Advanced R Markdown

Jeff Stevens

2025-05-05

Set-up

First, load tidyverse and {palmerpenguin} packages

library(tidyverse)
library(palmerpenguins)

Code chunks

Code chunk options

Go in the {r} header of code chunks (in one line)

• label = chunk-label - chunk label
• eval = TRUE - evaluates code chunk
• echo = TRUE - displays source code in document
• include = TRUE - displays chunk output in document
• message = TRUE - displays messages in document
• warning = TRUE - displays warnings in document
• error = TRUE - displays errors in document

Code chunk options

Go in the {r} header of code chunks (in one line)

```{r chunk-label, echo = FALSE, message = FALSE, warning = FALSE}

```

Code chunk options

Can also be separated from header using #| but must switch from = to :

```{r}

#| chunk-label

#| echo: FALSE

#| message: FALSE

#| warning: FALSE

```

Global options

Set options globally with knitr::opts_chunk$set()

```{r setup, include = FALSE}

knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)

```

Figures

Figures generated in chunks

ggplot(penguins, aes(bill_length_mm, bill_depth_mm)) + geom_point()

Figure scaling

fig.width = 5, fig.height = 5

ggplot(penguins, aes(bill_length_mm, bill_depth_mm)) + geom_point()

Figure scaling

fig.width = 3, fig.height = 3

ggplot(penguins, aes(bill_length_mm, bill_depth_mm)) + geom_point()

Output width/height

out.width = "30%", out.height = "30%"

ggplot(penguins, aes(bill_length_mm, bill_depth_mm)) + geom_point()

Output width/height

out.width = "300", out.height = "300"

ggplot(penguins, aes(bill_length_mm, bill_depth_mm)) + geom_point()

Figure alignment

fig.align = "center"

ggplot(penguins, aes(bill_length_mm, bill_depth_mm)) + geom_point()

Figure caption

fig.cap = "My figure caption"

ggplot(penguins, aes(bill_length_mm, bill_depth_mm)) + geom_point()

Figure 1: My figure caption

Figure alt text

fig.alt = "Scatterplot of penguin bill length by depth."

ggplot(penguins, aes(bill_length_mm, bill_depth_mm)) + geom_point()

My figure caption

Figure files

knitr::include_graphics()

knitr::include_graphics("https://quarto.org/docs/authoring/images/crossref-figure.png")

Cross-referencing

Cross reference figures/tables

• Make sure code chunk has a label and a caption

• Use a bookdown output format (e.g., pdf_document2, word_document2, papaja::apa6_pdf, thesisdown)

• Insert \@ref(fig:chunk-label) for figures and \@ref(tab:chunk-label) for tables (e.g., \@ref(fig:cap))

• Note for Quarto, labels must start with @fig- or @tbl- and reference with @fig-label or @tbl-label (e.g., Figure 1 yields Figure 1)

Cross reference sections

• Label sections with {#slug}
  (e.g., ## Cross reference figures/tables {#sec-cross-reference})

• Cross reference with \@ref(slug)

• For Quarto, cross references must start with #sec- and are referenced with @sec-label (e.g., @sec-cross-reference yields Section 3.1)

Citations and bibliographies

Zotero

Zotero

• Install Better BibTeX extension
• Create collection for project
• Add references to collection
• Export Collection (check Keep Updated) to BibTeX

Set bibliography

• In YAML header, assign bibliography to the project’s .bib file

bibliography: zotero-output.bib

• If using {papaja}’s r_ref() output

bibliography: ["zotero-output.bib", "r-references.bib"]

Insert citations

• Find BibTex key in Zotero (e.g., Stevens.etal.2023)
• Insert with [@citation.key]: [@Stevens.etal.2023] yields (Stevens et al., 2023)
• Separate multiple citations with ;: [@Stevens.etal.2022; @Stevens.etal.2023] yields (Stevens et al., 2022, 2023)
• Add prefixes and suffixes: [see @Stevens.etal.2023, pp. 25] yields (see Stevens et al., 2023, pp. 25)

Insert citations

• Use parentheses only for date by removing brackets: @Stevens.etal.2023 yields Stevens et al. (2023)
• Use only year by adding -: [-@Stevens.etal.2023] yields (2023)
• Add reference to bibliography without adding citation with

---
nocite: |
  @Stevens.etal.2023
...

Set citation style

• In YAML header, assign csl to citation style .csl file

csl: apa7.csl

• Get CSL files from Zotero Style Repository

Quarto

https://quarto.org/

• Documents, manuscripts, books, theses, websites, presentations, dashboards, interactive apps

• HTML, PDF, Word, ePub

• R, Python, Julia, Observable

Let’s code!

Advanced R Markdown