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This is material for a small tutorial on LaTeX and reproducible document generation.

• Install
• R
• Test
• Schedule
• Literature

For full productivity, install LaTeX and an editor, for which I suggest TexMaker.

To avoid installations, sign up at sharelatex or overleaf. Sharelatex seems to be slightly better and is open source.

For reprodicible research, automated report generation and syntax-higlighted code inclusion, use rmarkdown. To couple that with the power of LaTeX, you do have to install LaTeX locally.

Install a recent version of R and Rstudio.

In R, run install.packages("rmarkdown"), which will also install knitr.

In Rstudio, go to tools -> global options -> Sweave and set "weave Rnw files using" to knitr.

To check whether everything is running, download and unzip the example presentation.

Open rdwd_pres.Rnw and click "compile PDF" (CTRL+SHIFT+K).

If LaTeX produces errors because no figures are created, try the following:

• install the rdwd package manually with install.packages("rdwd") in R
• remove the cache folder
• compile again

For my presentations, I am now using a template:

install.packages("berryFunctions")
berryFunctions::instGit("brry/berryFunctions") # createPres is not on CRAN yet
library(berryFunctions)
?createPres

Part 1 (Berry, 1 hour)

• 05 min: general LaTeX intro
• 10: doc structure, document class beamer
• 10: compiling
• 05: sectioning
• 10: including figures
• 05: onslide, pause, <+->
• 05: knitr intro
• 10: real life example

10 min break

Part 2 (Irene, 45 min)

• 05: document class
• 10: subsections, Table of contents (TOC)
• 10: tables (Website tex table generator)
• 10: equations
• 10: templates

For literature management, I recommend to use zotero as a Firefox addon. On journal article pages, simply save references into zotero, then export as BibLaTex file, e.g. myreferences.bib.

If (instead of just bibtex) you want to use the modern biblatex with biber, set the following:

• In TexMaker - Options - configure TexMaker - Commands change the Bibtex entry from "bibtex %.aux" to "biber %" or "biber %.bcf".
• In TexMaker - Options - configure TexMaker - Quick build select "PdfLaTeX + Bib(la)tex + PdfLaTeX (x2) + View pdf"
• In the document itself, use \usepackage[backend=biber]{biblatex}, \bibliography{myreferences} and \printbibliography{}.

Here is a complete example (included as tex file along with myreferences.bib in the example folder):

\documentclass[11pt,a4paper]{article}
\usepackage[utf8]{inputenc}

\usepackage[backend=biber,
  citestyle=authoryear,
  natbib=true,              % for \citet etc
  maxcitenames=2]{biblatex}
\bibliography{myreferences} % filename without file extension!

\begin{document}
This is random sample text, so go ahead and read our paper \citet{boessenkool_effects_2016} and  maybe also
\citet{allan_anticipated_2010}.

\printbibliography{}

\end{document}