In RStudio/RMarkdown, how to setwd?

47
votes

setwd in an Rmd file in RStudio does not appear to change the directory in subsequent chunks. Is there a way to set the working directory for good?

Example:

```{r}
setwd("/tmp")
getwd()
```

```{r}
getwd()
```

Output:

setwd("/tmp")
getwd()
## [1] "/private/tmp"

getwd()
## [1] "/Users/me/src"

This is on Mac OS 10.8.5 using RStudio 0.97.551, R version 3.0.2 and knitr version 1.5.

I wish to set the directory once for all subsequent chunks.

2
rrstudior-markdown
I think this is a knitr issue. See github.com/yihui/knitr/issues/277#issuecomment-6528846 and see if it helps, though I don't think Yihui is a fan of globally setting setwd – Tyler Rinker
Solution is here, use opts_knit rather than opts_chunk – Nate Breznau

2 Answers

49
votes

See Issue #277 and for further background, the package author's comments here

What you are looking for is the root.dir option in knitr::opts_knit.

The following will set the root directory for subsequent code chunks (but not this chunk):

```{r setup}
knitr::opts_knit$set(root.dir = '/tmp')
```

EDIT: RStudio 1.0.44

as of RStudio's latest release (Oct/Nov 2016), the following snippet is needed for knitr's render default:

```{r setup}
knitr::opts_knit$set(root.dir = '/tmp')
```

see Etienne's comment about versions below.

2
votes

Here's what I've been using, and it seems to work well when using R Projects (.Rproj files):

knitr::opts_chunk$set(
    # This should allow Rmarkdown to locate the data
    root.dir = rprojroot::find_rstudio_root_file()
)