Code chunks

Enough about markdown, let's get to the fun part and include some code! Look at the last code chunk in the template R Markdown document that you just created, as an example:

```{r pressure, echo = FALSE}
plot(pressure)
```

The R code is surrounded by: ```{r} and ```. The r indicates that the code chunk contains R code (it is possible to add code chunks using other languages, e.g. Python). After that comes an optional chunk name, pressure in this case (this can be used to reference the code chunk as well as alleviate debugging). Last comes chunk options, separated by commas (in this case there is only one option: echo = FALSE).

Below are listed some useful chunk options related to evaluating and displaying code chunks in the final file:

• Go back to your template R Markdown document in RStudio and locate the cars code chunk.
• Add the option echo = FALSE:

```{r cars, echo = FALSE}
summary(cars)
```

• How do you think this will affect the rendered file? Press Knit and check if you were right.
• Remove the echo = FALSE option and add eval = FALSE instead:

```{r cars, eval = FALSE}
summary(cars)
```

• How do you think this will affect the rendered file? Press Knit and check if you were right.
• Remove the eval = FALSE option and add include = FALSE instead:

```{r cars, include = FALSE}
summary(cars)
```

There are also some chunk options related to plots:

• Go back to your template R Markdown document in RStudio and locate the pressure code chunk.
• Add the fig.width and fig.height options as below:

```{r pressure, echo = FALSE, fig.width = 6, fig.height = 4}
plot(pressure)
```

• Press Knit and look at the output. Can you see any differences?
• Now add a whole new code chunk to the end of the document. Give it the name pressure 2 (code chunks have to have unique names, or no name). Add the fig.width and out.width options like this:

```{r pressure 2, echo = FALSE, fig.width = 9, out.width = "560px"}
plot(pressure)
```

• Press Knit and look at the output. Notice the difference between the two plots? In the second chunk we have first plotted a figure that is a fair bit larger (9 inches wide) than that in the first chunk. Next we have down-sized it in the final output, using the out.width option (where we need to use a size metric recognized by the output format, in this case "560px" which works for HTML).

Have you noticed the first chunk?

```{r setup, include = FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

In this way we can set global chunk options, i.e. defaults for all chunks. In this example, echo will always be set to TRUE, unless otherwise specified in individual chunks.

It is also possible to create different types of interactive plots using R Markdown. You can see some examples of this here. If you want to try it out you can add the following code chunk to your document:

```{r}
library(networkD3)
data(MisLinks, MisNodes)
forceNetwork(Links = MisLinks, Nodes = MisNodes, Source = "source",
             Target = "target", Value = "value", NodeID = "name",
             Group = "group", opacity = 0.4)
```