3.4 Convert R Markdown to R script

3.4 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.,

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().