Reproducible Research

In this page we show how to create a minimal report using R + Latex + Markdown Resources. Lets create a minimal report from few R commands :

 
# loaddata
data(iris)

# summarydata
summary(iris)

# boxplot
boxplot(iris[,1]~iris[,5])

# table
table(iris[,5])

We can embbed those commands into a simple LaTeX file according to the example below :

 
\documentclass{article}

\title{Introduction to Reproducible Research in R}
\author{Bioinformatics Meeting}


\begin{document}

\maketitle

\section{Introduction}

This document contains a minimal example of reproducible research using R.

\section{Loading Data}
<<loaddata>>=
# loading data set
data(iris)
@


\section{Summary of Data}
<<summarydata>>=
# summary of the data set
summary(iris)
@

\section{A Box Plot}
<<boxplot>>=
# building a box plot
boxplot(iris$Sepal.Length~iris$Species)
@


\section{A Table}
 
<<table,results='asis'>>=
# loading xtable package
require(xtable)

# creating a table
tab<-table(iris$Species)

# buiding a table with all data
print(xtable(tab))
@
 
\section{Aditional Tips}

<<>>=
# let it commented
# purl("report.rnw")
# system("pandoc -s report.tex -o report.docx")
@

\end{document}

Save the commands above into a file called report.rnw and compile it into a LaTeX document according to the commands below.

library(knitr)
knit("report.rnw")

This will generate a .tex file that can be processed by a LaTex editor!

For linux and mac users, you can run :

> tex2pdf report.tex

to convert the result into a pdf