage{tabularx}
\usepackage{parskip}
\usepackage{threeparttable}
\renewcommand\Affilfont{\itshape\small}

\usepackage{csquotes}
\usepackage{setspace}

\doublespacing

\renewcommand{\topfraction}{0.85}
\renewcommand{\textfraction}{0.1}
\usepackage{graphicx}


\usepackage{mathptmx}% Times Roman font
\usepackage[scaled=.90]{helvet}% Helvetica, served as a model for arial

\usepackage{indentfirst}
\setlength{\parskip}{0pt}

\usepackage{courier}

\usepackage{titlesec}
\usepackage{titletoc}

\titleformat{\section}
  {\normalfont\sffamily\bfseries\LARGE}
  {\thesection}{0.5em}{}
\titleformat{\subsection}
  {\normalfont\sffamily\bfseries\Large}
  {\thesubsection}{0.5em}{}
\titleformat{\subsubsection}
  {\normalfont\sffamily\large}
  {\thesubsubsection}{0.5em}{}
  
\titlecontents{section}
[2em]                 % adjust left margin
{\sffamily}             % font formatting
{\contentslabel{2.3em}} % section label and offset
{\hspace*{-2.3em}}
{\titlerule*[0.25pc]{.}\contentspage}
  
\titlecontents{subsection}
[4.6em]                 % adjust left margin
{\sffamily}             % font formatting
{\contentslabel{2.3em}} % section label and offset
{\hspace*{-2.3em}}
{\titlerule*[0.25pc]{.}\contentspage}
  
\titlecontents{subsubsection}
[6.9em]                 % adjust left margin
{\sffamily}             % font formatting
{\contentslabel{2.3em}} % section label and offset
{\hspace*{-2.3em}}
{\titlerule*[0.25pc]{.}\contentspage}

\titlecontents{table}
[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}
[0em]                 % adjust left margin
{\sffamily}             % font formatting
{\textbf{Figure}\hspace*{2em} \contentslabel {2em}} % section label and offset
{\hspace*{4em}}
{\titlerule*[0.25pc]{.}\contentspage}

%Italisize and change font of urls:
\urlstyle{sf}
\renewcommand\UrlFont\itshape

\usepackage{caption}
\captionsetup{
  font={sf},
  labelfont={bf,sf},
  labelsep=period,
  justification=justified,
  singlelinecheck=false
}

\setlength\parindent{20pt}

\textwidth=6.5in
\textheight=9.2in
\parskip=.3cm
\oddsidemargin=.1in
\evensidemargin=.1in
\headheight=-.3in

%------------------------------------------------------------
% newcommand
%------------------------------------------------------------
\newcommand{\scscst}{\scriptscriptstyle}
\newcommand{\scst}{\scriptstyle}
\newcommand{\Robject}[1]{{\texttt{#1}}}
\newcommand{\Rfunction}[1]{{\texttt{#1}}}
\newcommand{\Rclass}[1]{\textit{#1}}
\newcommand{\Rpackage}[1]{\textit{#1}}
\newcommand{\Rexpression}[1]{\texttt{#1}}
\newcommand{\Rmethod}[1]{{\texttt{#1}}}
\newcommand{\Rfunarg}[1]{{\texttt{#1}}}

\begin{document}

\renewenvironment{knitrout}{\begin{singlespace}}{\end{singlespace}}
\renewcommand*\listfigurename{Figures}
\renewcommand*\listtablename{Tables}

<<openLibrary, echo=FALSE>>=
library(xtable)
options(continue=" ")
options(width=60)
library(knitr)

@


<<include=TRUE ,echo=FALSE,eval=TRUE>>=
opts_chunk$set(highlight=TRUE, tidy=TRUE, keep.space=TRUE, keep.blank.space=FALSE, keep.comment=TRUE, concordance=TRUE,tidy=FALSE,comment="")

knit_hooks$set(inline = function(x) {
   if (is.numeric(x)) round(x, 3)})
knit_hooks$set(crop = hook_pdfcrop)

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]","")

@

%------------------------------------------------------------
\title{Sample Title}
%------------------------------------------------------------
\author[1]{Laura De Cicco}
\affil[1]{United States Geological Survey}

% \maketitle

\noindent{\huge\textsf{\textbf{Sample Title}}}

\noindent\textsf{By Laura De Cicco}

\newpage 

\tableofcontents
\listoffigures
\listoftables

\newpage


%------------------------------------------------------------
\section{Header 1}
%------------------------------------------------------------ 

Some text. With a url: \url{http://www.cida.usgs.gov}. More text.

%------------------------------------------------------------
\section{Header 2}
%------------------------------------------------------------ 
Blah blah


<<workflowFlowHistory, echo=TRUE,eval=FALSE, message=FALSE>>=
library(boot)

# Some R code

@



%------------------------------------------------------------ 
\section{Header 3}
\label{sec:dataframes}
%------------------------------------------------------------ 
Text blah blah. Here's a table with xtable. Also, has a bit of formatting (in the ft$^3$/s).

<<tableParameterCodes, echo=FALSE,results='asis'>>=
pCode <- c('00060', '00065', '00010','00045','00400')
shortName <- c("Discharge [ft$^3$/s]","Gage height [ft]","Temperature [C]", "Precipitation [in]", "pH")

data.df <- data.frame(pCode, shortName, stringsAsFactors=FALSE)

print(xtable(data.df,
       label="tab:params",
       caption="Common USGS Parameter Codes"),
       caption.placement="top",
       size = "\\footnotesize",
       latex.environment=NULL,
       sanitize.text.function = function(x) {x},
       sanitize.colnames.function =  bold.colHeaders,
       sanitize.rownames.function = addSpace
      )

@


%------------------------------------------------------------ 
\subsection{Subsection 1}
\label{sec:dataframesDaily}
%------------------------------------------------------------ 
Here's a table without using xtable, table \ref{table:Daily1}).

\begin{table}[!ht]
{\footnotesize
\caption{Daily dataframe} 
\label{table:Daily1}
\begin{tabular}{llll}
  \hline
\multicolumn{1}{c}{\textbf{\textsf{ColumnName}}} &
\multicolumn{1}{c}{\textbf{\textsf{Type}}} &
\multicolumn{1}{c}{\textbf{\textsf{Description}}} &
\multicolumn{1}{c}{\textbf{\textsf{Units}}} \\ 
  \hline
  Date & Date & Date & date \\ 
  [5pt]Q & number & Discharge in m\textsuperscript{3}/s & m\textsuperscript{3}/s \\ 
  [5pt]Qualifier & string & Qualifing code & character \\ 
  [5pt]Q7 & number & 7 day running average of Q & m\textsuperscript{3}/s \\ 
  [5pt]Q30 & number & 30 running average of Q & m\textsuperscript{3}/s \\ 
   \hline
\end{tabular}
}
\end{table}

\FloatBarrier

There's also a table with a footnote.

\begin{table}
{\footnotesize
  \begin{threeparttable}[b]
  \caption{Sample dataframe}
  \label{tab:SampleDataframe}
  \begin{tabular}{llll}
  \hline
\multicolumn{1}{c}{\textbf{\textsf{ColumnName}}} & 
\multicolumn{1}{c}{\textbf{\textsf{Type}}} & 
\multicolumn{1}{c}{\textbf{\textsf{Description}}} & 
\multicolumn{1}{c}{\textbf{\textsf{Units}}} \\ 
  \hline
  Date & Date & Date & date \\ 
  [5pt]CosDY & number & Cosine of DecYear & numeric \\ 
  [5pt]Q \tnote{1} & number & Discharge & m\textsuperscript{3}/s \\ 
  [5pt]LogQ \tnote{1} & number & Natural logarithm of discharge & numeric \\ 
   \hline
\end{tabular}

  \begin{tablenotes}
    \item[1] Discharge columns are populated from data in the Daily dataframe after calling the \texttt{mergeReport} function.
  \end{tablenotes}
 \end{threeparttable}
}
\end{table}

\FloatBarrier

%------------------------------------------------------------ 
\subsection{Subsection 2}
\label{sec:dataframesSample}
%------------------------------------------------------------ 

\FloatBarrier


%------------------------------------------------------------ 
\section{Next Section}
\label{sec:flowHistory}
%------------------------------------------------------------ 


We will walk through an example from Columbia River at The Dalles, OR.

<<flowHistory,echo=TRUE,eval=TRUE,message=FALSE>>=
#Some R stuff
x <- 1
@


\FloatBarrier

%------------------------------------------------------------ 
\subsection{Plotting Options}
\label{sec:plotOptions}
%------------------------------------------------------------ 



<<plotSingleandSD, echo=TRUE, fig.cap="Plots of discharge statistics",fig.subcap=c("plot(1:10)","plot(rnorm(10))"),out.width='.5\\linewidth',out.height='.5\\linewidth',fig.show='hold',fig.pos="h">>=
plot(1:10)
plot(rnorm(10))
@

\clearpage



%------------------------------------------------------------ 
\subsection{Plotting Options}
\label{sec:plotOptionsWQ}
%------------------------------------------------------------ 

More text

<<plotBoxes, echo=TRUE, fig.cap="Concentration box plots",out.width='.5\\linewidth',out.height='.5\\linewidth',fig.show='hold',fig.pos="h">>=
plot(rnorm(10))
@

\clearpage



\end{document}