rmd4sci-melbourne

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.

Overview

• Teaching 10 minutes
• Exercises 15 minutes

Questions

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

Objectives

• Link to tables or figures in text.

How to refer to tables and figures in text? {.demo}

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”.

Your Turn {.exercise}

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

Referencing a figure

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

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

Demo {.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()

(\#fig:gg-oz-plot)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 \@ref(fig:gg-oz-plot))

Your Turn {.exercise}

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

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 \@ref(tab:gg-oz-tab) the raw data used to create Figure \@ref(fig:gg-oz-plot)).

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

Table: (#tab:gg-oz-tab)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

Your Turn {.exercise}

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

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 \@ref(start)) 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}

Your Turn {.exercise}

1. Reference a section in the report.

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

This site is open source. Improve this page.