Reference sections

library(ggplot2)

1 Bibliography style

Use a csl file to change the referencing style, both in-text and in-bib. Put

csl: ecology.csl

in the header to use a different file. Get CSL files from their github, and look at what they actually look like from CSL’s visual editor (which seems to kick over to something managed by Zotero.

2 References (bibliography)

To put the bibliography wherever you want, include a div ::: {#refs} wherever you want it to be. If we cite Holt and Chesson (2018), we can put the bib right here.

Note, we need square brackets around the citation to get the author in parentheses. This one has square brackets (Holt and Chesson 2018) and this one Holt and Chesson (2018) does not.

Holt, Galen, and Peter Chesson. 2018. “The Role of Branching in the Maintenance of Diversity in Watersheds.” Freshwater Science 37 (4): 712–30. https://doi.org/10.1086/700680.

3 Figures and tables with sections

I want to have figs and tables in different sections; e.g. in main text and supplement or different chapters. It seems to work different for figs generated from code and images loaded in.

In the main text, we just use tbl and fig, referenced with @tbl-iris (Table 1) for tables, @fig-branching (Figure 1) for read-in images, and @fig-iris (Figure 2) for code-generated figures:

```{r}
#| label: tbl-iris
#| tbl-cap: Head of iris dataframe
head(iris) |> knitr::kable()
```
Table 1: Head of iris dataframe
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
5.1 3.5 1.4 0.2 setosa
4.9 3.0 1.4 0.2 setosa
4.7 3.2 1.3 0.2 setosa
4.6 3.1 1.5 0.2 setosa
5.0 3.6 1.4 0.2 setosa
5.4 3.9 1.7 0.4 setosa

![An image of branching](../_images/branching.png){#fig-branching} gives

Figure 1: An image of branching 
```{r}
#| label: fig-iris
#| fig-cap: A figure of the iris dataframe

ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, color = Species)) +
  geom_point()
```
Figure 2: A figure of the iris dataframe

4 New section

Now, according to the Quarto docs, we can add a new kind of crossref. So I’ve put the following from that site in the yaml header:

crossref:
  custom:
    - kind: float
      key: suppfig
      latex-env: suppfig
      reference-prefix: Figure S
      space-before-numbering: false
    - kind: float
      key: supptbl
      latex-env: supptbl
      reference-prefix: Table S
      space-before-numbering: false
      caption-location: top

See docs for options.

Now, the trick, which I missed, is that it only works for fenced divs (see github issues). See quarto docs.

Now, it should work to use suppfig to reference loaded figures such as @suppfig-elephant (Figure S1) for read-in images, and @suppfig-iris (Figure S2) for code-generated figures and tables @supptbl-iris (Table S1) Only if we use divs:

![An image of Surus](../_images/surus.png){#suppfig-elephant} gives

Figure S1: An image of Surus

Wapping this in ::: {#suppfig-iris} and putting the caption inside:

```{r}
ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, color = Petal.Width)) +
  geom_point()
```

Figure S2: Another iris plot

Now tables. It captions at the bottom though unles we set caption-location: top in the yml.

Table S1: Tail of the iris df. 
```{r}
tail(iris) |> knitr::kable()
```
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
145 6.7 3.3 5.7 2.5 virginica
146 6.7 3.0 5.2 2.3 virginica
147 6.3 2.5 5.0 1.9 virginica
148 6.5 3.0 5.2 2.0 virginica
149 6.2 3.4 5.4 2.3 virginica
150 5.9 3.0 5.1 1.8 virginica

Unnumbered sections

If we have number-sections: true in the yaml, we can turn it off for some by putting {.unnumbered} next to their names (as I have for this section).