Markdown in Quarto
Including BibTex references
There are many ways to manage BibTex references. In ReadCube Papers, you just right-click to select Copy...>BibTex entry
and paste it into your BibTex file (I also have a script that formats your entire Papers library for BibTex with meaningful labels).
You can render citations in different ways to accommodate their sentence. Skov et al. reported strong selection on the human X chromosome (2023). Lineages in small populations have shorter coalescence times (see Nielsen and Slatkin 2016, chap. 1). The Neanderthal genome has been sequenced (Prüfer et al. 2012). The X chromosome is subject to recurrent sweeps (Nam et al. 2015; Dutheil et al. 2015). Following Munch et al. (2014), we blah blah…
Illustrations
You can see an elephant in Figure 12.1.
Elephants are big (Figure 12.2):
There are two elephants in Figure 12.3. The elephants in Figure 12.3 (a) and Figure 12.3 (b) look similar.
Asides
If you like,
Plot included from notebook
See plot Figure 12.4 below.
Or this really wide plot below (Figure 12.5).
Text included from notebook
Table included from notebook
These were selected to represent as many nationalities as possible (Table 12.1).
you can also allow the table to be wider
Margin content
You can anything in the margin like Figure 12.6.
Diagrams
Diagram in Figure 12.7.
Code
graph G {
layout=neato
run -- intr;
intr -- runbl;
runbl -- run;
run -- kernel;
kernel -- zombie;
kernel -- sleep;
kernel -- runmem;
sleep -- swap;
swap -- runswap;
runswap -- new;
runswap -- runmem;
new -- runmem;
sleep -- runmem;
}
Code
flowchart LR
A[Beginning] --> B[Middle] B --> C[End]
flowchart LR A[Beginning] --> B[Middle] B --> C[End]
Code
flowchart LR
A[Beginning] --> B[Middle] B --> C[End]
flowchart LR A[Beginning] --> B[Middle] B --> C[End]
This is a flow chart.
Code
Executed but hide code and any output:
Show and execute Python code:
Code
= 5 x
Values can be embedded in the text, too. The value of x
is 5.
Shown, not executed, Python code:
= 4 y
A for loop:
for i in range(10):
print(i)
Shown, not executed, R code:
<- 7 z
Math
This is calculated as \(\pi_k = \prod_{i=1}^K x_i\). You can crossref formulas (Equation 12.1).
\[ \lambda = \sum_{k=1}^N \pi_k \tag{12.1}\]
We know from the first fundamental theorem of calculus that for \(x\) in \([a, b]\):
\[\frac{d}{dx}\left( \int_{a}^{x} f(u)\,du\right)=f(x).\]
Bold and italics
This is bold, so is this. This is italics, so is this. This is both, so is this.
Section
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis sagittis posuere ligula sit amet lacinia. Duis dignissim pellentesque magna, rhoncus congue sapien finibus mollis. Ut eu sem laoreet, vehicula ipsum in, convallis erat. Vestibulum magna sem, blandit pulvinar augue sit amet, auctor malesuada sapien. Nullam faucibus leo eget eros hendrerit, non laoreet ipsum lacinia. Curabitur cursus diam elit, non tempus ante volutpat a. Quisque hendrerit blandit purus non fringilla. Integer sit amet elit viverra ante dapibus semper. Vestibulum viverra rutrum enim, at luctus enim posuere eu. Orci varius natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.
Subsection
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis sagittis posuere ligula sit amet lacinia. Duis dignissim pellentesque magna, rhoncus congue sapien finibus mollis. Ut eu sem laoreet, vehicula ipsum in, convallis erat. Vestibulum magna sem, blandit pulvinar augue sit amet, auctor malesuada sapien. Nullam faucibus leo eget eros hendrerit, non laoreet ipsum lacinia. Curabitur cursus diam elit, non tempus ante volutpat a. Quisque hendrerit blandit purus non fringilla. Integer sit amet elit viverra ante dapibus semper. Vestibulum viverra rutrum enim, at luctus enim posuere eu. Orci varius natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.
Subsubsection
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis sagittis posuere ligula sit amet lacinia. Duis dignissim pellentesque magna, rhoncus congue sapien finibus mollis. Ut eu sem laoreet, vehicula ipsum in, convallis erat. Vestibulum magna sem, blandit pulvinar augue sit amet, auctor malesuada sapien. Nullam faucibus leo eget eros hendrerit, non laoreet ipsum lacinia. Curabitur cursus diam elit, non tempus ante volutpat a. Quisque hendrerit blandit purus non fringilla. Integer sit amet elit viverra ante dapibus semper. Vestibulum viverra rutrum enim, at luctus enim posuere eu. Orci varius natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.