R Markdown : \@ref() not working

Question

I'm having a lot of trouble getting basic references to work in R Markdown. To reduce complexity from my original project, I've decided to use the bookdown example code, but I'm experiencing the same problem. Here's a link to the intro exmample code: https://github.com/rstudio/bookdown-demo/blob/master/01-intro.Rmd

When I use Knitr to HTML or PDF the file is being generated fine but the references are not working, instead the file will just containt "@ref(example)". Here is an image to show better the output (my emphasis added in red):

Direct link to image: https://i.imgur.com/2yxB5h3.png

Here is a minimal example:

---
title: "Minimal"
output: 
  pdf_document:
    fig_caption: yes
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

Here is a reference to the plot below \@ref(fig:minGraph)

```{r minGraph, echo=FALSE, fig.cap="\\label{fig:minGraph}test"}
plot(x=1)
```

With the output appearing as such: https://i.imgur.com/J3UECqn.png

Answer 1

If you want make use of the bookdown extensions in a normal rmarkdown document you can use bookdown::html_document2 and bookdown::pdf_document2 instead of rmarkdown::html_document and rmarkdown::pdf_document. Example:

---
title: "Minimal"
output: 
  bookdown::html_document2:
    fig_caption: yes
  bookdown::pdf_document2:
    fig_caption: yes
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

Here is a reference to the plot below \@ref(fig:minGraph)

```{r minGraph, echo=FALSE, fig.cap="test"}
plot(x=1)
```