Commit a2f9e7aa authored by Jeffrey Phillips Freeman's avatar Jeffrey Phillips Freeman 💥

updated directory structure and templates.

parent 295139d7
#!/bin/sh
for file in *.Rmd
do
Rscript -e "library(rmarkdown); rmarkdown::render('$file', 'pdf_document')"
done
for file in *.tex
do
pdflatex --shell-escape "$file"
done
% graphviz.sty
% by Mark Aufflick
% 2006-03-25
% mark@aufflick.com
% http://mark.aufflick.com/
%
% based on graphviz.tex by Derek Rayside 2003
% Modified by Mike Prentice (mjp44@buffalo.edu)
% 2011-02-21
% To use PDF output directly from dot
% dot -Tpdf
% Modified by Remi Dubot (remi.dubot@irit.fr)
% 2012-12-3
% To distinguish errors from tex and from dot.
% Report dot errors
% Indications for non english writers
% add the following lines to your preamble:
% \usepackage[pdftex]{graphicx}
% \usepackage{graphviz}
% parameters to \digraph:
% 1 - parameters for \includegraphics (optional; default value is "scale=1")
% 2 - name of the digraph
% 3 - body of the digraph
% parameters to \includedot
% 1 - parameters for \includegraphics (optional; default value is "scale=1")
% 2 - name of the dot file (w/out file extension, which must be `.dot')
% ASSUMES pdflatex
% If you are not using pdflatex, go back on an older version of this style.
% If you are not writing english, pay attention to your charset.
% If is not UTF-8, you may have to indicate your charset to dot with "-Gccharset=XXXX".
\ProvidesPackage{graphviz}
\newcommand{\includedot}[2][scale=1]{%
\ifnum\pdfshellescape=1
% Yes, enabled
\immediate\write18{bash -c "dot -Tpdf #2.dot -o #2.pdf 2> #2.log"}%
\IfFileExists{#2.pdf}
% the pdf exists: include it
{\includegraphics[#1]{#2}}
% the pdf was not created - show a hint
{ \fbox{ \begin{tabular}{l}
The file \texttt{#2.pdf} hasn't been created from
\texttt{#2.dot} yet. \\
We attempted to create it with:\\
`\texttt{dot -Tpdf #2.dot -o #2.pdf}' \\
but that seems not to have worked.\\
\texttt{dot} said : \\
"\texttt{\input{#2.log}}"
\end{tabular}}
}
\else
\fbox{ \begin{tabular}{l}
You need to execute `\texttt{pdflatex}' with the `\texttt{-shell-escape}' option.\\
This allows the graphviz package to execute the program dot.
\end{tabular}}
\fi
}
\newcommand{\digraph}[3][scale=1]{
\newwrite\dotfile
\immediate\openout\dotfile=#2.dot
\immediate\write\dotfile{digraph #2 {\string#3}}
\immediate\closeout\dotfile
\includedot[#1]{#2}
}
......@@ -5,7 +5,7 @@
% ---------------------------------------------------------------------
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{SyncleusWhite}[7/8/2013, v1.0]
\ProvidesClass{templates/syncleus-white}[7/8/2013, v1.0]
\RequirePackage{ifthen}
\RequirePackage{calc}
\AtEndOfClass{\RequirePackage{microtype}}
......@@ -20,7 +20,7 @@
% ---------------------------------------------------------------------
\RequirePackage[utf8]{inputenc}
\RequirePackage{amsmath,amsfonts,amssymb}
\RequirePackage{graphicx,xcolor}
\RequirePackage[pdftex]{graphicx,xcolor}
\RequirePackage[english]{babel}
\RequirePackage{booktabs}
\RequirePackage{eso-pic}
......
......@@ -4,9 +4,10 @@
\usepackage{mathtools}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{graphicx}
\usepackage{subcaption}
\usepackage{float}
\usepackage[pdftex]{graphicx}
\usepackage{./templates/graphviz}
\usepackage[$if(geometry)$$geometry$$else$left=2cm, right=2cm, top=2.25cm, bottom=2.25cm, headheight=13.6pt, letterpaper$endif$]{geometry}
......@@ -29,6 +30,8 @@ $if(draft)$\draft{$draft$}$endif$
\setlength{\parindent}{$if(indent)$$indent$$else$0pt$endif$}
\setlength{\parskip}{$if(parskip)$$parskip$$else$3mm$endif$}
\definecolor{color1}{RGB}{$if(title-color)$$title-color$$else$0,0,0$endif$}
\providecommand{\tightlist}{%
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
%----------------------------------------------------------------------------------------
% ARTICLE INFORMATION
......
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