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:

    1. ---
    2. title: Use `purl()` to extract R code
    3. ---
    5. The function `knitr::purl()` extracts R code chunks from
    6. a **knitr** document and save the code to an R script.
    8. Below is a simple chunk:
    10. ```{r, simple, echo=TRUE}
    11. 1 + 1
    12. ```
    14. Inline R expressions like `r 2 * pi` are ignored by default.
    16. If you do not want certain code chunks to be extracted,
    17. you can set the chunk option `purl = FALSE`, e.g.,
    19. ```{r, ignored, purl=FALSE}
    20. x = rnorm(1000)
    21. ```

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

    1. ## ----simple, echo=TRUE-------------------------------
    2. 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:

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

    1. #' ---
    2. #' title: Use `purl()` to extract R code
    3. #' ---
    4. #' 
    5. #' The function `knitr::purl()` extracts R code chunks from
    6. #' a **knitr** document and save the code to an R script.
    7. #' 
    8. #' Below is a simple chunk:
    9. #' 
    10. ## ----simple, echo=TRUE-------------------------------
    11. 1 + 1
    13. #' 
    14. #' Inline R expressions like `r 2 * pi` are ignored by default.
    15. #' 
    16. #' If you do not want certain code chunks to be extracted,
    17. #' you can set the chunk option `purl = FALSE`, e.g.,
    18. #'

    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().