Creating Notebooks from R Scripts
R Markdown provides an easy way to generate reports that include analysis, code, and results. However, if your code is in an R script rather than an R Markdown document you can still generate a report using the Compile Notebook command:
Compiling a notebook for an R script automatically generates an R Markdown document, executes it, and then writes the results as a standalone HTML file. You'll find the Compile Notebook command for R scripts both on the File menu as well as on the source editor toolbar.
A Simple Example
For example, compiling the following R script to an HTML notebook:
Results in a web page that looks like this:
Any images included in the HTML file are embedded, so the document can be easily distributed as standalone file.
Notebook Output Types
When you compile a notebook, you can choose from the three output types described below.
The default notebook output type is shown above. This type includes all R code in a single R Markdown code block and modifies two of the default knitr options:
- Disables code reformatting (so your code appears exactly as it did in the R source file).
- Disables prepending of ## to output blocks.
knitr stitch and spin
If you have knitr version 0.6 or higher, you can also choose to create a notebook by calling the
stitch function creates a report based on the template located in the knitr package directory at
misc/knitr-template.Rmd. It also automatically appends a call to
sessionInfo at the bottom of the script.
spin function takes a specially formatted R script and produces an R Markdown document. Roxygen style comments (i.e. lines starting with
#') are automatically turned into text and lines starting with
#+ are parsed as chunk options. The following is an example of an R script formatted for spinning: knitr spin example.