3.3 Cross-referencing within documents

Cross-referencing is a useful way of directing your readers through your document, and can be automatically done within R Markdown. While this has been explained in Chapter 2 from the bookdown book, we want to present a brief summary below.

To use cross-references, you have to:

  • Use a bookdown output format: cross-referencing is not provided directly within the base rmarkdown package, but is provided as an extension in bookdown. We must therefore use an output format from bookdown (e.g., html_document2, pdf_document2, and word_document2, etc.) in the YAML output field.

  • A caption to your figure (or table): figures without a caption will be included directly as images and will therefore not be a numbered figure.

  • A labeled code chunk: this provides the identifier for referencing the figure generated by the chunk.

After these conditions are met, we can make cross-references within the text using the syntax \@ref(type:label), where label is the chunk label and type is the environment being referenced (e.g. tab, fig, or eqn). An example is provided below:

title: Cross-referencing figures, tables, and equations
author: Generated by bookdown
  bookdown::html_document2: default
  bookdown::pdf_document2: default

See Figure \@ref(fig:cars-plot).

```{r cars-plot, fig.cap="The cars data.", echo=FALSE}
par(mar = c(4, 4, .2, .1))
plot(cars)  # a scatterplot

Also see Equation \@ref(eq:mean).

\bar{X} = \frac{\sum_{i=1}^n X_i}{n} (\#eq:mean)

And see Table \@ref(tab:mtcars).

```{r mtcars, echo=FALSE}
knitr::kable(mtcars[1:5, 1:5], caption = "The mtcars data.")

The output of this document is shown in Figure 3.1.

Example of cross-referencing within an R Markdown document.

FIGURE 3.1: Example of cross-referencing within an R Markdown document.

You can also cross-reference equations, theorems, and section headers. These types of references are explained further in Section 2.2 and Section 2.6 of the bookdown book.