A sample demo of R Markdown with pandoc

demo-rmd-pandoc.rmd

% A little demonstration of R Markdown and Pandoc
% Author
% Date

``` {r setup, cache=FALSE, include=FALSE}                                                                                      
opts_knit$set(aliases=c(h='fig.height', w='fig.width',                                                                         
                cap='fig.cap', scap='fig.scap'))                                                                               
opts_knit$set(eval.after = c('fig.cap','fig.scap'))                                                                            
knit_hooks$set(document = function(x) {                                                                                        
  gsub('(\\\\end\\{knitrout\\}[\n]+)', '\\1\\\\noindent ', x)                                                                  
})                                                                                                                             
options(width=80)                                                                                                              
library(latticeExtra)                                                                                                          
trellis.par.set(custom.theme.2())                                                                                              
```


## A little simulation

Here is a basic setup to illustrate linear regression. Let's generate some data like $y = 1.1+0.8x+\varepsilon$, where $\varepsilon\sim\mathcal{N}(0;1)$:

``` {r simulate, cache=TRUE}                                                                                                   
n <- 40                                                                                                                        
x <- runif(n, min=0, max=10)                                                                                                   
y <- 1.1 + 0.8*x + rnorm(n)                                                                                                    
```

and a basic scatter display of the artificial dataset

``` {r display, dev='quartz_png', cap='Figure caption goes here.'}                                                                                      
xyplot(y ~ x, type=c("p","g","r"))                                                                                             
```

Here is model output from `lm`:

``` {r estimate, echo=FALSE}                                                                                                   
summary(m <- lm(y ~ x))                                                                                                        
```

Of course, we can do many other fancy things, but see
**knitr**
[Chunk options and package options](http://yihui.name/knitr/options).

For example, if you have the `Hmisc` package (you should really have it),
you can try the following:

``` {r setup_birthwt, include=FALSE}                                                                                           
data(birthwt, package="MASS")                                                                                                  
birthwt <- within(birthwt, {                                                                                                   
  low <- factor(low, labels=c("No","Yes"))                                                                                     
  race <- factor(race, labels=c("White","Black","Other"))                                                                      
  smoke <- factor(smoke, labels=c("No","Yes"))                                                                                 
  ui <- factor(ui, labels=c("No","Yes"))                                                                                       
  ht <- factor(ht, labels=c("No","Yes"))                                                                                       
})                                                                                                                             
```

``` {r summary_birthwt, message=FALSE}                                                                                         
library(Hmisc)              
f <- function(x, digits=1) c(mean=round(colMeans(x), digits=digits), range=paste(apply(x, 2, range), collapse="-"))                                                                                                   
summary(low ~ ., data=birthwt, method="reverse",                                                                               
        overall=TRUE)                                                                                                          
summary(bwt ~ ., data=birthwt, fun=f)                                                                                                 
summary(low ~ smoke + ht + ui, data=birthwt, fun=table)                                                                        
```

## More with Pandoc

Pandoc allows to customize HTML or PDF output through default or custom
theme. It is also easy to include bibliographic entries the usual way,
e.g. `@wickham11` will read @wickham11.


## References

footer.html

</body>
</html>

header.html

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">

<!-- add this if you want to use a custom JS -->
<!--#include virtual="mathjax.html"-->

</head>
<body>

Makefile

RMDFILE=demo-rmd-pandoc
PANDOC=~/.cabal/bin/pandoc

all:
	Rscript -e "require(knitr); require(markdown); knit('$(RMDFILE).rmd', '$(RMDFILE).md'); purl('$(RMDFILE).rmd')"
	${PANDOC} --mathjax --toc -B header.html -A footer.html --bibliography refs.bib --css markdown.css -s $(RMDFILE).md -o $(RMDFILE).html
 

refs.bib

@Article{wickham11,
  author =       {Wickham, H},
  title =        {The Split-Apply-Combine Strategy for Data Analysis},
  journal =      {Journal of Statistical Software},
  year =         2011,
  volume =       40,
  number =       1}

Tested with R version 2.15.1 (2012-06-22) and

$ pandoc --version
pandoc 1.9.3
Compiled with citeproc-hs 0.3.4, texmath 0.6.0.3, highlighting-kate 0.5.0.6.

Note: I have some Md formatting issue with latest release of pandoc (1.10).