Markdown

Custom document header

For example, for grants with custom templates that include information at the top of the page.

In the yaml header:

geometry:
  - margin=2cm
  - top=1cm
  - includehead
  - headheight=1.1cm

In the header.tex, define a “table” for the header:

%% make header
\usepackage{fancyhdr}
\pagestyle{fancy}
\renewcommand{\headrulewidth}{0pt}
\fancypagestyle{plain}

% clear all headers and footers
\fancyhead{}
\renewcommand{\arraystretch}{1.2}
  
% set the C(entre) header location but no O or E
\fancyhead[C]{
  \begin{tabular}[c]{|l|l|l|r|}
    \hline
    {\large GRANT23} & \multicolumn{2}{l|}{\bf\large PROJECTNAME} & {\large GRANTNAME} \\
    \hline
    Coordinated by: & Jean MONLONG \hspace{12em} & X months &   Funding requested: \\
    \cline{1-3}
    \multicolumn{3}{|l|}{COMMITEE} &  3 000 000 000 € \\
    \hline
  \end{tabular}
}
    
%% shift title
\usepackage{titling}
\setlength{\droptitle}{-3em}
\posttitle{\par\end{center}\vspace{-5em}}

Comments

Define the LaTeX commands in the header.tex:

\usepackage[textsize=scriptsize]{todonotes}
\setlength{\marginparwidth}{4em} %% avoid the todo notes going out of the margin
\usepackage{xcolor}
\newcounter{mycomment}
\newcommand{\note}[1]{
  \refstepcounter{mycomment}
  {
    \todo[inline,color={red!100!green!33},size=\tiny]{
      \textbf{[\themycomment]:}~#1}
  }}
\newcommand{\comment}[1]{
  \refstepcounter{mycomment}
  {
    \todo[color={red!100!green!33},size=\tiny]{
      \textbf{[\themycomment]:}~#1}
  }}

Then use in the text as \note{A note} and \comment{a comment} for inline notes and comments in the margin, respectively.

Custom tables

To better control the table formatting, I write the content of the table in a file (e.g. TSV), then read it in a R code chunk and format it with knitr and kableExtra.

The code chunk, for example with echo=FALSE, message=TRUE, warnings=FALSE parameters, might look like:

library(knitr)
library(kableExtra)
df = read.table('table1.tsv', as.is=TRUE, header=TRUE, sep='\t',
                quote="", comment.char = "", check.names=FALSE)
kable(df, format='latex', booktabs=FALSE) %>%
  kable_styling(latex_options="scale_down", position='left') %>%
  column_spec(2:3, width = ".7in") %>% 
  column_spec(4, width = "3in") %>%
  column_spec(1, border_left = T) %>%
  column_spec(ncol(df), border_right=T, width = "1.5in") %>%
  row_spec(0,bold=TRUE)

Note: it’s possible to adapt the table’s format to the output format of the document. For example, to use markdown formatting for Word documents:

if(knitr::opts_knit$get("rmarkdown.pandoc.to") == 'docx'){
  kable(df, format='markdown')
} else {
    ## SEE ABOVE
}

PDF slides

Using Beamer:

---
output:
  beamer_presentation:
    slide_level: 2
    theme: "default"
    colortheme: "dolphin"
    fonttheme: "structurebold"
---

Pick a theme from https://hartwork.org/beamer-theme-matrix/ (for example).

HTML slides

Some YAML header options:

---
output: 
  ioslides_presentation:
    widescreen: true
    css: style.css
---

I used the style.css file to make sure the images are sized properly and don’t overflow. For example, this CSS code seemed to help:

img {
    max-width:100%;
    max-height:400px;
    height: auto;
    width:auto;
}

In this mode, the user can use key bindings such as f (fullscreen), w (widescreen), o (overview), p (presenter notes).

> - First things first
> - But also this

blogdown websites

blogdown is a R package extending R Markdown to build Hugo static websites. Hugo is easier to install than Jekyll and apparently faster. Most importantly blogdown makes it easier to write posts with R code like in a RMarkdown document.

I still use GitHub Pages to deploy the website. GH Pages doesn’t support Hugo, so I build the website in a docs folder (publishDir = "docs" in config.toml) which I set up on the website settings to be the source of the static website.

output:
  blogdown::html_page:
    toc: true

<script src="//yihui.name/js/math-code.js"></script>
<script async src="//cdn.bootcss.com/mathjax/2.7.1/MathJax.js?config=TeX-MML-AM_CHTML">
</script>

bibliography: [../../static/library.bib]
link-citations: true

Jekyll websites (deprecated)

Note: I now use blogdown for markdown-based websites, see above.

Jekyll websites are simple Markdown documents that can be converted into a website. GitHub uses it to provide a website for a repo.

* Is replaced by the TOC
{toc}

<nav>
  <h4>Table of Contents</h4>
  * TOC
  {:toc}
</nav>

\{\% include toc.html \%\}

<script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" ></script>