hand-merged knitr material

- branch is now knitrified
- added material to the gitignore for tex files

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
 /*.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
 
 #!/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))
 
 # 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 $<
 
 %.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 -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
 
 viewpdf: all
        evince *.pdf


@@ -27,4 +27,4 @@ vc:   resources/vc-git
 pdf: all
 
 .PHONY: clean all
 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.Rnw b/paper_template/text.Rnw
index a58ce9129e6821b96ef6d43542a745c3e0ee161e..1f38026e761982d040e11916f31f732fdcf27efe 100644 (file)
--- a/paper_template/text.Rnw
+++ b/paper_template/text.Rnw
@@ -10,6 +10,17 @@
 
 \usepackage[utf8]{inputenc}
 \usepackage{wrapfig}
 
 \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}
 \usepackage[T1]{fontenc}
 \usepackage{textcomp}
 \usepackage[garamond]{mathdesign}


@@ -26,9 +37,7 @@
 % \usepackage{endfloat}
 
 % import and customize urls
 % \usepackage{endfloat}
 
 % import and customize urls

-\usepackage[usenames,dvipsnames]{color}

 \usepackage[breaklinks]{hyperref}
 \usepackage[breaklinks]{hyperref}

-

 \hypersetup{colorlinks=true, linkcolor=Black, citecolor=Black, filecolor=Blue,
     urlcolor=Blue, unicode=true}
 
 \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}.
 
 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
 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