12 Citing Figures, Tables & Sections

When you’re writing a report, you often refer to a table or figure in text.

Australia’s life expectancy has increased a great deal over the past 50 years (Figure 1)

Figure 1. Life expectancy from 1952 - 2007 for Australia. Life expectancy increases steadily except from 1962 to 1969. We can safely say that our life expectancy is higher than it has ever been!

And sure, this is figure 1. But what happens if actually, that figure should be moved later in the paper? You need to do the following:

1. Update the reference to figure 1 in the text.
2. Update the figure 1 caption to not say figure 1.

This is fine.

Once.

But it is never once. After this, it is frustrating, and error prone.

There is a way to solve this, which this lesson discusses.

12.1 Overview

• Teaching 10 minutes
• Exercises 15 minutes

12.2 Questions

• How do I refer to the table or figure in text and link to it?

12.3 Objectives

• Link to tables or figures in text.

12.4 How to refer to tables and figures in text?

In order to use this referencing style, you must use the following in the YAML

output:
  bookdown::pdf_document2

Or for HTML:

output:
  bookdown::html_document2

Or for word:

output:
  bookdown::word_document2

This is a new version of document that supports a better way to reference things in text. This reads as:

Make the output the HTML/PDF/Word document from the bookdown package.

That is, the special :: after bookdown, bookdown::html_document2 read as “The html_document2 function from the bookdown package”.

12.5 Your Turn

1. Convert your output to use bookdown::html_document2 in your YAML.

12.6 Referencing a figure

To refer to a figure, you write the following in your text:

Figure \@ref(fig:chunk-name))

12.6.1 Demo

```{r gg-oz-plot, fig.cap = "Life expectancy from 1952 - 2007 for Australia. Life expentancy increases steadily except from 1962 to 1969. We can safely say that our life expectancy is higher than it has ever been!"}
library(ggplot2)
library(dplyr)
gapminder %>%
  filter(country == "Australia") %>%
  ggplot(aes(x = year,
             y = lifeExp)) + 
  geom_point()
```

Australia's life expectancy has increased a great deal over the past 50 years

(See Figure \@ref(fig:gg-oz-plot))

library(ggplot2)
library(dplyr)
gapminder %>%
  filter(country == "Australia") %>%
  ggplot(aes(x = year,
             y = lifeExp)) + 
  geom_point()

Figure 12.1: Life expectancy from 1952 - 2007 for Australia. Life expectancy increases steadily except from 1962 to 1969. We can safely say that our life expectancy is higher than it has ever been!

Australia’s life expectancy has increased a great deal over the past 50 years (See Figure 12.1)

12.6.2 Your Turn

1. Add a new plot in your document and reference it

12.7 Referencing a table

To cite a table, you write the following:

Table \@ref(tab:chunk-name))

```{r gg-oz-tab}
gapminder %>%
  filter(country == "Australia") %>%
  knitr::kable(caption = "Raw gapminder data for Australia.")
```

We can see below in Table 12.1 the raw data used to create Figure 12.1).

gapminder %>%
  filter(country == "Australia") %>%
  knitr::kable(caption = "Raw gapminder data for Australia.")

Table 12.1: Raw gapminder data for Australia.

country	continent	year	lifeExp	pop	gdpPercap
Australia	Oceania	1952	69.120	8691212	10039.60
Australia	Oceania	1957	70.330	9712569	10949.65
Australia	Oceania	1962	70.930	10794968	12217.23
Australia	Oceania	1967	71.100	11872264	14526.12
Australia	Oceania	1972	71.930	13177000	16788.63
Australia	Oceania	1977	73.490	14074100	18334.20
Australia	Oceania	1982	74.740	15184200	19477.01
Australia	Oceania	1987	76.320	16257249	21888.89
Australia	Oceania	1992	77.560	17481977	23424.77
Australia	Oceania	1997	78.830	18565243	26997.94
Australia	Oceania	2002	80.370	19546792	30687.75
Australia	Oceania	2007	81.235	20434176	34435.37

12.7.1 Your Turn

1. Create a table in your document and refer to it in text

12.8 Referencing a section

You can even reference a section in your report:

\@ref(slug))

However, in order to write this, you need to include slug in your markdown header, like so:

## your amazing header {#slug}

For example, I can refer to the first section (Section 12) in this document by referring to the section as

\@ref(start)

because it was written as:

# Citing Figures, Tables & Sections {#start}

One note here - your slug can not start with a number. Otherwise, it will print out the slug. So the following would not work:

## 10 rules {#10-rules}

You should instead write:

## 10 rules {#ten-rules}

12.8.1 Your Turn

1. Reference a section in the report.

12.9 One small note

If you are using a template of some kind, such as those in rticles, and want the full featured citation features, then your YAML will need to include something like this:

output:
  bookdown::pdf_book:
    base_format: rticles::plos_article