R-markdown: Add an empty line between echoed code and result output

To combine the echoed R code and outputted result in knitr there is a handy collapse=TRUE option. However by default it leaves no space between them i.e. given the following Rmd:

```{r, echo=TRUE, include=TRUE, collapse=TRUE}
x <- matrix(1:6, nrow=2)
x
```

It would produce this output wrapped in a <pre> tag:

x <- matrix(1:6, nrow=2)
x
##      [,1] [,2] [,3]
## [1,]    1    3    5
## [2,]    2    4    6

What I would like instead is to get an empty line separating the output and code, but still being combined into a single <pre> element.

x <- matrix(1:6, nrow=2)
x

##      [,1] [,2] [,3]
## [1,]    1    3    5
## [2,]    2    4    6

Is there a way to achieve this? I tried adding an empty line to the end of the R chunk, but seems like it was removed.

Solution

You can define a new chunk option instead of collapse using knitr chunk hooks that collapses code and output with additional whitespace. For instance, you could include in the setup chunk:

Rmarkdown

---
output: html_document
---

```{r setup, include=FALSE}
hook_chunk = knitr::knit_hooks$get('chunk')

knitr::knit_hooks$set(chunk = function(x, options) {
  regular_output = hook_chunk(x, options)
  # collapse with vspace if collapse_vspace is TRUE
  if (isTRUE(options$collapse_vspace))
    gsub("```\n\n```", "", regular_output)
  else
    regular_output
})

knitr::opts_chunk$set(collapse_vspace = TRUE)
```

```{r, echo = TRUE}
x <- matrix(1:6, nrow=2)
x
```

HTML output

Some useful references: