how to comment out R code blocks in R markdown?

Question

I'm editing an R markdown file (.Rmd) that has a lot of R code blocks to move groups of those code blocks into "child" documents to simplify rearranging sections (if nothing else). As I convert sections to child documents, I would like to test the new child document without running the rest of the blocks and other children. However, when I use to comment out those sections, the R blocks still run (but RStudio makes the sections "look" as though they were commented out).

If I eliminate the preceding and trailing "```"s (i.e., the code block signifiers), the commenting works fine. However, as I said, I've got lots of code blocks and something like would be more convenient.

So, how do I comment out the R code blocks so they won't run?

Answer 1

In RStudio, if you highlight from (at least) one row above an R code chunk to (at least) the last row of the R code chunk,¹ and then type ctrl-shift-C (in OSX or Windows) or command-shift-C (OSX only), RStudio will place html comment tags on the chunk.

For example:

```{r cars}
summary(cars)
plot(pressure)
```

After highlighting this and type ctrl-shift-C, this becomes:

<!-- ```{r cars} -->
<!-- summary(cars) -->
<!-- plot(pressure) -->
<!-- ``` -->

To selectively comment out multiple chunks, you can use the RStudio find/replace tool with the regex option checked. It takes two replacement steps (it can probably be done in one step, but I'm not sure how to do a regex to capture across multiple lines in RStudio).

Step 1: Comment out the first line of one or more chunks:

Find: (```{r.*)
Replace: <!--\1

Step 2: Comment out the last line of one or more chunks:

Find: (```)$
Replace: \1-->

---

^{1 You must include the row above the chunk in the highlight. Otherwise, RStudio will place R comment tags (#) at the beginning of each row of the chunk and the commented lines will appear as plain text in the output document.}

Answer 2

In an Rmarkdown document, we can apply certain options to each R code chunk that determines whether the code inside will be run, printed, show error messages, etc.

To have a specific code chunk not run, use:

```{r cars, eval=FALSE}
summary(cars)
```

To have a specific code chunk not run or print into the created doc, use:

```{r cars, eval=FALSE, echo=FALSE}
summary(cars)
```

"TRUE" is used for the opposite effects and is the default.

If you have many code chunks you need to comment out, you can take the suggestion from @eipi10 (thanks) and use find/replace with the regex option selected. So, the find would be "(```{r.*)", and the replace would be "\1, eval=FALSE, echo=FALSE}" (without the double quotes).