How to show code but hide output in RMarkdown?

80
votes

I want my html file to show the code, but not the output of this chunk:

```{r echo=True, include=FALSE}
fun <- function(b)
    {
    for(a in b)
        {print(a)
        return(a * a)}
    }
y <- fun(b)
```

When I run the code, i need the print to see the progress (it is quite a long function in reality).

But in the knitr file, I use the output in a further chunk, so I do not want to see it in this one (and there's no notion of progress, since the code has already been run).

This echo=True, include=FALSE here does not work: the whole thing is hidden (which is the normal behavior of include=FALSE).

What are the parameters I could use to hide the prints, but show my code?

6
rknitrr-markdown
Try {r echo=T, results='hide'} – J_F
Nice, that's exactly what I was looking for! I hadn't seen that results parameter before – Laurent
But how would one hide any and all output? Using results='hide' will still show things like warnings, like when an object is masked when using library(package). Is there an option to hide everything that would be printed to the console? – stragu
You can do that with warn.conflicts=F, quietly=T in your library command, like library(package, warn.conflicts=F, quietly=T) – Laurent
I have no idea why but this does not work for me – T.Omalley

6 Answers

79
votes

As @ J_F answered in the comments, using {r echo = T, results = 'hide'}.

I wanted to expand on their answer - there are great resources you can access to determine all possible options for your chunk and output display - I keep a printed copy at my desk!

You can find them either on the RStudio Website under Cheatsheets (look for the R Markdown cheatsheet and R Markdown Reference Guide) or, in RStudio, navigate to the "Help" tab, choose "Cheatsheets", and look for the same documents there.

Finally to set default chunk options, you can run (in your first chunk) something like the following code if you want most chunks to have the same behavior:

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T,
                      results = "hide")
```

Later, you can modify the behavior of individual chunks like this, which will replace the default value for just the results option.

```{r analysis, results="markup"}
# code here
```
37
votes

The results = 'hide' option doesn't prevent other messages to be printed. To hide them, the following options are useful:

  • {r, error=FALSE}
  • {r, warning=FALSE}
  • {r, message=FALSE}

In every case, the corresponding warning, error or message will be printed to the console instead.

19
votes

For what it's worth.

```{r eval=FALSE}

The document will display the code by default but will prevent the code block from being executed, and thus will also not display any results.

5
votes

For muting library("name_of_library") codes, meanly just showing the codes, {r loadlib, echo=T, results='hide', message=F, warning=F} is great. And imho a better way than library(package, warn.conflicts=F, quietly=T)

3
votes

To hide warnings, you can also do {r, warning=FALSE}

2
votes

For completely silencing the output, here what works for me

```{r error=FALSE, warning=FALSE, message=FALSE}
invisible({capture.output({


# Your code here
2 * 2
# etc etc


})})
```

The 5 measures used above are

  1. error = FALSE
  2. warning = FALSE
  3. message = FALSE
  4. invisible()
  5. capture.output()