R Notebooks

Execution Queue

When you execute code in a notebook, an indicator will appear in the gutter to show you execution progress.

Lines of code which have been sent to R are marked with dark green; lines which have not yet been sent to R are marked with light green.

If at least one chunk is waiting to be executed, you’ll see a progress meter appear in the editor’s status bar indicating the number of chunks remaining to be executed. You can click on this meter at any time to jump to the currently executing chunk.

When a chunk is waiting to execute, the Run button in its toolbar will change to a Queued icon. If you don’t want the chunk to run, you can click on the Queued icon to remove it from the execution queue.

Execution Environment

In general, when you execute code in a notebook chunk, it will do exactly the same thing as it would if that same code were typed into the console. There are however a few differences:

Output: The most obvious difference is that most forms of output produced from a notebook chunk are shown in the chunk output rather than e.g. the Viewer or Plots pane. Console output (including warnings and messages) appears both at the console and in the chunk output.

Working directory: The current working directory inside a notebook chunk is always the directory containing the notebook .Rmd file. This makes it easier to use relative paths inside notebook chunks, and also matches the behavior when knitting, making it easier to write code that works identically both interactively and in a standalone render.

You’ll get a warning if you try to change the working directory inside a notebook chunk, and the directory will revert back to the notebook’s directory once the chunk is finished executing. You can suppress this warning by using the warnings = FALSE chunk option.

If it’s necessary to execute notebook chunks in a different directory, you can change the working directory for all your chunks by using the knitr root.dir option. For instance, to execute all notebook chunks in the grandparent folder of the notebook:

knitr::opts_knit$set(root.dir = normalizePath("..")) 

This option is only effective when used inside the setup chunk. Note also that, as in knitr, the root.dir chunk option applies only to chunks; relative paths in Markdown are still relative to the notebook’s parent folder.

Warnings: Inside a notebook chunk, warnings are always displayed immediately rather than being held until the end, as in options(warn = 1).

Plots: Plots emitted from a chunk are rendered to match the width of the editor at the time the chunk was executed. The height of the plot is determined by the golden ratio. The plot’s display list is saved, too, and the plot is re-rendered to match the editor’s width when the editor is resized.

You can use the fig.width, fig.height, and fig.asp chunk options to manually specify the size of rendered plots in the notebook; you can also use knitr::opts_chunk$set(fig.width = ..., fig.height = ...) in the setup chunk to to set a default rendered size. Note however specifying a chunk size manually suppresses the generation of the display list, so plots with manually specified sizes will be resized using simple image scaling when the notebook editor is resized.

Executing Inline Chunks

An inline chunk is a chunk which is inline with the text rather than on its own line. For instance, “2 + 2 = `r 2 + 2`” will be rendered as “2 + 2 = 4”.

To execute an inline chunk in the notebook, put your cursor inside the chunk and press Ctrl + Shift + Enter (OS X: Cmd + Shift + Enter). As in the execution of ordinary chunks, the content of the chunk will be sent to the R console for evaluation. The results will appear in a small pop-up window next to the code:

In notebooks, inline R chunks can only produce text, not figures or other kinds of output. It’s also important that R code run inside inline chunks executes quickly and does not have side effects, as it’s executed whenever you save the notebook.

Executing External Chunks

Notebooks are typically self-contained. However, in some situations it’s preferable to re-use code from an R script as a notebook chunk, as in knitr’s code externalization. This can be done by using knitr::read_chunk in your notebook’s setup chunk, along with a special ## ---- chunkname annotation in the R file from which you intend to read code. Here is a minimal example:

example.Rmd

```{r setup}
knitr::read_chunk("example.R")
```

```{r chunk}
```

example.R

## ---- chunk
1 + 1

When you execute the empty chunk in the notebook, code from the external file will be inserted, and the results displayed inline, as though the chunk contained that code.

Managing Output

When code is executed in the notebook, its output appears beneath the code chunk that produced it. You can clear an individual chunk’s output by clicking the X in the upper right corner of the output, or collapse it by clicking the chevron.

It’s also possible to clear or collapse all of the output in the document at once using the Collapse All Output and Clear All Output commands; these commands are available on the gear menu in the editor toolbar.

If you want to fully reset the state of the notebook, the command Restart R and Clear All Output will do the job.

See Output Storage below for more information on where chunk output is saved.

Previewing Output

Ordinary R Markdown documents are “knit”, but notebooks are “previewed”. While the notebook preview looks similar to a rendered R Markdown document, the notebook preview does not execute any of your R code chunks; it simply shows you a rendered copy of the markdown in your document along with the most recent chunk output. This preview is generated automatically whenever you save the notebook (whether you are viewing it in RStudio or not); see the section beneath on the .nb.html file for details.

When html_notebook is the topmost (default) format in your YAML header, you’ll see a Preview button in the editor toolbar. Clicking it will show you the notebook preview:

If you have configured R Markdown previewing to use the Viewer pane (as illustrated above) then the preview will be automatically updated whenever you save your notebook.

Handling Errors

When an error occurs while a notebook chunk is executing:

1. Execution will stop; the remaining lines of that chunk (and any chunks that have not yet been run) will not be executed.
2. The editor will scroll to the error.
3. The line of code that caused the error will have a red indicator in the editor’s gutter.

If you want your notebook to keep running after an error, you can suppress the first two behaviors by specifying errors = TRUE in the chunk options.

Console Hiding

In most cases it shouldn’t be necessary to have the console open while using the notebook, as you can see all of the console output in the notebook itself. To preserve vertical space, the console will be automatically collapsed when you open a notebook or run a chunk in the notebook.

If you prefer not to have the console hidden when chunks are executed, uncheck Tools -> Global Options -> R Markdown -> Hide console automatically when executing notebook chunks.