Using knitr to create HTML slides and separate R code file

Question

Following on from this question... I am not sure where to set knitr option if I want to output a separate file of R code. The following does not provide the expected additional .R files in my working directory.

---
output: ioslides_presentation
---

```{r setup, include=FALSE}
library("knitr"); purl("myfile.rmd")
#library("knitr"); knit("test_tangle.Rmd", tangle = TRUE)
#opts_knit$set(tangle=TRUE)
```

## Slide with Plot
```{r, echo=TRUE}
plot(cars)
```

but an error message...

Quitting from lines 6-7 (myfile.rmd) 
Error in readLines(if (is.character(input2)) { : 
  cannot open the connection
Calls: <Anonymous> ... withVisible -> eval -> eval -> purl -> knit ->     readLines
Execution halted

@BenBolker Both suggestions give an error message? I created the file using File | New File | R Markdown... | Presentation and then did a Save As before hitting the Knit HTML button — guyabel
– guyabel, Commented Apr 17, 2015 at 13:04
I think @RomanLuštrik and I are both suggesting that you try running our commands from the console. — Ben Bolker
– Ben Bolker, Commented Apr 17, 2015 at 13:19
@BenBolker. I see, I was fixated on trying to do it within the .Rmd file and hence oblivious to your approaches. Many thanks. — guyabel
– guyabel, Commented Apr 17, 2015 at 13:30

Yihui Xie · Accepted Answer · 2015-04-18 03:56:54Z

1

I recommend you to use the hook_purl function instead. The function purl() (or equivalently, knit(tangle = TRUE)) may fail to work in certain cases, and the hook function hook_purl() is more reliable. See ?hook_purl for more information.

---
output: ioslides_presentation
---

```{r setup, include=FALSE}
library("knitr")
knit_hooks$set(purl = hook_purl)
```

## Slide with Plot
```{r, echo=TRUE}
plot(cars)
```

Then as you knit the document, the R script will be automatically generated.

answered Apr 18, 2015 at 3:56

Yihui Xie

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1 Comment

guyabel Over a year ago

Thanks @Yihui. Just what I wanted. Awesome!

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