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.

Figure 12.1: Some caption for an illustration showing an elephant

Elephants are big (Figure 12.2):

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.

(a)

(b)

Figure 12.3: Some caption you wrote for an illustration of two elephants.

Asides

If you like,

you can make comments in the margin without footnote a reference.

Plot included from notebook

See plot Figure 12.4 below.

Figure 12.4: Figure legends are defined alongside the figure in the notebook. The figure size in the notebook is determines its size when embedded in a document 4x3 inches.

Or this really wide plot below (Figure 12.5).

Figure 12.5: Figure legends are defined alongside the figure in the notebook. The figure size in the notebook is determines its size when embedded in a document 4x3 inches.

Text included from notebook

The 24 subjects from workplaces in Denmark were interviewed …. blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah

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

Table 12.1: People included in the analysis.

name	age	sex	position	nationality
Julie	27	F	PhDstudent	DK
Thomas	33	M	Postdoc	GB
Emilie	23	F	PhDstudent	CH
Sofie	31	F	Postdoc	DK
Sara	29	F	Postdoc	US
Cecilie	34	F	Postdoc	DK
Anders	32	M	PhDstudent	UK
Emma	42	F	Professor	DK
Caroline	31	F	PhDstudent	DK
Laura	30	F	Postdoc	DK
Mikkel	33	M	Postdoc	NL
Jens	27	M	PhDstudent	DK
Andreas	29	M	PhDstudent	DK
Jakob	28	M	PhDstudent	DK
Mathilde	61	F	Professor	DK
Katrine	35	F	Postdoc	DK
Poul	30	M	Postdoc	DK
Anna	26	F	PhDstudent	DK
Peter	42	M	Professor	GB
Ida	53	F	Postdoc	DK
Freja	30	F	Postdoc	DK
Maria	39	F	Professor	UK
Amalie	29	F	PhDstudent	DK
Camilla	35	F	Postdoc	DK

Margin content

You can anything in the margin like Figure 12.6.

Figure 12.6: Figure legends are defined alongside the figure in the notebook. The figure size in the notebook is determines its size when embedded in a document 4x3 inches.

Diagrams

Diagram in Figure 12.7.

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;
}

(a) This is a simple graphviz graph.

Figure 12.7

flowchart LR
  A[Beginning] --> B[Middle]
  B --> C[End]

flowchart LR
  A[Beginning] --> B[Middle]
  B --> C[End]

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:

x = 5

Values can be embedded in the text, too. The value of x is 5.

Shown, not executed, Python code:

y = 4

A for loop:

for i in range(10):
    print(i)

Shown, not executed, R code:

z <- 7

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.

Dutheil, Julien Y, Kasper Munch, Kiwoong Nam, Thomas Mailund, and Mikkel H Schierup. 2015. “Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence.” PLOS Genetics 11 (8): e1005451. https://doi.org/10.1371/journal.pgen.1005451.

Munch, Kasper, Thomas Mailund, Julien Y Dutheil, and Mikkel Schierup. 2014. “A fine-scale recombination map of the human–chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion.” Genome Research 24 (3): 467–74. https://doi.org/10.1101/gr.158469.113.

Nam, Kiwoong, Kasper Munch, Asger Hobolth, Julien Dutheil, Krishna R Veeramah, August E Woerner, Michael F Hammer, et al. 2015. “Extreme selective sweeps independently targeted the X chromosomes of the great apes.” Proceedings of the National Academy of Sciences 112 (20): 6413–18. https://doi.org/10.1073/pnas.1419306112.

Nielsen, Rasmgb, and Montgomery Slatkin. 2016. An Introduction to Population Genetics: Theory and Applications.

Prüfer, Kay, Kasper Munch, Ines Hellmann, Keiko Akagi, Jason R. Miller, Brian Walenz, Sergey Koren, et al. 2012. “The bonobo genome compared with the chimpanzee and human genomes.” Nature 486 (7404): 527–31. https://doi.org/10.1038/nature11128.

Skov, Laurits, Moisès Coll Macià, Elise Anne Lucotte, Maria Izabel Alvez Cavassim, David Castellano, Mikkel Heide Schierup, and Kasper Munch. 2023. “Extraordinary selection on the human X chromosome associated with archaic admixture.” Cell Genomics, 100274. https://doi.org/10.1016/j.xgen.2023.100274.