Merge branch 'master' into knitr

moving both versions from color to xcolor

assignment_template/HW1.tex

@@ -0,0 +1,67 @@
+\documentclass[12pt]{memoir}
+
+% article-1 and article-2 styles were originally based on kieran healy's
+% templates
+\usepackage{mako-mem}
+\chapterstyle{article-2}
+
+% with article-3 \chapterstyle, change to: \pagestyle{memo}
+\pagestyle{mako-mem}
+
+\usepackage[utf8]{inputenc}
+
+\usepackage[T1]{fontenc}
+\usepackage{textcomp}
+\usepackage[garamond]{mathdesign}
+
+\usepackage[letterpaper,left=1.65in,right=1.65in,top=1.3in,bottom=1.2in]{geometry}
+
+% packages i use in essentially every document
+\usepackage{graphicx}
+\usepackage{enumerate}
+
+% packages i use in many documents but leave off by default
+% \usepackage{amsmath, amsthm, amssymb}
+% \usepackage{dcolumn}
+% \usepackage{endfloat}
+
+% import and customize urls
+\usepackage[usenames,dvipsnames]{color}
+\usepackage[breaklinks]{hyperref}
+
+\hypersetup{colorlinks=true, linkcolor=Black, citecolor=Black, filecolor=Blue,
+    urlcolor=Blue, unicode=true}
+
+% add bibliographic stuff 
+% memoir function to take out of the space out of the whitespace lists
+\firmlists
+
+% LATEX NOTE: these lines will import vc stuff after running `make vc` which
+% will add version control information to the bottom of each page. This can be
+% useful for keeping track of which version of a document somebody has:
+% \input{vc}
+% \pagestyle{mako-mem-git}
+
+\begin{document}
+
+\setlength{\parskip}{4.5pt}
+% LATEX NOTE: Ideal linespacing is usually said to be between 120-140% the
+% typeface size. So, for 12pt (default in this document, we're looking for
+% somewhere between a 14.4-17.4pt \baselineskip.  Single; 1.5 lines; and Double
+% in MSWord are equivalent to ~117%, 175%, and 233%.
+
+\baselineskip 16pt
+
+\title{Title}
+\author{Nathan TeGrotenhuis\\
+        \href{mailto:nathante@uw.edu}{nathante@uw.edu}}
+\date{\today}
+
+\maketitle
+
+\section{Section}
+
+
+\end{document}
+
+%  LocalWords:  

assignment_template/Makefile

@@ -8,7 +8,7 @@ all: $(patsubst %.tex,%.pdf,$(wildcard *.tex))
 #	Rscript -e "library(knitr); knit('$<')"
 
 %.pdf: %.tex 
-	latexmk -f -lualatex $<
+	latexmk -f -pdf $<
 
 clean: 
 	latexmk -C *.tex

assignment_template/mako-mem.sty

@@ -21,6 +21,9 @@
 
 % >> article-1 << 
 \makechapterstyle{article-1}{
+ \renewcommand{\rmdefault}{ugm}
+ \renewcommand{\sfdefault}{phv}
+
  \setsecheadstyle{\large\scshape}
  \setsubsecheadstyle{\normalsize\itshape}
  \renewcommand{\printchaptername}{}
@@ -57,6 +60,9 @@
 
 % >> article-2 <<
 \makechapterstyle{article-2}{
+ \renewcommand{\rmdefault}{ugm}
+ \renewcommand{\sfdefault}{phv}
+
  \setsecheadstyle{\large\scshape} 
  \setsubsecheadstyle{\normalsize\itshape} 
  \setaftersubsubsecskip{-1em}
@@ -112,6 +118,9 @@
 
 % >> article-3 <<
 \makechapterstyle{article-3}{
+ \renewcommand{\rmdefault}{ugm}
+ \renewcommand{\sfdefault}{phv}
+
  \setsecheadstyle{\large\sffamily\bfseries\MakeUppercase} 
  \setsubsecheadstyle{\normalsize\itshape} 
  \setaftersubsubsecskip{-1em}

assignment_template/text.tex

@@ -8,9 +8,11 @@
 % with article-3 \chapterstyle, change to: \pagestyle{memo}
 \pagestyle{mako-mem}
 
-\usepackage{fontspec}
-\setmainfont{EB Garamond}
-\setsansfont{TeX Gyre Heros}
+\usepackage[utf8]{inputenc}
+
+\usepackage[T1]{fontenc}
+\usepackage{textcomp}
+\usepackage[garamond]{mathdesign}
 
 \usepackage[letterpaper,left=1.65in,right=1.65in,top=1.3in,bottom=1.2in]{geometry}
 

letter_template/Makefile

@@ -3,7 +3,7 @@
 all: $(patsubst %.tex,%.pdf,$(wildcard *.tex)) 
 
 %.pdf: %.tex 
-	latexmk -f -lualatex $<
+	latexmk -f -pdf $<
 
 clean: 
 	latexmk -C *.tex

letter_template/text.tex

@@ -1,8 +1,13 @@
 \documentclass[12pt]{letter}
 
-\usepackage{fontspec}
-\setmainfont{EB Garamond}
-\setsansfont{TeX Gyre Heros}
+\usepackage{ucs}
+\usepackage[utf8x]{inputenc}
+
+\usepackage[T1]{fontenc}
+\usepackage{textcomp}
+\renewcommand{\rmdefault}{ugm}
+\renewcommand{\sfdefault}{phv}
+\usepackage[garamond]{mathdesign}
 
 \usepackage[letterpaper,left=1.3in,right=1.3in,top=0.8in,bottom=0.8in]{geometry}
 

paper_template/.gitignore

@@ -13,3 +13,5 @@
 /*.ttt
 /*.bcf
 /*.run.xml
+/figures/*
+/*.tex

paper_template/Makefile

@@ -1,23 +1,21 @@
 #!/usr/bin/make
 
-all: $(patsubst %.tex,%.pdf,$(wildcard *.tex)) 
+all: $(patsubst %.Rtex,%.pdf,$(wildcard *.Rtex)) 
 
-# use the following section for Rnw/knitr documents
-# all: $(patsubst %.Rnw,%.pdf,$(wildcard *.Rnw))
-# %.tex: %.Rnw
-#	Rscript -e "library(knitr); knit('$<')"
+%.tex: %.Rtex
+	Rscript -e "library(knitr); knit('$<')"
 
 %.pdf: %.tex 
-	latexmk -f -lualatex $<
+	latexmk -f -pdf $<
 
 clean: 
 	latexmk -C *.tex
 	rm -f *.tmp *.run.xml
 	rm -f vc
 	rm -f *.bbl
-	# the following lines are useful for Rnw/knitr
-	# rm -rf cache/ figure/
-	# rm -f *.tex
+	# the following lines are useful for Rtex/knitr
+	rm -rf cache/ figure/
+	rm -f *.tex
 
 viewpdf: all
 	evince *.pdf
@@ -27,4 +25,4 @@ vc:	resources/vc-git
 pdf: all
 
 .PHONY: clean all
-# .PRECIOUS: %.tex
+.PRECIOUS: %.tex

paper_template/cdsc-memoir.sty

@@ -103,6 +103,10 @@
 % put a period after the section numbers
 \setsecnumformat{\csname the#1\endcsname.\enspace}
 
+% set fonts to garamond and helvetica
+\renewcommand{\rmdefault}{ugm}
+\renewcommand{\sfdefault}{phv}
+
 % material shared between the two modes
 
 \setsubsecheadstyle{\normalsize\itshape} 

paper_template/resources/preamble.R

@@ -0,0 +1,50 @@
+bold <- function(x) {paste('{\\textbf{',x,'}}', sep ='')}
+gray <- function(x) {paste('{\\textcolor{gray}{',x,'}}', sep ='')}
+wrapify <- function (x) {paste("{", x, "}", sep="")}
+
+# load("knitr_data.RData"); now broken up into small files so we'll bring 'em all in together
+r <- do.call("c", lapply(paste("knitr_rdata/", list.files("knitr_rdata"), sep=""),
+                         function (x) {load(x); return(r)}))
+
+attach(r)
+
+f <- function (x) {formatC(x, format="d", big.mark=',')}
+
+format.percent <- function(x) {paste(f(x*100),"\\%",sep='')}
+
+format.day.ordinal <- function(x) {
+    day <- format(x,format="%d")
+    daylast <- substr(day,nchar(day),nchar(day))
+    dayfirst <- substr(day,1,1)
+    if(dayfirst == '0')
+        day = daylast
+
+    if( daylast == "1")
+        day <- paste0(day,"st")
+    else if(daylast == "2")
+        day <- paste0(day,"nd")
+    else if (daylast == "3")
+        day <- paste0(day,"rd")
+    else
+        day <- paste0(day,"th")
+        
+    return(day)
+}
+
+format.month <- function(x){
+    return( format(x,format='%B %Y'))
+}
+
+format.date <- function(x) {
+    return(paste(format(x,format = '%B'),format.day.ordinal(x),format(x,format='%Y'),sep=' '))
+}
+
+format.pvalue <- function (x, digits=3) {
+    threshold <- 1*10^(-1*digits)
+    x <- round(x, digits)
+    if (x < threshold) {
+        return(paste("p<", threshold, sep=""))
+    } else {
+        return(paste("p=", x, sep=""))
+    }
+}

paper_template/text.Rtex

@@ -7,11 +7,24 @@
 % \published tag
 \chapterstyle{cdsc-article}
 
-\usepackage{fontspec}
-\setmainfont{EB Garamond}
-\setsansfont{TeX Gyre Heros}
+\usepackage[utf8]{inputenc}
 \usepackage{wrapfig}
 
+<<init, echo=FALSE>>=
+knit_hooks$set(document = function(x) {
+  x <- sub('\\usepackage[]{xcolor}',
+           '\\usepackage[dvipsnames]{xcolor}', x, fixed = TRUE)
+  x
+})
+opts_chunk$set(fig.path="figures/knitr-")
+
+source("resources/preamble.R")
+@
+
+\usepackage[T1]{fontenc}
+\usepackage{textcomp}
+\usepackage[garamond]{mathdesign}
+
 \usepackage[letterpaper,left=1.65in,right=1.65in,top=1.3in,bottom=1.2in]{geometry}
 
 % packages i use in essentially every document
@@ -26,7 +39,6 @@
 % import and customize urls
 \usepackage[dvipsnames]{xcolor}
 \usepackage[breaklinks]{hyperref}
-
 \hypersetup{colorlinks=true, linkcolor=Black, citecolor=Black, filecolor=Blue,
     urlcolor=Blue, unicode=true}
 
@@ -133,6 +145,15 @@ brown fox jumps over the lazy dog.  The quick brown fox jumps over the
 lazy dog.  The quick brown fox jumps over the lazy dog.  The quick brown
 fox jumps over the lazy dog \citep{989866}.
 
+\begin{table}
+  \centering
+<<test_table, echo=FALSE>>=
+kable(form.copy, format="latex")
+@
+\caption{This is a test table. There are \Sexpr{f(nrow(form.copy))} rows in the table.}
+\label{tab:test}
+\end{table}
+
 The quick brown fox jumps over the lazy dog.  The quick brown fox jumps
 over the lazy dog.  The quick brown fox jumps over the lazy dog.  The
 quick brown fox jumps over the lazy dog.  The quick brown fox jumps over

poster_template/main.tex

@@ -88,13 +88,13 @@
 \usepackage{url}
 % \usepackage{dcolumn}
 % \usepackage{booktabs}
-% bibliography stuff — uncomment these if you load biblatex
-% \DeclareLanguageMapping{american}{american-apa}
-% \defbibheading{secbib}[\bibname]{%
-%   \section{#1}%
-%   \markboth{#1}{#1}%
-%   \baselineskip 14.2pt%
-%   \prebibhook}
+% bibliography stuff
+\DeclareLanguageMapping{american}{american-apa}
+\defbibheading{secbib}[\bibname]{%
+  \section{#1}%
+  \markboth{#1}{#1}%
+  \baselineskip 14.2pt%
+  \prebibhook}
 
 \def\citepos#1{\citeauthor{#1}'s (\citeyear{#1})}
 \def\citespos#1{\citeauthor{#1}' (\citeyear{#1})}