Source code

After compiling

Source code

After compiling

Early stage – Sweave

• To "weave" S
• Developed by R Core, very powerful

Today – knitr

• To "knit" R
• Pronounced as "neater", and neater indeed
• Developed by Yihui Xie, even more powerful (almost surely)
• http://yihui.name/knitr

• Default option, show both source code and output

<<>>=
x <- seq(1, 6, by = 0.5)
x
sin(x)
@

• Show R source code only

<<eval=FALSE>>=
@

• Show code output only

<<echo=FALSE>>=
@

• Whether to format the code or not

<<tidy=FALSE>>=
x<-                 seq(1,6,
    by=0.5)
x
@

• Only evaluate the code, do not show anything. Mainly used to create variables for later use.

<<include=FALSE>>=
dat = rnorm(100)
@

• Figure width and height (in R side)

<<fig.width=6, fig.height=6>>=
plot(density(dat))
@

• Figure width and height (in output document side)

<<out.width='0.7\\textwidth'>>=
plot(density(dat))
@

• Alignment and caption

<<fig.align='center', fig.cap="A density plot">>=
plot(density(dat))
@

• Headers

## Methodology 
In this section we introduce our methodology.

### Algorithm
The algorithm is blablabla...

### Simulation
Now we show our simulation result.

• Similar to \section{} and \subsection{} in \(\LaTeX\)

• Decorations (bold, italic, etc.)

You should **NEVER** claim to _accept_ a null hypothesis

You just say **_do not reject_**

• Rendered result

You should NEVER claim to accept a null hypothesis

You just say do not reject

• Code

There is some inline code: `print(x)`

And code blocks:
```
x <- rnorm(100)
summary(x)
```

• Rendered result

There is some inline code: print(x)

And code blocks:

x <- rnorm(100)
summary(x)

• Math formulas

The series $\sum_i \frac{1}{n}$ is divergent, i.e.,
$$\sum_i \frac{1}{n}=\infty$$

• Rendered result

The series \(\sum_i \frac{1}{n}\) is divergent, i.e.,

\[\sum_i \frac{1}{n}=\infty\]

• Item lists

There are three kinds of lies:

- Lies
- Damned lies
- Statistics
    - Frequentists
    - Bayesian

There are three kinds of lies:

• Lies
• Damned lies
• Statistics
  • Frequentists
  • Bayesian

• Links and images

[A 5-minute tutorial of Markdown](http://goo.gl/JqhpOf)

The talk is boring, but please wake up! ![](images/tuzki31.gif)

• Rendered result

A 5-minute tutorial of Markdown

The talk is boring, but please wake up!

• 3-D interactive plots
  • Demo
• Animation
  • Demo
• Slides
  • Did I tell you this slide was written using Markdown+knitr?
• More data analysis reports at RPubs
• More visualization examples at Vistat

• Official website of knitr of knitr @ Yihui
• 100+ examples of knitr
• A 5-minute tutorial of Markdown
• Details about Markdown

Thanks to Yihui Xie, the creator of knitr, for creating this wonderful tool, and for providing me lots of help in using knitr.

Questions?