Using RMarkdown I always generate pdf documents via Rmd -> pandoc -> TeX -> pdflatex -> pdf and accomplish figure references using \\label{something} in the fig.cap as in the follow example:
---
title: "Foo"
author: "Mark Andrews"
date: "10 January 2019"
output: pdf_document
---
See Figure \ref{figfoo} and see Figure \ref{figbar}.
```{r fig1, fig.cap='A figure\\label{figfoo}'}
plot(rnorm(10))
```
```{r fig2, fig.cap='Another figure\\label{figbar}'}
plot(rnorm(10))
```
If I change output: pdf_document to output: html_document, that does not work, understandably because it is relying on LaTeX's cross referencing system.
So how do Figure references work with html_document in RMarkdown?
The following does not work:
---
title: "Foo"
author: "Mark Andrews"
date: "10 January 2019"
output: html_document
---
See Figure \@ref(fig:fig1) and see Figure \@ref(fig:fig2).
```{r fig1, fig.cap='A figure}'}
plot(rnorm(10))
```
```{r fig2, fig.cap='Another figure'}
plot(rnorm(10))
```
But the following does work:
---
title: "Foo"
author: "Mark Andrews"
date: "10 January 2019"
output: bookdown::html_document2
---
See Figure \@ref(fig:fig1) and see Figure \@ref(fig:fig2).
```{r fig1, fig.cap='A figure}'}
plot(rnorm(10))
```
```{r fig2, fig.cap='Another figure'}
plot(rnorm(10))
```
Does that mean that the only way to cross-reference figures when producing html from Rmarkdown is to use output: bookdown::html_document2. That's fine, if so, but am I missing something?