Template for contribution to Computo

1 Introduction

1.1 About this document

This document, accompanied with the hopefully finely tuned git repos, provides a template for writing contributions to Computo (Computo Team 2020).

TipNote

This document provides only the key formatting principles. For a detailed, step-by-step guide on preparing your article and submitting it to Computo, please consult the guidelines for authors.

1.2 Quarto

Quarto is a versatile formatting system for authoring documents integrating markdown, LaTeX and code blocks interpreted either via Jupyter or Knitr (thus supporting Python, R and Julia). It relies on the Pandoc document converter.

1.3 Requirements

You need quarto installed on your system and the Computo extension to prepare your document. For the latter, once quarto is installed, run the following to install the extension in the current directory (it creates a _extension directory which is ignored by git thanks to .gitignore by default):

quarto add computorg/computo-quarto-extension

Julia and Jupyter must be installed on your computer.

2 Formatting

This section covers basic formatting guidelines for quarto documents.

To render a document, run quarto render. By default, both PDF and HTML documents are generated:

quarto render # will render both to html and PDF

TipNote

To check the syntax of the formatting below, you can use the </> source button at the top left of this document.

2.1 Basic markdown formatting

Bold text or italic

• This is a list
• With more elements
• It isn’t numbered.

But we can also do a numbered list

1. This is my first item
2. This is my second item
3. This is my third item

2.2 Mathematics

2.2.1 Mathematical formulae

LaTeX code is natively supported¹, which makes it possible to use mathematical formulae:

f(x_1, \dots, x_n; \mu, \sigma^2) = \frac{1}{\sigma \sqrt{2\pi}} \exp{\left(- \frac{1}{2\sigma^2}\sum_{i=1}^n(x_i - \mu)^2\right)}

It is also posible to cross-reference an equation, see Equation 1:

\begin{aligned} D_{x_N} & = \frac12 \left[\begin{array}{cc} x_L^\top & x_N^\top \end{array}\right] \, \left[\begin{array}{cc} L_L & B \\ B^\top & L_N \end{array}\right] \, \left[\begin{array}{c} x_L \\ x_N \end{array}\right] \\ & = \frac12 (x_L^\top L_L x_L + 2 x_N^\top B^\top x_L + x_N^\top L_N x_N), \end{aligned} \tag{1}

2.2.2 Theorems and other amsthem-like environments

Quarto includes a nice support for theorems, with predefined prefix labels for theorems, lemmas, proposition, etc. see this page. Here is a simple example:

Theorem 1 (Strong law of large numbers) The sample average converges almost surely to the expected value:

\overline{X}_n\ \xrightarrow{\text{a.s.}}\ \mu \qquad\textrm{when}\ n \to \infty.

See Theorem 1.

2.3 Julia Code

Quarto uses either Jupyter or knitr to render code chunks. This can be triggered in the yaml header. In this tutorial, we use Jupyter, (Julia and Jupyter must be installed on your computer)

---
title: "My Document"
author "Jane Doe"
jupyter: julia-1.10
---

julia code chunks may be embedded as follows:

using Random
rng = MersenneTwister(1234)
x = randn(rng, ComplexF32, (10,1))
x

2.4 Figures

Plots can be generated as follows:

#| label: fig-parametric
#| fig-cap: "Parametric Plots"

using Plots

plot(sin, 
     x->sin(2x), 
     0, 
     2π, 
     leg=false, 
     fill=(0,:lavender))

It is also possible to create figures from static images:

Figure 1: Computo logo (label)

Note: Until Quarto version 1.3+ is released, including a remote image (from a web URL) in a document (like the image above) will work in the rendered HTML document but will generate an error when building the PDF document (c.f. related bug report).

2.5 Tables

Tables (with label: @tbl-mylabel renders Table 1) can be generated with markdown as follows

Table 1: my table caption

Tables	Are	Cool
col 1 is	left-aligned	$1600
col 2 is	centered	$12
col 3 is	right-aligned	$1

2.6 Handling references

2.6.1 Bibliographic references

References are displayed as footnotes using BibTeX, e.g. [@computo] will be displayed as (Computo Team 2020), where computo is the bibtex key for this specific entry. The bibliographic information is automatically retrieved from the .bib file specified in the header of this document (here: references.bib).

2.6.2 Other cross-references

As already (partially) seen, Quarto includes a mechanism similar to the bibliographic references for sections, equations, theorems, figures, lists, etc. Have a look at this page.

2.7 Advanced formatting

Advanced formatting features are possible and documented (including interactive plots, pseudo-code, (Tikz) diagrams, Lua filters, mixing R + Python in the same document), but are beyond the scope of this simple introduction. We point several entries in this direction.

WarningMore information

• The Quarto web site for comprehensive documentation, including:

  • Tutorial
  • User guide
  • Options reference

• The template distributed with the Computo Quarto extension, which uses such advanced features.

• Our mock version of the t-SNE paper, a full and advanced example using Python and the Jupyter kernel.

• The previously published papers in Computo can be used as references.

References

Computo Team. 2020. “Computo: Reproducible Computational/Algorithmic Contributions in Statistics and Machine Learning.”

Footnotes

1. We use lualatex for this purpose.