latex-aez-notes

\documentclass[preview,varwidth=true]{standalone}

\usepackage{amsmath}
\usepackage{amssymb}

\begin{document}

\begin{equation}
  h^2 = a^2 + b^2
\end{equation}

\end{document}

\documentclass[preview,border=0.7cm,varwidth=11.8cm,convert={density=300,size=1080x800,outext=.png}]{standalone}

%% r0-in-words.tex
%% ===============
%%
%% This produces a simple image spelling out the effective
%% reproduction number of a birth-death-sampling model.
%%
%% Usage
%% -----
%%
%% pdflatex -shell-escape r0-in-words
%%

\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{xcolor}

\begin{document}

{\fontfamily{phv}\fontsize{12}{10}\selectfont
  The \emph{effective reproduction number}, \(R\), is the expected number
  of secondary cases per infectious individual.

  \vspace{0.7cm}
  \noindent
  For the birth-death-sampling model
\begin{align*}
  R \quad=&\quad  \frac{\text{birth rate}}{\text{net removal rate}} \hspace{3.0cm} \\
  =& \quad\frac{\lambda}{\mu + \psi + \omega}
\end{align*}
}

\end{document}

pdflatex -shell-escape r0-in-words

\documentclass[
  preview,border=0.7cm,varwidth=12.8cm,
  convert={density=300,size=1080x800,outext=.png}]{standalone}

%% bibliography-slide.tex
%% ======================
%%
%% Usage
%% -----
%%
%% To create a slide with the bibliography, run the following command:
%%
%% pdflatex bibliography-slide
%% pdflatex bibliography-slide
%% biber bibliography-slide
%% pdflatex -shell-escape bibliography-slide
%%
%% This will create a file called `bibliography-slide.png` which can
%% be included in a presentation. It reads the references from
%% references.bib

\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{xcolor}

%% Since slides often use helvetica, these lines ensure the references
%% are printed in helvetica.
\usepackage[scaled]{helvet}
\renewcommand{\sfdefault}{phv}
\renewcommand{\familydefault}{\sfdefault}

\usepackage[
  backend=biber,
  style=authoryear,
  dashed=false,
  maxcitenames=2,
  maxbibnames=2]{biblatex}
\addbibresource{references.bib}

\begin{document}

\printbibliography[heading=none]
\nocite{*}

\end{document}

@article{stadler2009incomplete,
  title =        {{O}n incomplete sampling under birth-death models and
                  connections to the sampling-based coalescent},
  journal =      "Journal of Theoretical Biology",
  volume =       261,
  number =       1,
  pages =        "58--66",
  year =         2009,
  doi =          "10.1016/j.jtbi.2009.07.018",
  author =       "Tanja Stadler"
}

@article{stadler2010sampling,
  title =        {{S}ampling-through-time in birth-death trees},
  author =       "Tanja Stadler",
  journal =      "Journal of Theoretical Biology",
  volume =       267,
  number =       3,
  pages =        "396--404",
  year =         2010,
  doi =          "10.1016/j.jtbi.2010.09.010"
}

@article{stadler2011estimating,
  author =       {Stadler, Tanja and Kouyos, Roger and Bonhoeffer, Sebastian and
                  Joos, Beda and G\"{u}nthard, Huldrych F. and Rieder, Philip and
                  von Wyl, Viktor and Yerly, Sabine and B\"{o}ni, J\"{u}rg and
                  B\"{u}rgisser, Philippe and Klimkait, Thomas and Drummond, Alexei
                  J. and Xie, Dong and the Swiss HIV Cohort Study},
  title =        {{Estimating the Basic Reproductive Number from Viral Sequence
                  Data}},
  journal =      {Molecular Biology and Evolution},
  volume =       29,
  number =       1,
  pages =        {347-357},
  year =         2011,
  month =        09,
  issn =         {0737-4038},
  doi =          {10.1093/molbev/msr217}
}

pdflatex bibliography-slide
pdflatex bibliography-slide
biber bibliography-slide
pdflatex -shell-escape bibliography-slide

\documentclass[9pt,twocolumn]{scrartcl}
% \documentclass{article}

% ------------------------------------------------------------
% Packages
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage[a4paper]{geometry}
\geometry{margin=0.75in}
\usepackage{hyperref}
% ------------------------------------------------------------

% ------------------------------------------------------------
% Macros
\newcommand{\name}[0]{}
% ------------------------------------------------------------

% ------------------------------------------------------------
% Title information
\title{Fleeb}
\date{}
\author{Squanchy}
% ------------------------------------------------------------

\begin{document}

\maketitle

Here is some text

\end{document}

\documentclass[12pt,a4paper]{letter}

% -------------------------------------------------------------------------------
%       PAPER MARGINS
%-------------------------------------------------------------------------------

\textwidth 5.50in
\textheight 9.25in
\oddsidemargin 0.40in
\evensidemargin 0.00in
\topmargin -0.50in
\longindentation 0.50\textwidth
\parindent 0.2in

%-------------------------------------------------------------------------------
%       SENDER INFORMATION
%-------------------------------------------------------------------------------

\def\Who{Alexander E. Zarebski}
\def\Where{Department of Zoology\\University of Oxford}
\def\Address{South Parks Road}
\def\CityZip{Oxford OX1 3SY}
\def\Email{alexander.zarebski@zoo.ox.ac.uk}
% \def\URL{http://www.rmit.edu.au/}

%-------------------------------------------------------------------------------
%       HEADER AND FROM ADDRESS STRUCTURE
%-------------------------------------------------------------------------------

\address{
\hspace{5in}
\vskip -1.1in~\\
~\\[-0.11in]
\hspace{\fill}\parbox[t]{2.85in}{
\footnotesize
\Who \\
\Where\\
\Address\\
\CityZip\\
\Email\\
% \URL
}
\hspace{-1.3in} % Horizontal position of this block
\vspace{-1in}
}

%-------------------------------------------------------------------------------
%       TO ADDRESS STRUCTURE
%-------------------------------------------------------------------------------

\def\opening#1{\thispagestyle{empty}
{\centering\fromaddress \vspace{1.5in} \\
\today \hspace*{\fill}\par}
{\raggedright \toname \\ \toaddress \par}
\vspace{0.5in} % White space after the to address
\noindent #1
}

%-------------------------------------------------------------------------------
%       SIGNATURE
%-------------------------------------------------------------------------------

\signature{\Who}

\long\def\closing#1{
\vspace{0.2in}
\noindent
% \hspace*{\longindentation} % Move the signature right
\parbox{\indentedwidth}{\raggedright
#1 % Print the signature text
\vskip 0.2in % Whitespace between the signature text and your name
\fromsig}}

% -------------------------------------------------------------------------------

\begin{document}

%-------------------------------------------------------------------------------
%       TO ADDRESS
%-------------------------------------------------------------------------------

\begin{letter}
  {
    Prof. Donald E. Knuth \\
    Computer Science Department \\
    Gates Building 4B \\
    Stanford University \\
    Stanford, CA 94305-9045 USA. \\
    \vspace{0.3in}
    \textbf{Re: Letters with \LaTeX}}

%-------------------------------------------------------------------------------
%       LETTER CONTENT
%-------------------------------------------------------------------------------

\opening{Dear Prof. Knuth,}\\

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor
incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu
fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in
culpa qui officia deserunt mollit anim id est laborum.

\vspace{0.2in}
\closing{Kind Regards,}
%-------------------------------------------------------------------------------
\end{letter}
\end{document}

\documentclass{letter}
\usepackage{graphicx}
\usepackage{lipsum}

% -------------------------------------------------------------------------------
%       PAPER MARGINS
%-------------------------------------------------------------------------------

\topmargin -0.70in
\textwidth 6.00in
\textheight 9.25in
\oddsidemargin 0.20in
\evensidemargin -0.20in

% -------------------------------------------------------------------------------
%       LETTER
%-------------------------------------------------------------------------------

\begin{document}

\begin{letter}{
    Admissions Committee \\
    Master of Science in Data Science Programme \\
    School of Computer Science and Engineering \\
    Nanyang Technological University \\
    Singapore}

\begin{minipage}[t]{0.48\textwidth}
    Dr Alexander E. Zarebski \\
    Lecturer in Applied Mathematics \\
    School of Mathematics \& Statistics \\
    University of Melbourne \\
    Peter Hall Building \\
    Parkville, VIC, 3010 \\
    Email: azarebski@unimelb.edu.au
\end{minipage}
\hfill
\begin{minipage}[t]{0.48\textwidth}
  \raggedleft
    \raisebox{-0.9\height}{\includegraphics[width=0.4\linewidth]{../resources/UoM_Logo_Vert_Housed_RGB.png}} % Adjust width as needed
\end{minipage}

\vspace{1cm}

\opening{Dear Admissions Committee,}
\vspace{5mm}

\lipsum[1-2] % Replace this with your actual letter content

\vspace{5mm}
\closing{Sincerely,\\[5mm]Alexander}

\end{letter}
\end{document}

\documentclass{beamer}
\usetheme{Madrid}
\usecolortheme{seagull}
\setbeamertemplate{navigation symbols}{}
\setbeamertemplate{footline}{}
\usefonttheme[onlymath]{serif}

\title{How to be cool}
\author{Arthur Herbert Fonzarelli}
\institute{Department of Cool, University of Cool}
\date{1 January 1974}

\begin{document}

\frame[plain]{\titlepage}

\begin{frame}[c]
  \frametitle{Foobar}
  123
\end{frame}

\begin{frame}[c]
  \frametitle{Barfoo}
  abc
\end{frame}

\end{document}

\documentclass[preview,varwidth=true]{standalone}

\usepackage{algorithm}
\usepackage{algorithmic}

\begin{document}

\begin{algorithmic}
\REQUIRE $n \geq 0$
\ENSURE $y = x^n$
\STATE $y \leftarrow 1$
\STATE $X \leftarrow x$
\STATE $N \leftarrow n$
\WHILE{$N \neq 0$}
\IF{$N$ is even}
\STATE $X \leftarrow X \times X$
\STATE $N \leftarrow N / 2$
\ELSE[$N$ is odd]
\STATE $y \leftarrow y \times X$
\STATE $N \leftarrow N - 1$
\ENDIF
\ENDWHILE
\end{algorithmic}

\end{document}

\documentclass{standalone}
\usepackage{pgfgantt}

\begin{document}

\begin{ganttchart}[
  hgrid,
  vgrid,
  title/.style={fill=blue!20},
  title label font=\bfseries\color{black},
  bar/.style={fill=orange!50},
  bar height=0.7,
  group right shift=0,
  group height=.3,
  y unit chart=0.8cm
  ]{1}{12}

  \gantttitle{Week}{12} \\
  \gantttitlelist{1,...,12}{1} \\

  \ganttgroup{Preparation}{1}{3} \\
  \ganttbar{Choose recipe}{1}{1} \\
  \ganttbar{Buy ingredients}{2}{2} \\
  \ganttlinkedbar{Mix ingredients}{3}{3} \ganttnewline

  \ganttgroup{Baking}{4}{9} \\
  \ganttbar{Preheat oven}{4}{4} \\
  \ganttlinkedbar{Bake the cake}{5}{9} \ganttnewline

  \ganttgroup{Decoration}{10}{12} \\
  \ganttbar{Cool the cake}{10}{10} \\
  \ganttlinkedbar{Decorate the cake}{11}{12}
\end{ganttchart}

\end{document}

\newcommand{\R}{\mathbb{R}}
\newcommand{\bb}[1]{\mathbb{#1}}

sudo apt-get install texlive-full

tlmgr install <PACKGENAME>

\usepackage[doublespacing]{setspace}

% or

\usepackage{setspace}
\doublespacing

\usepackage{nopageno}

\documentclass{article}
\usepackage{xcolor}
\newcommand\ytl[2]{
\parbox[b]{8em}{\hfill{\color{cyan}\bfseries\sffamily #1}~$\cdots\cdots$~}\makebox[0pt][c]{$\bullet$}\vrule\quad \parbox[c]{4.5cm}{\vspace{7pt}\color{red!40!black!80}\raggedright\sffamily #2.\\[7pt]}\\[-3pt]}
\begin{document}
\begin{table}
\caption{Timeline of something.}
\centering
\begin{minipage}[t]{.7\linewidth}
\color{gray}
\rule{\linewidth}{1pt}
\ytl{1947}{AT and T Bell Labs develop the idea of cellular phones}
\ytl{1968}{Xerox Palo Alto Research Centre envisage the `Dynabook'}
\ytl{1971}{Busicom 'Handy-LE' Calculator}
\ytl{1973}{First mobile handset invented by Martin Cooper}
\ytl{1978}{Parker Bros. Merlin Computer Toy}
\ytl{1981}{Osborne 1 Portable Computer}
\ytl{1982}{Grid Compass 1100 Clamshell Laptop}
\ytl{1983}{TRS-80 Model 100 Portable PC}
\ytl{1984}{Psion Organiser Handheld Computer}
\ytl{1991}{Psion Series 3 Minicomputer}
\bigskip
\rule{\linewidth}{1pt}%
\end{minipage}%
\end{table}
\end{document}

\begin{table}
  \caption{\label{tab:demo}Go tabular data!}
  \centering
  \fbox{
    \begin{tabular}{lll}
Sepal Length & Sepal Width & Species\\
\hline
5.1 & 3.5 & setosa\\
4.9 & 3.0 & setosa\\
    \end{tabular}
  }
\end{table}

\setcounter{secnumdepth}{1}

\documentclass{article}

\usepackage{authblk}            % provides author affiliations.

\title{Fleeb}
\date{}
\author[1]{Morty Smith\thanks{For correspondence email: yolo@hotmail.com}}
\author[2]{Rick Sanchez}
\affil[1]{Princeton University}
\affil[2]{School of Hard Knocks}

\begin{document}

\maketitle

Here is some text

\end{document}

library(argparse)

parser <- ArgumentParser()
parser$add_argument(
         "tex",
         default = "",
         help = "Input tex file."
       )

main <- function(args) {
  input_tex <- args$tex

  if (!file.exists(input_tex)) {
    stop("Could not find given file: ", input_tex)
  }

  tex_lines <- readLines(input_tex)

  non_comments <- grep(
    pattern = "^%",
    x = tex_lines,
    value = TRUE,
    invert = TRUE)

  cite_pattern <- "[[:alpha:]]+[[:digit:]]+[[:alpha:]]*"
  pattern <- sprintf("%s(,[ ]*%s)*", cite_pattern, cite_pattern)
  matches <- regmatches(non_comments, regexpr(pattern, non_comments))

  for (m in matches) {
    if (grepl(pattern = ",", x = m)) {
      for (mx in unlist(strsplit(x = m, ","))) {
        cat(mx, "\n")
      }
    } else {
      cat(m, "\n")
    }
  }
}

if (!interactive()) {
  args <- parser$parse_args()
  main(args)
}

\documentclass[10pt,a4paper]{article}

\usepackage{hyperref} % for better urls


\begin{document}

This is text with \cite{foo1984bar}.

\nocite{*} % to test all bib entrys
\bibliographystyle{plos2015}
\bibliography{references} % file mwe.bib

\end{document}

pdflatex demo
bibtex demo
pdflatex demo
pdflatex demo

\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[english]{babel}

\usepackage[
natbib=true,
backend=bibtex,
maxcitenames=2,
style=authoryear
]{biblatex}

\addbibresource{references.bib}

\begin{document}

foobar

\printbibliography{}

\end{document}

\usepackage[
natbib=true,
backend=bibtex,
maxcitenames=1,
minbibnames=1,
maxbibnames=1,
style=numeric-comp
]{biblatex}
\renewcommand{\bibfont}{\small}        % small font (approx 10pt)
\defbibheading{bibliography}[\relax]{} % remove title
\setlength{\bibitemsep}{0mm}    % spacing

LANG=C grep --color=always '[^ -~]\+' <path/to/bibliography.bib>

\documentclass[preview]{standalone}
\usepackage[utf8]{inputenc}

\usepackage{tikz}
\usetikzlibrary{positioning}

\begin{document}

\begin{figure}
  \begin{tikzpicture}

    % Put the marvelous tikz diagram code here!!!

  \end{tikzpicture}
\end{figure}

\end{document}

\begin{tikzpicture}[
  roundnode/.style={circle, draw=green!60, fill=green!5, very thick, minimum size=7mm},
  squarednode/.style={rectangle, draw=red!60, fill=red!5, very thick, minimum size=5mm},
  ]

  % Nodes
  \node[squarednode]      (maintopic)                              {2};
  \node[roundnode]        (uppercircle)       [above=of maintopic] {1};
  \node[squarednode]      (rightsquare)       [right=of maintopic] {3};

  % Lines
  \draw[->] (uppercircle.south) -- (maintopic.north);
  \draw[->] (maintopic.east) -- (rightsquare.west);
  \draw[->] (rightsquare.north) .. controls +(up:7mm) and +(right:7mm) .. (uppercircle.east);

\end{tikzpicture}