Advanced R Markdown

Jeff Stevens

2023-05-08

Set-up

First, load tidyverse and {palmerpenguin} packages

Code chunks

Code chunk options

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

  • label = my-chunk - 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 my-chunk, echo = FALSE, message = FALSE, warning = FALSE}

```

Code chunk options

Can also be separated from header using #|

```{r}

#| my-chunk, 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()

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()
Scatterplot of penguin bill length by depth.

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., bookdown::pdf_document2, papaja::apa6_pdf, thesisdown)

  • Insert \ref{fig:chunk-label} for figures and \ref{tab:chunk-label} for tables

  • Note for Quarto, labels must start with fig- or tbl- and reference with @fig-label or @tbl-label (e.g., 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., Section 4.1)

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 manually

  • 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 manually

  • 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: |
  @Barela.etal.2023
...

Insert with {citr} add-in

  • Install {citr} with remotes::install_github("crsh/citr")
  • Restart RStudio
  • Start Zotero
  • Start citr add-in, select Insert citations

Set citation style

  • In YAML header, assign csl to citation style .csl file
csl: apa7.csl

DPaViR 2023