Merge branch 'master' into knitr

Newer knitr injects \usepackage[]{xcolor} instead of \usepackage[]{color},
so the old hook never matched and dvipsnames colors (e.g. Blue) were undefined.

paper_template/.gitignore

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

paper_template/Makefile

@@ -1,11 +1,9 @@
 #!/usr/bin/make
 
-all: $(patsubst %.tex,%.pdf,$(wildcard *.tex)) 
+all: $(patsubst %.Rtex,%.pdf,$(wildcard *.Rtex)) 
 
-# use the following section for Rnw/knitr documents
+%.tex: %.Rtex
-# all: $(patsubst %.Rnw,%.pdf,$(wildcard *.Rnw))
+	Rscript -e "library(knitr); knit('$<')"
-# %.tex: %.Rnw
-#	Rscript -e "library(knitr); knit('$<')"
 
 %.pdf: %.tex 
 	latexmk -f -pdf $<
@@ -15,9 +13,9 @@ clean:
 	rm -f *.tmp *.run.xml
 	rm -f vc
 	rm -f *.bbl
-	# the following lines are useful for Rnw/knitr
+	# the following lines are useful for Rtex/knitr
-	# rm -rf cache/ figure/
+	rm -rf cache/ figure/
-	# rm -f *.tex
+	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/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

@@ -9,6 +9,20 @@
 
 \usepackage[utf8]{inputenc}
 \usepackage{wrapfig}
+
+<<init, echo=FALSE>>=
+knit_hooks$set(document = function(x) {
+  x <- sub('\\usepackage[]{color}',
+           '\\usepackage[usenames,dvipsnames]{color}', x, fixed = TRUE)
+  x <- sub('\\usepackage[]{xcolor}',
+           '\\usepackage[usenames,dvipsnames]{xcolor}', x, fixed = TRUE)
+  x
+})
+opts_chunk$set(fig.path="figures/knitr-")
+
+source("resources/preamble.R")
+@
+
 \usepackage[T1]{fontenc}
 \usepackage{textcomp}
 \usepackage[garamond]{mathdesign}
@@ -25,9 +39,7 @@
 % \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}
 
@@ -134,6 +146,15 @@ 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