Bookdown Cross-Referencing Skill

Bookdown Cross-Referencing

Output Formats

Use bookdown:: output formats for cross-referencing support:

output:
  bookdown::html_document2:
    toc: true
  bookdown::pdf_document2:
    toc: true

Other formats: gitbook, word_document2, epub_book.

Figures

Chunk name becomes the reference ID. Requires fig.cap:

```{r myplot, fig.cap="Distribution of values."}
plot(x)


Reference: `Figure \@ref(fig:myplot)` → "Figure 1"

### Long Captions (Text Reference)

Define caption outside chunk, reference inside:

```markdown
(ref:myplot) This is a very long caption with **markdown** and citations [@smith2020].

```{r myplot, fig.cap="(ref:myplot)"}
plot(x)


## Tables

Use `knitr::kable()` with `caption`:

```r
```{r mytable}
knitr::kable(df, caption = "Summary statistics.")


Reference: `Table \@ref(tab:mytable)` → "Table 1"

## Sections

Headers auto-generate IDs from text (lowercase, hyphens):

```markdown
# My Analysis Section
See Section \@ref(my-analysis-section).

Custom ID: # My Section {#custom-id}

Equations

\begin{equation}
y = mx + b
(\#eq:linear)
\end{equation}

See Equation \@ref(eq:linear).

Quick Reference

| Element | Chunk/Label | Reference Syntax | |----------|-------------|------------------| | Figure | myplot | \@ref(fig:myplot) | | Table | mytable | \@ref(tab:mytable) | | Section | my-section| \@ref(my-section) | | Equation | eq:model | \@ref(eq:model) |

Common Issues

References show as ??: Missing fig.cap or wrong output format
Duplicate labels: Each chunk name must be unique
Backslash required: Use \@ref() not @ref()

Agent Skills: Bookdown Cross-Referencing