From ce30e1ac617c570564b72a6ab73b143061886b1a Mon Sep 17 00:00:00 2001
From: Benjamin Mako Hill <mako@atdot.cc>
Date: Sat, 4 Aug 2018 10:44:15 -0700
Subject: [PATCH] hand-merged knitr material

- branch is now knitrified
- added material to the gitignore for tex files
---
 paper_template/.gitignore                   |   2 +
 paper_template/Makefile                     |  12 ++---
 paper_template/knitr_rdata/knitr_data.RData | Bin 0 -> 239 bytes
 paper_template/resources/preamble.R         |  50 ++++++++++++++++++++
 paper_template/text.Rnw                     |  22 ++++++++-
 5 files changed, 78 insertions(+), 8 deletions(-)
 create mode 100644 paper_template/knitr_rdata/knitr_data.RData
 create mode 100644 paper_template/resources/preamble.R

diff --git a/paper_template/.gitignore b/paper_template/.gitignore
index 5504ab4..1ae77e6 100644
--- a/paper_template/.gitignore
+++ b/paper_template/.gitignore
@@ -13,3 +13,5 @@
 /*.ttt
 /*.bcf
 /*.run.xml
+/figures/*
+/*.tex
diff --git a/paper_template/Makefile b/paper_template/Makefile
index 0bca574..d7e6678 100644
--- a/paper_template/Makefile
+++ b/paper_template/Makefile
@@ -1,11 +1,11 @@
 #!/usr/bin/make
 
-all: $(patsubst %.tex,%.pdf,$(wildcard *.tex)) 
+all: $(patsubst %.Rnw,%.pdf,$(wildcard *.Rnw)) 
 
 # use the following section for Rnw/knitr documents
 # all: $(patsubst %.Rnw,%.pdf,$(wildcard *.Rnw))
-# %.tex: %.Rnw
-#	Rscript -e "library(knitr); knit('$<')"
+%.tex: %.Rnw
+	Rscript -e "library(knitr); knit('$<')"
 
 %.pdf: %.tex 
 	latexmk -f -pdf $<
@@ -16,8 +16,8 @@ clean:
 	rm -f vc
 	rm -f *.bbl
 	# the following lines are useful for Rnw/knitr
-	# rm -rf cache/ figure/
-	# rm -f *.tex
+	rm -rf cache/ figure/
+	rm -f *.tex
 
 viewpdf: all
 	evince *.pdf
@@ -27,4 +27,4 @@ vc:	resources/vc-git
 pdf: all
 
 .PHONY: clean all
-# .PRECIOUS: %.tex
+.PRECIOUS: %.tex
diff --git a/paper_template/knitr_rdata/knitr_data.RData b/paper_template/knitr_rdata/knitr_data.RData
new file mode 100644
index 0000000000000000000000000000000000000000..c6f661ff18711317039b8ace2d85522cc79fb2c8
GIT binary patch
literal 239
zcmV<L01*EliwFP!000000}FDAFye~fVqjokVqj(klFUFR3lorFWME<71kpu6QDLwE
z1G6w#Ap-*+5VP6uoCyN6>@ORGf&BvpFtC3N<v&XU1N%2;K;SG~-!>MB$t8QT>@S*o
zA6x!@p8cI}=c$css`d||{3jfSYA-9U+P`E|xvMX=0L?+Hd5O8H#XyDt*f9`6mgK~u
zBq*CLzn~-~H4j}|a!z6~OdCv)D<!ccQ7^3sXd;?&&Z7KsJ!G5MVBuj1V;I30#xRBn
pjA066m;s4@5Tlv?qgl?GmS2>smz-Zv2~ouG4*;}zvG0xn001@KV^jbD

literal 0
HcmV?d00001

diff --git a/paper_template/resources/preamble.R b/paper_template/resources/preamble.R
new file mode 100644
index 0000000..dbdc279
--- /dev/null
+++ b/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=""))
+    }
+}
diff --git a/paper_template/text.Rnw b/paper_template/text.Rnw
index a58ce91..1f38026 100644
--- a/paper_template/text.Rnw
+++ b/paper_template/text.Rnw
@@ -10,6 +10,17 @@
 
 \usepackage[utf8]{inputenc}
 \usepackage{wrapfig}
+
+<<init, echo=FALSE>>=
+knit_hooks$set(document = function(x) {
+  sub('\\usepackage[]{color}',
+'\\usepackage[usenames,dvipsnames]{color}', x, fixed = TRUE)
+})
+opts_chunk$set(fig.path="figures/knitr-")
+
+source("resources/preamble.R")
+@
+
 \usepackage[T1]{fontenc}
 \usepackage{textcomp}
 \usepackage[garamond]{mathdesign}
@@ -26,9 +37,7 @@
 % \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}
 
@@ -135,6 +144,15 @@ 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
-- 
2.39.2