From: Benjamin Mako Hill <mako@atdot.cc>
Date: Sat, 4 Aug 2018 18:22:33 +0000 (-0700)
Subject: Merge branch 'master' into knitr
X-Git-Url: https://code.communitydata.science/cdsc_tex.git/commitdiff_plain/54c07cb9f5ecf1e3c990801c150a9526ccb2c6b0?hp=2a0962338f4e2212b121747c82d7c2927912b3f6

Merge branch 'master' into knitr

- copied over the new scripts
---

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 0000000..c6f661f
Binary files /dev/null and b/paper_template/knitr_rdata/knitr_data.RData differ
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.tex b/paper_template/text.Rnw
similarity index 94%
rename from paper_template/text.tex
rename to paper_template/text.Rnw
index 1a316cd..faf5f9c 100644
--- a/paper_template/text.tex
+++ b/paper_template/text.Rnw
@@ -9,6 +9,17 @@
 
 \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}
@@ -25,9 +36,7 @@
 % \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 +143,15 @@ 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