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% packages
\usepackage{hyperref} % allows clickable urls
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% define title page
\title{\LaTeX \ for scientists }
\subtitle{ }
\author{Julien Riou}
\date{13 February 2019}
\institute{institute}
% begin document
\begin{document}
\frame{\titlepage}
\frame{
\frametitle{Plan}
\begin{itemize}
\item What is \LaTeX ?
\item Writing and compiling \LaTeX \ code
\item Basic formatting
\item Advanced topics
\item \LaTeX \ templates for scientists:
\begin{itemize}
\item[-] cover letter
\item[-] scholarly article
\item[-] journal submission
\item[-] presentation
\end{itemize}
\end{itemize}
}
\frame{
\frametitle{\LaTeX \ is \ldots}
\ldots a sophisticated \alert{typesetting system}.
\medskip\pause
Different from a ``\textit{what you see is what you get}" word processor:
\begin{itemize}
\item \alert{program} the structure and contents of a document
\item compile the \LaTeX \ code into an output file (PDF)
\end{itemize}
\medskip\pause
Very good for:
\begin{itemize}
\item professional-looking documents with a \alert{pre-specified format}
\item structure, reproductibility
\item maths, cross-referencing, bibliographies
\end{itemize}
\medskip\pause
Less good for:
\begin{itemize}
\item creating highly personalized documents
\end{itemize}
}
\frame{
\frametitle{Writing and compiling \LaTeX \ code}
\textit{In principle}, you only need a text editor and a \LaTeX \ compiler:
\begin{itemize}
\item write your code and save it as a \texttt{.tex} file
\begin{itemize}
\item[-] e.g. with notepad in Windows
\end{itemize}
\item compile the \texttt{.tex} file into an output file (generally \texttt{.pdf})
\begin{itemize}
\item[-] e.g. with MiK\TeX \ for Windows or \TeX \ Live for MacOS and Linux
\end{itemize}
\end{itemize}
\bigskip\pause
\textit{In practice}, it is easier to use an integrated development environment:
\begin{itemize}
\item installed on your computer: \alert{\TeX Studio} (\url{www.texstudio.org})
\begin{itemize}
\item[-] but you still need to install a compiler!
\end{itemize}
\item online: \alert{Overleaf} (\url{www.overleaf.com})
\end{itemize}
}
\frame{
\frametitle{Commands}
\LaTeX~ commands start with \alert{\textbackslash} and are of two kinds:
\begin{block}{Declarations}
\begin{itemize}
\item Are stated once and take effect until further notice
\end{itemize}
e.g. \texttt{\textbackslash documentclass}, \texttt{\textbackslash centering}, \texttt{\textbackslash textit\{\}}
\end{block}
\begin{block}{Environments}
\begin{itemize}
\item Have matching \texttt{begin} and \texttt{end} declarations
\end{itemize}
e.g. \texttt{\textbackslash begin\{itemize\} \ldots \textbackslash end\{itemize\}}
\end{block}
\medskip
\alert{Beware}, forgetting closing braces or end declarations will give an error!
}
\frame{
\frametitle{Arguments}
\begin{block}{Required arguments\ldots}
\begin{itemize}
\item Are contained in curly braces
\item Must be included
\end{itemize}
e.g. \texttt{\textbackslash documentclass\{\underline{letter}\}}
\end{block}
\begin{block}{Optional arguments\ldots}
\begin{itemize}
\item Are contained in square brackets
\item Can be left out
\item Give you more control over the commands
\end{itemize}
e.g. \texttt{\textbackslash documentclass[\underline{12pt}]\{letter\}}
\end{block}
}
\frame{
\frametitle{A basic \texttt{.tex} file}
\begin{enumerate}
\item Declare the type of document you want (\texttt{book, article, letter, report}\ldots) with \texttt{\textbackslash documentclass} \vspace{.5em}
\item Declare additional options or packages (\texttt{float, amsmath, geometry}\ldots) with \texttt{\textbackslash usepackage} \vspace{.5em}
\item Write your content within a \texttt{document} environment \vspace{1em} \pause
\hspace{1em}\texttt{\textbackslash documentclass\{\}} \\
\hspace{1em}\texttt{\%\textbackslash usepackage\{\}} \\
\hspace{1em}\texttt{\textbackslash begin\{document\}} \\
\hspace{2em}\ldots\\
\hspace{1em}\texttt{\textbackslash end\{document\}}
\end{enumerate}
}
%
%\frame{
% \frametitle{Document class}
% \LaTeX~has several basic templates selected using \texttt{\textbackslash documentclass}:
% \begin{itemize}
% \item book, article, report, letter \ldots
% \end{itemize}
%
% \pause
% \begin{block}{Options:}
% \begin{itemize}
% \item Default font size: \texttt{10pt}, \texttt{11pt}, \texttt{12pt}
% \item Paper size: \texttt{a4paper}, \texttt{letterpaper}
% \item Printing: \texttt{twoside}, \texttt{oneside}
% \end{itemize}
% \end{block}
% For example, if you want a report to be in 12pt type on A4, but printed one-sided, you would use:\vspace{.3em}
%
% \hspace{1em}\texttt{\textbackslash documentclass[12pt,a4paper,oneside]\{report\}}
%
%}
\frame{
\frametitle{Hello, world!}
Let's try a simple ``Hello, world!'' example with \LaTeX~and Overleaf:
\begin{itemize}
\item Go to \url{www.overleaf.com} and log in with your credentials
\item Create a new project, then an empty document named \texttt{helloworld.tex}
\item Create a \texttt{letter} that says ``Hello, world!'' \pause
\begin{block}{Solution}
\vspace{.3em}
\hspace{5em}\texttt{\textbackslash documentclass\{letter\}} \\
\hspace{5em}\texttt{\%\textbackslash usepackage\{\}} \\
\hspace{5em}\texttt{\textbackslash begin\{document\}} \\
\hspace{8em}Hello, world! \\
\hspace{5em}\texttt{\textbackslash end\{document\}}
\end{block}
\end{itemize}
}
\frame{
\frametitle{Basic formatting}
\begin{itemize}
\item font styles
\item special characters
\item lists
\item sectioning
\item figures
\item cross-referencing
\item bibliography
\item equations
\end{itemize}
}
\frame{
\frametitle{Font style}
\begin{block}{Font face:}
\texttt{\textbackslash textit\{}\textit{Text}\texttt{\}},
\texttt{\textbackslash textbf\{}\textbf{Text}\texttt{\}},
\texttt{\textbackslash texttt\{}\texttt{Text}\texttt{\}},
\texttt{\textbackslash textsc\{}\textsc{Text}\texttt{\}} \ldots
\end{block}\pause
\begin{block}{Font size:}
\texttt{\textbackslash tiny\{\tiny{Text}}\texttt{\}},
\texttt{\textbackslash scriptsize\{\scriptsize{Text}}\texttt{\}},
\texttt{\textbackslash footnotesize\{\footnotesize{Text}}\texttt{\}},
\texttt{\textbackslash small\{\small{Text}}\texttt{\}},
\texttt{\textbackslash large\{\large{Text}}\texttt{\}},
\texttt{\textbackslash Large\{\Large{Text}}\texttt{\}},
\texttt{\textbackslash huge\{\huge{Text}}\texttt{\}}
\end{block}\pause
\begin{block}{Alignment:}
\texttt{\textbackslash begin\{center/flushright/flushleft\}\\
\ldots\\
\textbackslash end\{center/flushright/flushleft\}}
\end{block}
}
\frame{
\frametitle{Special characters and commands}
\begin{block}{Special commands}
\texttt{\textbackslash} or $\sim$ $\rightarrow$ extra single space \\
\texttt{\textbackslash \textbackslash} $\rightarrow$ new line \\
\texttt{\textbackslash hspace\{1cm\}} or \texttt{\textbackslash vspace\{5mm\}} $\rightarrow$ custom space \\
\texttt{\textbackslash clearpage} $\rightarrow$ new page \\
\end{block} \pause
\begin{block}{Non-standard characters:}
\texttt{\textbackslash \%} $\rightarrow$ \% (used for commenting out)\\
\texttt{\textbackslash \&} $\rightarrow$ \& (used for separations) \\
\texttt{\textbackslash \{} $\rightarrow$ \{ (used in commands) \\
\texttt{\textbackslash textbackslash} $\rightarrow$ \textbackslash \ (used in commands) \\ \vspace{.2cm}
\textit{and lots of other symbols:} $\spadesuit$, $\phi$, $\mathfrak{R}$, $\mathcal{R}$, $\dagger$, $\lll$, $\notin$, $\triangle$\ldots (try \texttt{detexify}) \\
\end{block}
}
\frame{
\frametitle{Lists}
\begin{block}{Bullet list:}
\vspace{2mm}
\begin{columns}
\column{0.6\textwidth}
\hspace{1.5cm}\texttt{\textbackslash begin\{itemize\} \\
\hspace{2cm}\text\textbackslash item} Text \\
\hspace{2cm}\texttt{\textbackslash item}[-] Text \\
\hspace{1.5cm}\texttt{\textbackslash end\{itemize\}}
\column{0.4\textwidth}
\begin{itemize}
\item Text
\item[-] Text
\end{itemize}
\end{columns}
\end{block}\pause
\begin{block}{Numbered list:}
\vspace{2mm}
\begin{columns}
\column{0.6\textwidth}
\hspace{1.5cm}\texttt{\textbackslash begin\{enumerate\} \\
\hspace{2cm}\text\textbackslash item} Text \\
\hspace{2cm}\texttt{\textbackslash item} Text \\
\hspace{1.5cm}\texttt{\textbackslash end\{enumerate\}}
\column{0.4\textwidth}
\begin{enumerate}
\item Text
\item Text
\end{enumerate}
\end{columns}
\end{block}\pause
\vspace{1em}
Note: Lists can be nested within other lists.
}
\frame{
\frametitle{Sectioning}
\LaTeX~ can \alert{organize, number, and index} sections of document: \\\vspace{.5em}
\hspace{1em}\texttt{\textbackslash section\{Introduction\}}\vspace{.7em} \hspace{3em}{\large \textbf{1 Introduction}}
\hspace{1em}\texttt{\textbackslash subsection\{Context\}}\vspace{.7em} \hspace{4.5em}\textbf{1.1 Context}
\pause
\begin{block}{Layers of sectioning}
\hspace{2mm} \textcolor{gray}{\large{ \textbackslash part\{\}}
\textbackslash chapter\{\} }
{\small \textbackslash section\{\}}
{\footnotesize \textbackslash subsection\{\}}
{\scriptsize \textbackslash subsubsection\{\}}
{\tiny \textbackslash paragraph\{\}}
\end{block}
\vspace{1em}\pause
For the unnumbered version, add an asterisk: \\\vspace{.5em}
\hspace{1em}\texttt{\textbackslash section*\{Introduction\}} \hspace{3em}{\large \textbf{ Introduction}} \pause
\vspace{1.5em}Note: Add a table of contents with \texttt{\textbackslash tableofcontents}
}
\frame{
\frametitle{Figures}
Figures must be added as \alert{independent files} in the same repertory. \\\vspace{.3em} \pause
\texttt{\hspace{1cm}\textbackslash begin\{figure\}[h] \\
\hspace{1.5cm}\textbackslash centering \\
\hspace{1.5cm}\textbackslash includegraphics[width=2cm,height=3cm]\{cat.png\} \\
\hspace{1.5cm}\textbackslash caption\{This is my cat.\} \\
\hspace{1cm}\textbackslash end\{figure\}}\pause
\begin{block}{Placement options:}
\vspace{-3mm}
\begin{itemize}
\item \texttt{h}: approximately at the same point it occurs in the code
\item \texttt{t}/\texttt{b}: at the top/bottom of the page
\item \texttt{p}: on a special page for figures only
\item \texttt{H}: \textit{precisely} at the same point in the code (requires a package: \texttt{\textbackslash usepackage\{float\}})
\end{itemize}
\end{block}
}
\frame{
\frametitle{Cross-referencing}
\LaTeX \ handles all references using \alert{unique identifiers}.
\begin{itemize}
\item place a label after something (section, figure caption...) \\
\texttt{
\hspace{.7cm}\textcolor{gray}{\textbackslash begin\{figure\}[ht]} \\
\hspace{1.5cm}\textcolor{gray}{\textbackslash centering} \\
\hspace{1.5cm}\textcolor{gray}{\textbackslash includegraphics\{cat.png\}} \\
\hspace{1.5cm}\textcolor{gray}{\textbackslash caption\{This is my cat.\}} \\
\hspace{1.5cm}\textbackslash label\{\textcolor{blue}{refcat}\} \\
\hspace{1cm}\textcolor{gray}{\textbackslash end\{figure\}}
}\vspace{.5em}\pause
\item then refer to the same identifier at any point in the text \\\vspace{.5em}
\hspace{1cm}\texttt{My cat is very cute (see Fig.\textbackslash ref\{\textcolor{blue}{refcat}\}}).\\\vspace{.3em}
\hspace{2cm}$\rightarrow$ My cat is very cute (see Fig. 1).
\end{itemize}
}
\frame{
\frametitle{Bibliography I}
Same principle for citing books or articles, except that the information must be placed in a \alert{separate bib\TeX~file} in the same repertory.
\begin{itemize}
\item use the \texttt{\textbackslash cite} command instead:\vspace{.3em}
\hspace{-.9cm}\texttt{My cat is the product of evolution\textbackslash cite\{\textcolor{blue}{darwin1859origin}\}}. \vspace{.3em}\pause
\item place the corresponding information in a separate \texttt{foo.bib} file:\\\vspace{.3em}
\texttt{
\hspace{.7cm}@book\{\textcolor{blue}{darwin1859origin}, \\
\hspace{1.5cm}title=\{On the origin of species\},\\
\hspace{1.5cm}author=\{Darwin, Charles\},\\
\hspace{1.5cm}year=\{1859\} \}
}
\vspace{.3em}\pause
\item add a reference to the \texttt{foo.bib} file at the end of the source file:\\\vspace{.3em}
\texttt{
\hspace{.7cm}\textbackslash bibliographystyle\{plain\} \\
\hspace{.9cm}\textbackslash bibliography\{foo\}
}
\end{itemize}
}
\frame{
\frametitle{Bibliography II}
Several basic \alert{styles} are included (\texttt{apalike, unsrt, abbrv}) and journal-specific styles can be added. \\\vspace{2em}
The bib\TeX~ file can be created:
\begin{itemize}
\item manually
\item copied from e.g. \url{https://scholar.google.ch/}
\begin{figure}[h]
\centering
\includegraphics[height=2cm]{google_scholar.png}
\end{figure}
\item directly from Zotero or Endnote (export as bibtex)
\end{itemize}
}
\frame{
\frametitle{Equations I}
\LaTeX~allows you to typeset any sort of equations with \alert{reliability}.
\begin{block}{Using math mode}
Inline math mode: \texttt{\$\ldots\$}
\begin{center}
Consider subject $i \in \{1,\ldots,n\}$...
\end{center}
Numbered equations: \texttt{\small \textbackslash begin\{equation\}\ldots\textbackslash end\{equation\}}
\begin{equation}
\text{logit} \ \mathds{E}(Y) = \alpha+\beta x
\end{equation}
\end{block}
}
\frame{
\frametitle{Equations II}
Some commands:
\begin{center}
\begin{tabular}{rl}
$4+2$ & \texttt{\$4+2\$} \\ \pause
$\sqrt{5}$ & \texttt{\$\textbackslash sqrt\{5\}\$} \\ \pause
$\frac{x}{y}$ & \texttt{\$\textbackslash frac\{x\}\{y\}\$} \\ \pause
$Y^{m}_{i}$ & \texttt{\$Y\^{}\{m\}\_\{i\}\$} \\ \pause
$\sum_{i=1}^n x_i$ & \texttt{\$\textbackslash sum\_\{i=1\}\^{}n x\_i\$} \\ \pause
$Y \sim \mathcal{N}(0,1)$ & \texttt{\$Y \textbackslash sim \textbackslash mathcal\{N\}(0,1) \$} \\ \pause
$\alpha \in \{\alpha,\beta\}$ & \texttt{\$\textbackslash alpha \textbackslash in \textbackslash \{\textbackslash alpha,\textbackslash beta\}\$} \\ \pause
$f''(\xi)$ & \texttt{\$f''(\textbackslash xi)\$} \\ \pause
180$^{\circ}$C & \texttt{180\$\^{}\{\textbackslash circ\}\$C} \\
\end{tabular}
\end{center}
}
\frame{
\frametitle{Advanced topics}
\framesubtitle{Tables I}
Creating tables manually can be \alert{tricky}. \\\vspace{1em}
\begin{columns}
\column{0.7\textwidth}
\texttt{
\textbackslash begin\{table\}[h] \\
\hspace{.5cm}\textbackslash centering \\
\hspace{.3cm} \only<2->{\textbackslash begin\{tabular\}\{\textcolor{blue}{r|c|c}\} } \\
\hspace{.8cm} \only<3->{Trial \& n \& t \textbackslash\textbackslash~\textbackslash hline} \\
\hspace{.8cm} \only<4->{1 \& 23 \& 2 \textbackslash\textbackslash~\textbackslash hline} \\
\hspace{.8cm} \only<5->{2 \& 15 \& 10 \textbackslash\textbackslash~\textbackslash hline} \\
\hspace{.8cm} \only<6->{3 \& 100 \& 20 \textbackslash\textbackslash~} \\
\hspace{.3cm} \only<2->{\textbackslash end\{tabular\}} \\
\hspace{.2cm}\textbackslash end\{table\}
}
\column{0.3\textwidth}
\begin{table}
\centering
\begin{tabular}{r|c|c}
Trial & n & t \\ \hline
1 & 23 & 2 \\ \hline
2 & 15 & 10 \\ \hline
3 & 100 & 20 \\
\end{tabular}
\end{table}
\end{columns}
\vspace{-3em}
}
\frame{
\frametitle{Advanced topics}
\framesubtitle{Tables II}
Beyond simple tables it is preferable to use \alert{dedicated tools}:
\begin{itemize}
\item online convertors (e.g. \url{https://tablesgenerator.com/})
\item R package: \texttt{xtable}
\item Stata function: \texttt{esttab}
\end{itemize}
}
\frame{
\frametitle{Advanced topics}
\framesubtitle{Collaborating}
From simple to more difficult (but more powerful):
\begin{itemize}
\item drafting in Word and pasting the final version into \LaTeX \pause
\item using comments in the source code \\
\texttt{\hspace{1em}\% this sentence is really stupid}\pause
\item inline additions in the compiled PDF \\
\texttt{\hspace{1em}\textbackslash textcolor\{red\}\{SAD!\}}\pause
\item writing in margins (or in boxes with package \texttt{\alert{todonotes}})\\
\texttt{\hspace{1em}\textbackslash marginpar\{you are fired\}}\pause
\item highlighting modifications using \texttt{\alert{latexdiff}} \pause
\item version control: paid overleaf account, \texttt{svn}, \texttt{\alert{git}}
\end{itemize}
\vspace{-1cm}
}
\frame{
\frametitle{\LaTeX \ templates for scientists}
Templates to fill the needs of scientists:
\begin{itemize}
\item \alert{scholarly article}
\item journal submission
\item letters (cover letter, answer to reviewers)
\item presentation
\end{itemize}
\vspace{1em}
Download the files from: \\
\centering\underline{\smash{\url{https://github.com/jriou/LaTeX_for_scientists}}}
}
\frame{
\frametitle{\LaTeX \ templates for scientists}
\framesubtitle{Scholarly article}
Creating \alert{professional-looking} articles with the same methods used by journal publishers.
\vspace{1em}
Very important for \alert{directly published} academic documents:
\begin{itemize}
\item preprints (e.g. for bioRxiv)
\item supplementary appendices
\end{itemize}\pause
\begin{block}{How to use it}
\begin{itemize}
\item upload all 3 files in \texttt{/scholarly\_article} to Overleaf
\item select \texttt{scholarly\_article.tex} and hit the ``recompile'' button
\end{itemize}
\end{block}
\vspace{-2.5em}
}
\frame{
\frametitle{\LaTeX \ templates for scientists}
\framesubtitle{Journal submission}
Some academic journals provide \LaTeX~templates for submissions (e.g., PLoS Medicine \href{https://journals.plos.org/plosmedicine/s/latex}{\underline{here}}). \pause
\begin{block}{How to use it}
\begin{itemize}
\item upload all 2 files in \texttt{/plos\_submission\_template} to Overleaf
\item select \texttt{plos\_latex\_template.tex} and hit the ``recompile'' button
\end{itemize}
\end{block}
}
\frame{
\frametitle{\LaTeX \ templates for scientists}
\framesubtitle{Letters}
Provided by the University (\href{http://intern.unibe.ch/dienstleistungen/corporate_design_und_vorlagen/index_ger.html}{\underline{here}})\\\vspace{.3em}
Especially useful for \alert{cover letters} and \alert{responses to reviewers} \pause
\begin{block}{How to use it}
\begin{itemize}
\item open the \texttt{/cover\_letter} repertory
\item open the \texttt{.clo} file in any editor to modify the personal settings
\item comment out the 5th line (starting with ``\texttt{\textbackslash PackageError}'')
\item upload all 5 files to Overleaf
\item start your letter from the \texttt{.tex} file
\begin{itemize}
\item[-] options in \textbackslash \texttt{documentclass[]}: english/german, color/bw...
\item[-] recipient address, subject, opening, main text, closing
\end{itemize}
\end{itemize}
\end{block}
\vspace{-1.3cm}
}
\frame{
\frametitle{\LaTeX \ templates for scientists}
\framesubtitle{Presentation}
\alert{Surprise} (?) this presentation was made in \LaTeX! \\\vspace{.5em}
There is a document class called \texttt{\alert{beamer}} that allows to do presentations (a template is provided by the University \href{http://intern.unibe.ch/dienstleistungen/corporate_design_und_vorlagen/praesentationen/index_ger.html}{\underline{here}}).\\\vspace{.3em} \pause
\begin{block}{How to use it}
\begin{itemize}
\item upload all 4 files in \texttt{/beamer} to Overleaf
\item select \texttt{unibern-demo.tex} and hit the ``recompile'' button
\end{itemize}
\end{block}
}
\frame{
\frametitle{Acknowledgments}
\begin{itemize}
\item MIT Introduction to \LaTeX~(\underline{\href{https://web.mit.edu/rsi/www/pdfs/new-latex.pdf}{link}})
\item Peter Flom, \LaTeX~for academics and researchers who (think they) don't need it. (\underline{\href{https://www.tug.org/TUGboat/tb28-1/tb88flom.pdf}{link}})
\item \LaTeX~wikibook (\underline{\href{https://en.wikibooks.org/wiki/LaTeX}{link}})
\item \LaTeX~cheat sheet (\underline{\href{http://wch.github.io/latexsheet/}{Winston Chang}})
\end{itemize}
}
\end{document}
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