Knitr

Knitr is a engine having in mind dynamic report generation with R, a statistics-oriented programming language. This article explains how to add R code to your LaTeX document to generate a dynamic output.

In a standard LaTeX distribution you must have R set up in your operating system and run some special commands to compile it. ShareLaTeX can save you the trouble, knitr works out of the box.

Introduction

Documents that contain R code must be saved with the extension .Rtex, otherwise the code won't work. Let's see an example:

\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[english]{babel}

\begin{document}
You can type R commands in your \LaTeX{} document and they will be properly run and the output printed in the document.

<<>>=
# Create a sequence of numbers
X = 2:10

# Display basic statistical measures
summary(X)

@
\end{document}

As you see, the text in between the characters <<>>= and @ is R code, this code and its output is printed in a listing-like format.

This chunk of code can take some extra parameters to customize the dynamic output. See the next section.

  Open an example of the knitr package in ShareLaTeX

Chunks of code

A code block as the one presented in the previous section is usually called a chunk. You can set some extra options in knitr chunks. See the example below:

You can type R commands in your \LaTeX{} document and they will be properly run and the output printed in the document.

<<echo=FALSE, cache=TRUE>>=
# Create a sequence of numbers
X = 2:10

# Display basic statistical measures
summary(X)

@

There are three additional options passed inside << and >>.

echo=FALSE

This hides the code and only prints the output generated by R.

cache=TRUE

If cache is set to true the chunk is not run, only the objects generated by it. This saves time if the data in that chunk haven't changed. Note that the cache=TRUE option is not currently supported in ShareLaTeX, but it should work locally.

See the reference guide for more options.

  Open an example of the knitr package in ShareLaTeX

Inline commands

It is possible to access objects generated in a chunk and print them in-line.

You can type R commands in your \LaTeX{} document and they will be 
properly run and the output printed in the document.

<<echo=FALSE, cache=TRUE>>=
# Create a sequence of numbers
X = 2:10

# Display basic statistical measures
summary(X)

@

So, the mean of the data is $\Sexpr{mean(X)}$

The command \Sexpr{mean(X)} prints the output returned by the R code mean(X). Inside the braces any R command can be passed.

  Open an example of the knitr package in ShareLaTeX

Plots

Plots can also be added to a knitr document. See the next example

<<plot1, fig.pos="t", fig.height=4, fig.width=4, fig.cap="First plot">>=

xdata = read.csv(file="data.txt", head=TRUE,sep=" ")

hist(xdata$data, main="ShareLaTeX histogram", xlab="Data")

@

The figure \ref{fig:plot1} is simple histogram.

This histogram uses data stored in "data.txt", saved in the current working directory. A few figure-related options are passed to the chunk.

plot1

This is the label used to reference the plot. The prefix "fig:" is mandatory. You can see in the example that the figure is referenced with \ref{fig:plot1}.

fig.pos="t"

Positioning parameter. This is the same used in the figure environment.

fig.height=4, fig.width=4

Figure width and height

fig.cap="First plot"

Caption for the figure.

  Open an example of the knitr package in ShareLaTeX

External R scripts

You can import parts of an external R script into a knitr document. This is very helpful since is fairly common to write and debug the script in an external program prior to including it in your document. Let's see an example, suppose you need the next file to be included in you latex document:

## ---- myrcode1
# Create a sequence of numbers
 X = 2:10

## ---- myrcode2
# Display basic statistical measures
summary(X)

Notice the lines

## ---- myrcode1

These mark the beginning of a chunk of code and are mandatory if you want to use this script in your document.

The chunk below will not be printed

<<echo=FALSE, cache=FALSE>>=
read_chunk("mycode.R")
@

The code must show up here

<<myrcode2>>=

@

The first chunk is not printed, is only used to import the script with the command read_chunk("mycoder.R"), that's why the option echo=FALSE is set. Also, scripts mus not be cached. Once the script is imported, you can print a chunk using the label you set after ## ----. In this case it's myrcode2

  Open an example of the knitr package in ShareLaTeX

Reference guide

Some chunk options

• results. Changes the behaviour of the results generated by the R code, possible values are
  • markup Use LaTeX for format the output.
  • asis Prints raw results from R.
  • hold Holds the output results and to push them at the end of the chunk.
  • hide Hide results.

• echo. Whether to include the R source code. Can take other parameters, echo=2:3 prints only the second and third lines; echo=-2:-3 excludes the second and third lines only.

• cache. Whether to cache the code chunk. Possible values are TRUE and FALSE

• highlight. Whether to highlight the source code. Possible values are TRUE and FALSE

• background. Background colour of the chunk, rgb and HTML formats can be used, the default value is "#F7F7F7".

Further reading

For more information see

• Code Highlighting with minted
• Using colours in LaTeX
• plots in LaTeX
• Inserting Images
• Tables
• Positioning images and tables
• TikZ package
• Mathematical expressions
• the knitr web page
• the knitr package manual