galaaz 0.4.10 → 0.5.0

data/examples/latex_templates/Test-ieee_article/Test-ieee_article.Rmd

@@ -0,0 +1,175 @@
+---
+title: Bare Demo of IEEEtran.cls for IEEE Conferences
+affiliation:
+  ## use one only of the following
+  # author-columnar: true         ## one column per author
+  institution-columnar: true  ## one column per institution (multiple autors eventually)
+  # wide: true                  ## one column wide author/affiliation fields
+
+  institution:
+    - name: Georgia Institute of Technology
+      department: School of Electrical and Computer Engineering
+      location: Atlanta, Georgia 30332--0250
+      email: ece@datech.edu
+      mark: 1
+      author:
+        - name: Michael Shell
+    - name: Twentieth Century Fox
+      location: Springfield, USA
+      mark: 2
+      author:
+        - name: Homer Simpson
+          email: homer@thesimpsons.com
+    - name: Starfleet Academy
+      location: San Francisco, California 96678-2391
+      other: "Telephone: (800) 555--1212, Fax: (888) 555--1212"
+      mark: 3
+      author:
+        - name: Montgomery Scott
+    - name: Tyrell Inc.
+      location: 123 Replicant Street, Los Angeles, USA 90210--4321
+      mark: 4
+      author:
+        - name: Eldon Tyrell
+          email: eldon@starfleet-academy.star
+        - name: Roy Batty
+          email: roy@replicant.offworld
+abstract: |
+  The abstract goes here.
+  On multiple lines eventually.
+
+bibliography: mybibfile.bib
+output: rticles::ieee_article
+---
+
+Introduction
+=============
+<!-- no \IEEEPARstart -->
+This demo file is intended to serve as a ``starter file''
+for IEEE conference papers produced under \LaTeX\ using
+IEEEtran.cls version 1.8b and later.
+<!-- You must have at least 2 lines in the paragraph with the drop letter -->
+<!-- (should never be an issue) -->
+I wish you the best of success.
+
+
+## Subsection Heading Here
+Subsection text here.
+
+### Subsubsection Heading Here
+Subsubsection text here.
+
+<!-- An example of a floating figure using the graphicx package. -->
+<!-- Note that \label must occur AFTER (or within) \caption. -->
+<!-- For figures, \caption should occur after the \includegraphics. -->
+<!-- Note that IEEEtran v1.7 and later has special internal code that -->
+<!-- is designed to preserve the operation of \label within \caption -->
+<!-- even when the captionsoff option is in effect. However, because -->
+<!-- of issues like this, it may be the safest practice to put all your -->
+<!-- \label just after \caption rather than within \caption{}. -->
+
+<!-- Reminder: the "draftcls" or "draftclsnofoot", not "draft", class -->
+<!-- option should be used if it is desired that the figures are to be -->
+<!-- displayed while in draft mode. -->
+
+<!-- \begin{figure}[!t] -->
+<!-- \centering -->
+<!-- \includegraphics[width=2.5in]{myfigure} -->
+<!-- where an .eps filename suffix will be assumed under latex,  -->
+<!-- and a .pdf suffix will be assumed for pdflatex; or what has been declared -->
+<!-- via \DeclareGraphicsExtensions. -->
+<!-- \caption{Simulation results for the network.} -->
+<!-- \label{fig_sim} -->
+<!-- \end{figure} -->
+
+<!-- Note that the IEEE typically puts floats only at the top, even when this -->
+<!-- results in a large percentage of a column being occupied by floats. -->
+
+
+<!-- An example of a double column floating figure using two subfigures. -->
+<!-- (The subfig.sty package must be loaded for this to work.) -->
+<!-- The subfigure \label commands are set within each subfloat command, -->
+<!-- and the \label for the overall figure must come after \caption. -->
+<!-- \hfil is used as a separator to get equal spacing. -->
+<!-- Watch out that the combined width of all the subfigures on a  -->
+<!-- line do not exceed the text width or a line break will occur. -->
+
+<!-- \begin{figure*}[!t] -->
+<!-- \centering -->
+<!-- \subfloat[Case I]{\includegraphics[width=2.5in]{box}% -->
+<!-- \label{fig_first_case}} -->
+<!-- \hfil -->
+<!-- \subfloat[Case II]{\includegraphics[width=2.5in]{box}% -->
+<!-- \label{fig_second_case}} -->
+<!-- \caption{Simulation results for the network.} -->
+<!-- \label{fig_sim} -->
+<!-- \end{figure*} -->
+
+<!-- Note that often IEEE papers with subfigures do not employ subfigure -->
+<!-- captions (using the optional argument to \subfloat[]), but instead will -->
+<!-- reference/describe all of them (a), (b), etc., within the main caption. -->
+<!-- Be aware that for subfig.sty to generate the (a), (b), etc., subfigure -->
+<!-- labels, the optional argument to \subfloat must be present. If a -->
+<!-- subcaption is not desired, just leave its contents blank, -->
+<!-- e.g., \subfloat[]. -->
+
+
+<!-- An example of a floating table. Note that, for IEEE style tables, the -->
+<!-- \caption command should come BEFORE the table and, given that table -->
+<!-- captions serve much like titles, are usually capitalized except for words -->
+<!-- such as a, an, and, as, at, but, by, for, in, nor, of, on, or, the, to -->
+<!-- and up, which are usually not capitalized unless they are the first or -->
+<!-- last word of the caption. Table text will default to \footnotesize as -->
+<!-- the IEEE normally uses this smaller font for tables. -->
+<!-- The \label must come after \caption as always. -->
+
+<!-- \begin{table}[!t] -->
+<!-- % increase table row spacing, adjust to taste -->
+<!-- \renewcommand{\arraystretch}{1.3} -->
+<!-- if using array.sty, it might be a good idea to tweak the value of -->
+<!-- \extrarowheight as needed to properly center the text within the cells -->
+<!-- \caption{An Example of a Table} -->
+<!-- \label{table_example} -->
+<!-- \centering -->
+<!-- % Some packages, such as MDW tools, offer better commands for making tables -->
+<!-- % than the plain LaTeX2e tabular which is used here. -->
+<!-- \begin{tabular}{|c||c|} -->
+<!-- \hline -->
+<!-- One & Two\\ -->
+<!-- \hline -->
+<!-- Three & Four\\ -->
+<!-- \hline -->
+<!-- \end{tabular} -->
+<!-- \end{table} -->
+
+
+<!-- Note that the IEEE does not put floats in the very first column -->
+<!-- - or typically anywhere on the first page for that matter. Also, -->
+<!-- in-text middle ("here") positioning is typically not used, but it -->
+<!-- is allowed and encouraged for Computer Society conferences (but -->
+<!-- not Computer Society journals). Most IEEE journals/conferences use -->
+<!-- top floats exclusively.  -->
+<!-- Note that, LaTeX2e, unlike IEEE journals/conferences, places -->
+<!-- footnotes above bottom floats. This can be corrected via the -->
+<!-- \fnbelowfloat command of the stfloats package. -->
+
+
+Conclusion
+============
+The conclusion goes here.
+
+<!-- conference papers do not normally have an appendix -->
+
+Acknowledgment {#acknowledgment}
+==============
+
+The authors would like to thank...
+
+Bibliography styles
+===================
+
+Here are two sample references: @Feynman1963118 [@Dirac1953888].
+
+\newpage
+References {#references .numbered}
+==========

data/examples/latex_templates/Test-ieee_article/mybibfile.bib

@@ -0,0 +1,20 @@
+@article{Dirac1953888,
+  title   = "The lorentz transformation and absolute time",
+  journal = "Physica",
+  volume  = "19",
+  number  = "1--12",
+  pages   = "888--896",
+  year    = "1953",
+  doi     = "10.1016/S0031-8914(53)80099-6",
+  author  = "P.A.M. Dirac"
+}
+
+@article{Feynman1963118,
+  title   = "The theory of a general quantum system interacting with a linear dissipative system",
+  journal = "Annals of Physics ",
+  volume  = "24",
+  pages   = "118--173",
+  year    = "1963",
+  doi     = "10.1016/0003-4916(63)90068-X",
+  author  = "R.P Feynman and F.L {Vernon Jr.}"
+}

data/examples/latex_templates/Test-rjournal_article/RJournal.sty

@@ -0,0 +1,335 @@
+% Package `RJournal' to use with LaTeX2e
+% Copyright (C) 2010 by the R Foundation
+% Copyright (C) 2013 by the R Journal
+%
+% Originally written by Kurt Hornik and Friedrich Leisch with subsequent 
+% edits by the editorial board
+
+\NeedsTeXFormat{LaTeX2e}[1995/12/01]
+\ProvidesPackage{RJournal}[2013/08/27 v0.13 RJournal package]
+
+\RequirePackage{tikz}
+
+% Overall page layout, fonts etc -----------------------------------------------
+
+% Issues of of \emph{The R Journal} are created from the standard \LaTeX{}
+% document class \pkg{report}. 
+
+\RequirePackage{geometry}
+\geometry{a4paper, 
+   textwidth=14cm, top=1cm, bottom=1cm,
+   includehead,includefoot,centering,
+   footskip=1.5cm}
+\raggedbottom
+
+\RequirePackage{fancyhdr}
+\fancyhead{}
+\fancyheadoffset{2cm} 
+\fancyhead[L]{\textsc{\RJ@sectionhead}}
+\fancyhead[R]{\thepage}
+\fancyfoot{}
+\fancyfoot[L]{The R Journal Vol. \RJ@volume/\RJ@number, \RJ@month}
+\fancyfoot[R]{ISSN 2073-4859}
+\pagestyle{fancy}
+
+% We use the following fonts (all with T1 encoding):
+% 
+%   rm   & palatino
+%   tt   & inconsolata
+%   sf   & helvetica
+%   math & palatino
+
+\RequirePackage{microtype}
+
+\RequirePackage[scaled=0.92]{helvet}
+\RequirePackage{palatino,mathpazo}
+\RequirePackage[scaled=1.02]{inconsolata}
+\RequirePackage[T1]{fontenc}
+
+\RequirePackage[hyphens]{url}
+\RequirePackage[pagebackref]{hyperref}
+\renewcommand{\backref}[1]{[p#1]}
+
+% Dark blue colour for all links
+\RequirePackage{color}
+\definecolor{link}{rgb}{0.45,0.51,0.67}
+\hypersetup{
+  colorlinks,%
+  citecolor=link,%
+  filecolor=link,%
+  linkcolor=link,%
+  urlcolor=link
+}
+
+% Give the text a little room to breath
+\setlength{\parskip}{3pt}
+\RequirePackage{setspace}
+\setstretch{1.05}
+
+% Issue and article metadata ---------------------------------------------------
+
+% Basic front matter information about the issue: volume, number, and
+% date.
+
+\newcommand{\volume}[1]{\def\RJ@volume{#1}}
+\newcommand{\volnumber}[1]{\def\RJ@number{#1}}
+\renewcommand{\month}[1]{\def\RJ@month{#1}}
+\renewcommand{\year}[1]{\def\RJ@year{#1}}
+
+
+% Individual articles correspond to
+% chapters, and are contained in |article| environments.  This makes it
+% easy to have figures counted within articles and hence hyperlinked
+% correctly.
+
+% An article has an author, a title, and optionally a subtitle.  We use
+% the obvious commands for specifying these. Articles will be put in certain
+% journal sections, named by \sectionhead.
+
+\newcommand  {\sectionhead}  [1]{\def\RJ@sectionhead{#1}}
+\renewcommand{\author}       [1]{\def\RJ@author{#1}}
+\renewcommand{\title}        [1]{\def\RJ@title{#1}}
+\newcommand  {\subtitle}     [1]{\def\RJ@subtitle{#1}}
+
+% Control appearance of titles: make slightly smaller than usual, and 
+% suppress section numbering. See http://tex.stackexchange.com/questions/69749
+% for why we don't use \setcounter{secnumdepth}{-1} 
+
+\usepackage[medium]{titlesec}
+\usepackage{titletoc}
+\titleformat{\section}   {\normalfont\large\bfseries}{}{0em}{}
+\titleformat{\subsection}{\normalfont\normalsize\bfseries}{}{0em}{}
+\titlecontents{chapter}   [0em]{}{}{}{\titlerule*[1em]{.}\contentspage}
+
+% Article layout ---------------------------------------------------------------
+
+% Environment |article| clears the article header information at its beginning. 
+% We use |\FloatBarrier| from the placeins package to keep floats within
+% the article.
+\RequirePackage{placeins}
+\newenvironment{article}{\author{}\title{}\subtitle{}\FloatBarrier}{\FloatBarrier}
+
+% Refereed articles should have an abstract, so we redefine |\abstract| to
+% give the desired style
+
+\renewcommand{\abstract}[1]{%
+\setstretch{1}%
+\noindent%
+\small%
+\textbf{Abstract} #1 
+}
+
+% The real work is done by a redefined version of |\maketitle|.  Note
+% that even though we do not want chapters (articles) numbered, we
+% need to increment the chapter counter, so that figures get correct
+% labelling.
+
+\renewcommand{\maketitle}{%
+\noindent
+  \chapter{\RJ@title}\refstepcounter{chapter}
+  \ifx\empty\RJ@subtitle
+  \else
+    \noindent\textbf{\RJ@subtitle}
+    \par\nobreak\addvspace{\baselineskip}
+  \fi
+  \ifx\empty\RJ@author
+  \else
+    \noindent\textit{\RJ@author}
+    \par\nobreak\addvspace{\baselineskip}
+  \fi
+  \@afterindentfalse\@nobreaktrue\@afterheading
+}
+
+% Now for some ugly redefinitions.  We do not want articles to start a
+% new page. (Actually, we do, but this is handled via explicit
+% \newpage
+%
+% The name@of@eq is a hack to get hyperlinks to equations to work
+% within each article, even though there may be multiple eq.(1)
+%    \begin{macrocode}
+\renewcommand\chapter{\secdef\RJ@chapter\@schapter}
+\providecommand{\nohyphens}{%
+  \hyphenpenalty=10000\exhyphenpenalty=10000\relax}
+\newcommand{\RJ@chapter}{%
+  \edef\name@of@eq{equation.\@arabic{\c@chapter}}%
+  \renewcommand{\@seccntformat}[1]{}%
+  \@startsection{chapter}{0}{0mm}{%
+    -2\baselineskip \@plus -\baselineskip \@minus -.2ex}{\p@}{%
+    \phantomsection\normalfont\huge\bfseries\raggedright}}
+
+% Book reviews should appear as sections in the text and in the pdf bookmarks,
+% however we wish them to appear as chapters in the TOC. Thus we define an
+% alternative to |\maketitle| for reviews.
+\newcommand{\review}[1]{
+  \pdfbookmark[1]{#1}{#1}
+  \section*{#1}
+  \addtocontents{toc}{\protect\contentsline{chapter}{#1}{\thepage}{#1.1}}
+}
+
+% We want bibliographies as starred sections within articles.
+% 
+\RequirePackage[sectionbib,round]{natbib}
+\bibliographystyle{abbrvnat}
+
+% Equations, figures and tables are counted within articles, but we do
+% not show the article number. For equations it becomes a bit messy to avoid
+% having hyperref getting it wrong. 
+
+% \numberwithin{equation}{chapter}
+\renewcommand{\theequation}{\@arabic\c@equation}
+\renewcommand{\thefigure}{\@arabic\c@figure}
+\renewcommand{\thetable}{\@arabic\c@table}
+
+% Issue layout -----------------------------------------------------------------
+
+% Need to provide our own version of |\tableofcontents|. We use the
+% tikz package to get the rounded rectangle. Notice that |\section*|
+% is really the same as |\chapter*|.
+\renewcommand{\contentsname}{Contents}
+\renewcommand\tableofcontents{%
+   \vspace{1cm}
+   \section*{\contentsname}
+   { \@starttoc{toc} }
+}
+
+\renewcommand{\titlepage}{%
+  \thispagestyle{empty}
+  \hypersetup{
+    pdftitle={The R Journal Volume \RJ@volume/\RJ@number, \RJ@month \RJ@year},%
+    pdfauthor={R Foundation for Statistical Computing},%
+  }
+  \noindent
+  \begin{center}
+    \fontsize{50pt}{50pt}\selectfont
+    The \raisebox{-8pt}{\includegraphics[height=77pt]{Rlogo-4}}\hspace{10pt}
+    Journal
+  
+  \end{center}
+  {\large \hfill Volume \RJ@volume/\RJ@number, \RJ@month{} \RJ@year \quad}
+
+  \rule{\textwidth}{1pt}
+  \begin{center}
+    {\Large A peer-reviewed, open-access publication of the \\
+    R Foundation for Statistical Computing}
+  \end{center}
+
+  % And finally, put in the TOC box. Note the way |tocdepth| is adjusted
+  % before and after producing the TOC: thus, we can ensure that only
+  % articles show up in the printed TOC, but that in the PDF version,
+  % bookmarks are created for sections and subsections as well (provided
+  % that the non-starred forms are used).
+  \setcounter{tocdepth}{0}
+  \tableofcontents
+  \setcounter{tocdepth}{2}
+  \clearpage
+}
+
+% Text formatting --------------------------------------------------------------
+
+\newcommand{\R}{R}
+\newcommand{\address}[1]{\addvspace{\baselineskip}\noindent\emph{#1}}
+\newcommand{\email}[1]{\href{mailto:#1}{\normalfont\texttt{#1}}}
+
+% Simple font selection is not good enough.  For example, |\texttt{--}|
+% gives `\texttt{--}', i.e., an endash in typewriter font.  Hence, we
+% need to turn off ligatures, which currently only happens for commands
+% |\code| and |\samp| and the ones derived from them.  Hyphenation is
+% another issue; it should really be turned off inside |\samp|.  And
+% most importantly, \LaTeX{} special characters are a nightmare.  E.g.,
+% one needs |\~{}| to produce a tilde in a file name marked by |\file|.
+% Perhaps a few years ago, most users would have agreed that this may be
+% unfortunate but should not be changed to ensure consistency.  But with
+% the advent of the WWW and the need for getting `|~|' and `|#|' into
+% URLs, commands which only treat the escape and grouping characters
+% specially have gained acceptance
+
+\DeclareRobustCommand\code{\bgroup\@noligs\@codex}
+\def\@codex#1{\texorpdfstring%
+{{\normalfont\ttfamily\hyphenchar\font=-1 #1}}%
+{#1}\egroup}
+\newcommand{\kbd}[1]{{\normalfont\texttt{#1}}}
+\newcommand{\key}[1]{{\normalfont\texttt{\uppercase{#1}}}}
+\DeclareRobustCommand\samp{`\bgroup\@noligs\@sampx}
+\def\@sampx#1{{\normalfont\texttt{#1}}\egroup'}
+\newcommand{\var}[1]{{\normalfont\textsl{#1}}}
+\let\env=\code
+\newcommand{\file}[1]{{`\normalfont\textsf{#1}'}}
+\let\command=\code
+\let\option=\samp
+\newcommand{\dfn}[1]{{\normalfont\textsl{#1}}}
+% \acronym is effectively disabled since not used consistently
+\newcommand{\acronym}[1]{#1}
+\newcommand{\strong}[1]{\texorpdfstring%
+{{\normalfont\fontseries{b}\selectfont #1}}%
+{#1}}
+\let\pkg=\strong
+\newcommand{\CRANpkg}[1]{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}%
+\let\cpkg=\CRANpkg
+\newcommand{\ctv}[1]{\href{http://CRAN.R-project.org/view=#1}{\emph{#1}}}
+\newcommand{\BIOpkg}[1]{\href{http://www.bioconductor.org/packages/release/bioc/html/#1.html}{\pkg{#1}}}
+
+% Example environments ---------------------------------------------------------
+\RequirePackage{fancyvrb}
+\RequirePackage{alltt}
+
+\DefineVerbatimEnvironment{example}{Verbatim}{}
+\renewenvironment{example*}{\begin{alltt}}{\end{alltt}}
+
+% Support for output from Sweave, and generic session style code
+% These used to have fontshape=sl for Sinput/Scode/Sin, but pslatex
+% won't use a condensed font in that case.
+
+\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontsize=\small}
+\DefineVerbatimEnvironment{Soutput}{Verbatim}{fontsize=\small}
+\DefineVerbatimEnvironment{Scode}{Verbatim}{fontsize=\small}
+\DefineVerbatimEnvironment{Sin}{Verbatim}{fontsize=\small}
+\DefineVerbatimEnvironment{Sout}{Verbatim}{fontsize=\small}
+\newenvironment{Schunk}{}{}
+
+% Mathematics ------------------------------------------------------------------
+
+% The implementation of |\operatorname| is similar to the mechanism
+% \LaTeXe{} uses for functions like sin and cos, and simpler than the
+% one of \AmSLaTeX{}.  We use |\providecommand| for the definition in
+% order to keep the one of the \pkg{amstex} if this package has
+% already been loaded.
+%    \begin{macrocode}
+\providecommand{\operatorname}[1]{%
+  \mathop{\operator@font#1}\nolimits}
+\RequirePackage{amsfonts}
+
+\renewcommand{\P}{%
+  \mathop{\operator@font I\hspace{-1.5pt}P\hspace{.13pt}}}
+\newcommand{\E}{%
+  \mathop{\operator@font I\hspace{-1.5pt}E\hspace{.13pt}}}
+\newcommand{\VAR}{\operatorname{var}}
+\newcommand{\COV}{\operatorname{cov}}
+\newcommand{\COR}{\operatorname{cor}}
+
+% Figures ----------------------------------------------------------------------
+
+\RequirePackage[font=small,labelfont=bf]{caption}
+
+% Wide environments for figures and tables -------------------------------------
+\RequirePackage{environ}
+
+% An easy way to make a figure span the full width of the page
+\NewEnviron{widefigure}[1][]{
+\begin{figure}[#1]
+\advance\leftskip-2cm
+\begin{minipage}{\dimexpr\textwidth+4cm\relax}%
+  \captionsetup{margin=2cm}
+  \BODY
+\end{minipage}%
+\end{figure}
+}
+
+\NewEnviron{widetable}[1][]{
+\begin{table}[#1]
+\advance\leftskip-2cm
+\begin{minipage}{\dimexpr\textwidth+4cm\relax}%
+  \captionsetup{margin=2cm}
+  \BODY
+\end{minipage}%
+\end{table}
+}