Merge branch 'master' into knitr

- merged in CDSC branding from the master branch

diff --git a/paper_template/.gitignore b/paper_template/.gitignore
index 5504ab4b64f0476f77393d88b61806ab11a195a6..1ae77e62ae48f2cfa80856dfa14e4ee045c23dc8 100644 (file)
--- 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 0bca5740262c882c4324015fee6d543b687f1a61..d7e66787a590c04afec660cccd987cfe48bd9a4b 100644 (file)
--- 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 (file)
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 (file)
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 1a316cdca414f14f76caf424394da9b0c46f02c8..faf5f9c80567f8f1d805e591bafc7def448a0e69 100644 (file)
--- 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