2.3 Convert R Markdown to R script

When you want to extract all R code from an R Markdown document, you can call the function knitr::purl(). Below is a simple Rmd example with the filename purl.Rmd:

---
title: Use `purl()` to extract R code
---

The function `knitr::purl()` extracts R code chunks from
a **knitr** document and save the code to an R script.

Below is a simple chunk:

```{r, simple, echo=TRUE}
1 + 1
```

Inline R expressions like `r 2 * pi` are ignored by default.

If you do not want certain code chunks to be extracted,
you can set the chunk option `purl = FALSE`, e.g.,

```{r, ignored, purl=FALSE}
x = rnorm(1000)
```

If we call knitr::purl("purl.Rmd"), it generates the following R script (with the filename purl.R by default):

## ---- simple, echo=TRUE------------------------------
1 + 1

The above R script contains the chunk options in a comment. If you want pure R code, you may call knitr::purl() with the argument documentation = 0, which will generate the R script below:

1 + 1

If you want to retain all the text, you may use the argument documentation = 2, which generates the R script below:

#' ---
#' title: Use `purl()` to extract R code
#' ---
#' 
#' The function `knitr::purl()` extracts R code chunks from
#' a **knitr** document and save the code to an R script.
#' 
#' Below is a simple chunk:
#' 
## ---- simple, echo=TRUE------------------------------
1 + 1

#' 
#' Inline R expressions like `r 2 * pi` are ignored by default.
#' 
#' If you do not want certain code chunks to be extracted,
#' you can set the chunk option `purl = FALSE`, e.g.,
#' 

Note that code chunks with the option purl = FALSE will be excluded in the R script.

Inline R expressions are ignored by default. If you want to include them in the R script, you need to set the global R option options(knitr.purl.inline = TRUE) before calling knitr::purl().