intermediate latex file

tufte.tex

\documentclass[a4paper,]{tufte-book}

% ams
\usepackage{amssymb,amsmath}

\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[T1]{fontenc}
  \usepackage[utf8]{inputenc}
\else % if luatex or xelatex
  \makeatletter
  \@ifpackageloaded{fontspec}{}{\usepackage{fontspec}}
  \makeatother
  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
  \makeatletter
  \@ifpackageloaded{soul}{
     \renewcommand\allcapsspacing[1]{{\addfontfeature{LetterSpace=15}#1}}
     \renewcommand\smallcapsspacing[1]{{\addfontfeature{LetterSpace=10}#1}}
   }{}
  \makeatother

\fi

% graphix
\usepackage{graphicx}
\setkeys{Gin}{width=\linewidth,totalheight=\textheight,keepaspectratio}

% booktabs
\usepackage{booktabs}

% url
\usepackage{url}

% hyperref
\usepackage{hyperref}

% units.
\usepackage{units}


\setcounter{secnumdepth}{2}

% citations
\usepackage{natbib}
\bibliographystyle{apalike}


% pandoc syntax highlighting
\usepackage{color}
\usepackage{fancyvrb}
\newcommand{\VerbBar}{|}
\newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
% Add ',fontsize=\small' for more characters per line
\newenvironment{Shaded}{}{}
\newcommand{\AlertTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{#1}}}
\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{#1}}}}
\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.49,0.56,0.16}{#1}}
\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{#1}}
\newcommand{\BuiltInTok}[1]{#1}
\newcommand{\CharTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{#1}}
\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textit{#1}}}
\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{#1}}}}
\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.53,0.00,0.00}{#1}}
\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{\textbf{#1}}}
\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.56,0.13,0.00}{#1}}
\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{#1}}
\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.73,0.13,0.13}{\textit{#1}}}
\newcommand{\ErrorTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{#1}}}
\newcommand{\ExtensionTok}[1]{#1}
\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{#1}}
\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.02,0.16,0.49}{#1}}
\newcommand{\ImportTok}[1]{#1}
\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{#1}}}}
\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{\textbf{#1}}}
\newcommand{\NormalTok}[1]{#1}
\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.40,0.40,0.40}{#1}}
\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{#1}}
\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.74,0.48,0.00}{#1}}
\newcommand{\RegionMarkerTok}[1]{#1}
\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{#1}}
\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.73,0.40,0.53}{#1}}
\newcommand{\StringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{#1}}
\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.10,0.09,0.49}{#1}}
\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{#1}}
\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{#1}}}}

% longtable
\usepackage{longtable,booktabs}

% multiplecol
\usepackage{multicol}

% strikeout
\usepackage[normalem]{ulem}

% morefloats
\usepackage{morefloats}


% tightlist macro required by pandoc >= 1.14
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}

% title / author / date
\title{Global Health Research}
\author{Eric P. Green}
\date{2021-08-28}

\usepackage{booktabs}

\usepackage{fontspec}
\setmainfont{LibreBaskerville-Regular}
\setsansfont{SourceSansPro-ExtraLight}
\setmonofont{Inconsolata}

\usepackage[svgnames]{xcolor}
\usepackage{titlesec}
\usepackage{xhfill}
\colorlet{rulecolor}{Gainsboro!40!Lavender}
\usepackage{lipsum}

\titleformat{\chapter}[display]
{\filcenter}{\mbox{}\xrfill[0.4ex]{3pt}[rulecolor]\textsc{\large\enspace\chaptername \thechapter}\enspace\xrfill[0.4ex]{3pt}[rulecolor]\mbox{}}{0.3ex} {{\color{rulecolor}\titlerule[1pt]}\vskip3ex\huge\bfseries}[\medskip{\color{rulecolor}\titlerule[1pt]}]
\usepackage{titling}
\pretitle{\begin{flushleft}\LARGE\bfseries}
\posttitle{\par\end{flushleft}}
\titleformat*{\section}{\Large\bfseries\sffamily}
\titleformat*{\subsection}{\large\bfseries\sffamily}
\usepackage[svgnames]{xcolor}

\usepackage{amsthm}
\newtheorem{theorem}{Theorem}[chapter]
\newtheorem{lemma}{Lemma}[chapter]
\newtheorem{corollary}{Corollary}[chapter]
\newtheorem{proposition}{Proposition}[chapter]
\newtheorem{conjecture}{Conjecture}[chapter]
\theoremstyle{definition}
\newtheorem{definition}{Definition}[chapter]
\theoremstyle{definition}
\newtheorem{example}{Example}[chapter]
\theoremstyle{definition}
\newtheorem{exercise}{Exercise}[chapter]
\theoremstyle{definition}
\newtheorem{hypothesis}{Hypothesis}[chapter]
\theoremstyle{remark}
\newtheorem*{remark}{Remark}
\newtheorem*{solution}{Solution}
\begin{document}

\maketitle



{
\setcounter{tocdepth}{1}
\tableofcontents
}

\hypertarget{about}{%
\chapter{About}\label{about}}

This is a \emph{sample} book written in \textbf{Markdown}. You can use anything that Pandoc's Markdown supports; for example, a math equation \(a^2 + b^2 = c^2\).

\hypertarget{usage}{%
\section{Usage}\label{usage}}

Each \textbf{bookdown} chapter is an .Rmd file, and each .Rmd file can contain one (and only one) chapter. A chapter \emph{must} start with a first-level heading: \texttt{\#\ A\ good\ chapter}, and can contain one (and only one) first-level heading.

Use second-level and higher headings within chapters like: \texttt{\#\#\ A\ short\ section} or \texttt{\#\#\#\ An\ even\ shorter\ section}.

The \texttt{index.Rmd} file is required, and is also your first book chapter. It will be the homepage when you render the book.

\begin{marginfigure}
Testing the use of margin notes.
\end{marginfigure}

\hypertarget{test}{%
\subsection{Test}\label{test}}

??

\hypertarget{render-book}{%
\section{Render book}\label{render-book}}

You can render the HTML version of this example book without changing anything:

\begin{enumerate}
\def\labelenumi{\arabic{enumi}.}
\item
  Find the \textbf{Build} pane in the RStudio IDE, and
\item
  Click on \textbf{Build Book}, then select your output format, or select ``All formats'' if you'd like to use multiple formats from the same book source files.
\end{enumerate}

Or build the book from the R console:

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{bookdown}\SpecialCharTok{::}\FunctionTok{render\_book}\NormalTok{()}
\end{Highlighting}
\end{Shaded}

To render this example to PDF as a \texttt{bookdown::pdf\_book}, you'll need to install XeLaTeX. You are recommended to install TinyTeX (which includes XeLaTeX): \url{https://yihui.org/tinytex/}.

\hypertarget{preview-book}{%
\section{Preview book}\label{preview-book}}

As you work, you may start a local server to live preview this HTML book. This preview will update as you edit the book when you save individual .Rmd files. You can start the server in a work session by using the RStudio add-in ``Preview book'', or from the R console:

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{bookdown}\SpecialCharTok{::}\FunctionTok{serve\_book}\NormalTok{()}
\end{Highlighting}
\end{Shaded}

\hypertarget{hello-bookdown}{%
\chapter{Hello bookdown}\label{hello-bookdown}}

All chapters start with a first-level heading followed by your chapter title, like the line above. There should be only one first-level heading (\texttt{\#}) per .Rmd file.

\hypertarget{a-section}{%
\section{A section}\label{a-section}}

All chapter sections start with a second-level (\texttt{\#\#}) or higher heading followed by your section title, like the sections above and below here. You can have as many as you want within a chapter.

\hypertarget{an-unnumbered-section}{%
\subsection*{An unnumbered section}\label{an-unnumbered-section}}
\addcontentsline{toc}{subsection}{An unnumbered section}

Chapters and sections are numbered by default. To un-number a heading, add a \texttt{\{.unnumbered\}} or the shorter \texttt{\{-\}} at the end of the heading, like in this section.

\hypertarget{cross}{%
\chapter{Cross-references}\label{cross}}

Cross-references make it easier for your readers to find and link to elements in your book.

\hypertarget{chapters-and-sub-chapters}{%
\section{Chapters and sub-chapters}\label{chapters-and-sub-chapters}}

There are two steps to cross-reference any heading:

\begin{enumerate}
\def\labelenumi{\arabic{enumi}.}
\tightlist
\item
  Label the heading: \texttt{\#\ Hello\ world\ \{\#nice-label\}}.

  \begin{itemize}
  \tightlist
  \item
    Leave the label off if you like the automated heading generated based on your heading title: for example, \texttt{\#\ Hello\ world} = \texttt{\#\ Hello\ world\ \{\#hello-world\}}.
  \item
    To label an un-numbered heading, use: \texttt{\#\ Hello\ world\ \{-\#nice-label\}} or \texttt{\{\#\ Hello\ world\ .unnumbered\}}.
  \end{itemize}
\item
  Next, reference the labeled heading anywhere in the text using \texttt{\textbackslash{}@ref(nice-label)}; for example, please see Chapter \ref{cross}.

  \begin{itemize}
  \tightlist
  \item
    If you prefer text as the link instead of a numbered reference use: \protect\hyperlink{cross}{any text you want can go here}.
  \end{itemize}
\end{enumerate}

\hypertarget{captioned-figures-and-tables}{%
\section{Captioned figures and tables}\label{captioned-figures-and-tables}}

Figures and tables \emph{with captions} can also be cross-referenced from elsewhere in your book using \texttt{\textbackslash{}@ref(fig:chunk-label)} and \texttt{\textbackslash{}@ref(tag:chunk-label)}, respectively.

See Figure \ref{fig:nice-fig}.

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{par}\NormalTok{(}\AttributeTok{mar =} \FunctionTok{c}\NormalTok{(}\DecValTok{4}\NormalTok{, }\DecValTok{4}\NormalTok{, .}\DecValTok{1}\NormalTok{, .}\DecValTok{1}\NormalTok{))}
\FunctionTok{plot}\NormalTok{(pressure, }\AttributeTok{type =} \StringTok{\textquotesingle{}b\textquotesingle{}}\NormalTok{, }\AttributeTok{pch =} \DecValTok{19}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

\begin{figure}

{\centering \includegraphics[width=0.8\linewidth]{02-cross-refs_files/figure-latex/nice-fig-1} 

}

\caption[Here is a nice figure!]{Here is a nice figure!}\label{fig:nice-fig}
\end{figure}

Don't miss Table \ref{tab:nice-tab}.

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{knitr}\SpecialCharTok{::}\FunctionTok{kable}\NormalTok{(}
  \FunctionTok{head}\NormalTok{(pressure, }\DecValTok{10}\NormalTok{), }\AttributeTok{caption =} \StringTok{\textquotesingle{}Here is a nice table!\textquotesingle{}}\NormalTok{,}
  \AttributeTok{booktabs =} \ConstantTok{TRUE}
\NormalTok{)}
\end{Highlighting}
\end{Shaded}

\begin{table}

\caption{\label{tab:nice-tab}Here is a nice table!}
\centering
\begin{tabular}[t]{rr}
\toprule
temperature & pressure\\
\midrule
0 & 0.0002\\
20 & 0.0012\\
40 & 0.0060\\
60 & 0.0300\\
80 & 0.0900\\
\addlinespace
100 & 0.2700\\
120 & 0.7500\\
140 & 1.8500\\
160 & 4.2000\\
180 & 8.8000\\
\bottomrule
\end{tabular}
\end{table}

\hypertarget{parts}{%
\chapter{Parts}\label{parts}}

You can add parts to organize one or more book chapters together. Parts can be inserted at the top of an .Rmd file, before the first-level chapter heading in that same file.

Add a numbered part: \texttt{\#\ (PART)\ Act\ one\ \{-\}} (followed by \texttt{\#\ A\ chapter})

Add an unnumbered part: \texttt{\#\ (PART\textbackslash{}*)\ Act\ one\ \{-\}} (followed by \texttt{\#\ A\ chapter})

Add an appendix as a special kind of un-numbered part: \texttt{\#\ (APPENDIX)\ Other\ stuff\ \{-\}} (followed by \texttt{\#\ A\ chapter}). Chapters in an appendix are prepended with letters instead of numbers.

\hypertarget{footnotes-and-citations}{%
\chapter{Footnotes and citations}\label{footnotes-and-citations}}

\hypertarget{footnotes}{%
\section{Footnotes}\label{footnotes}}

Footnotes are put inside the square brackets after a caret \texttt{\^{}{[}{]}}. Like this one \footnote{This is a footnote.}.

\hypertarget{citations}{%
\section{Citations}\label{citations}}

Reference items in your bibliography file(s) using \texttt{@key}.

For example, we are using the \textbf{bookdown} package \citep{R-bookdown} (check out the last code chunk in index.Rmd to see how this citation key was added) in this sample book, which was built on top of R Markdown and \textbf{knitr} \citep{xie2015} (this citation was added manually in an external file book.bib).
Note that the \texttt{.bib} files need to be listed in the index.Rmd with the YAML \texttt{bibliography} key.

The \texttt{bs4\_book} theme makes footnotes appear inline when you click on them. In this example book, we added \texttt{csl:\ chicago-fullnote-bibliography.csl} to the \texttt{index.Rmd} YAML, and include the \texttt{.csl} file. To download a new style, we recommend: \url{https://www.zotero.org/styles/}

The RStudio Visual Markdown Editor can also make it easier to insert citations: \url{https://rstudio.github.io/visual-markdown-editing/\#/citations}

\hypertarget{blocks}{%
\chapter{Blocks}\label{blocks}}

\hypertarget{equations}{%
\section{Equations}\label{equations}}

Here is an equation.

\begin{equation} 
  f\left(k\right) = \binom{n}{k} p^k\left(1-p\right)^{n-k}
  \label{eq:binom}
\end{equation}

You may refer to using \texttt{\textbackslash{}@ref(eq:binom)}, like see Equation \eqref{eq:binom}.

\hypertarget{theorems-and-proofs}{%
\section{Theorems and proofs}\label{theorems-and-proofs}}

Labeled theorems can be referenced in text using \texttt{\textbackslash{}@ref(thm:tri)}, for example, check out this smart theorem \ref{thm:tri}.

\begin{theorem}
\protect\hypertarget{thm:tri}{}\label{thm:tri}For a right triangle, if \(c\) denotes the \emph{length} of the hypotenuse
and \(a\) and \(b\) denote the lengths of the \textbf{other} two sides, we have
\[a^2 + b^2 = c^2\]
\end{theorem}

Read more here \url{https://bookdown.org/yihui/bookdown/markdown-extensions-by-bookdown.html}.

\hypertarget{callout-blocks}{%
\section{Callout blocks}\label{callout-blocks}}

The \texttt{bs4\_book} theme also includes special callout blocks, like this \texttt{.rmdnote}.

You can use \textbf{markdown} inside a block.

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{head}\NormalTok{(beaver1, }\AttributeTok{n =} \DecValTok{5}\NormalTok{)}
\CommentTok{\#\textgreater{}   day time  temp activ}
\CommentTok{\#\textgreater{} 1 346  840 36.33     0}
\CommentTok{\#\textgreater{} 2 346  850 36.34     0}
\CommentTok{\#\textgreater{} 3 346  900 36.35     0}
\CommentTok{\#\textgreater{} 4 346  910 36.42     0}
\CommentTok{\#\textgreater{} 5 346  920 36.55     0}
\end{Highlighting}
\end{Shaded}

It is up to the user to define the appearance of these blocks for LaTeX output.

You may also use: \texttt{.rmdcaution}, \texttt{.rmdimportant}, \texttt{.rmdtip}, or \texttt{.rmdwarning} as the block name.

The R Markdown Cookbook provides more help on how to use custom blocks to design your own callouts: \url{https://bookdown.org/yihui/rmarkdown-cookbook/custom-blocks.html}

\hypertarget{sharing-your-book}{%
\chapter{Sharing your book}\label{sharing-your-book}}

\hypertarget{publishing}{%
\section{Publishing}\label{publishing}}

HTML books can be published online, see: \url{https://bookdown.org/yihui/bookdown/publishing.html}

\hypertarget{pages}{%
\section{404 pages}\label{pages}}

By default, users will be directed to a 404 page if they try to access a webpage that cannot be found. If you'd like to customize your 404 page instead of using the default, you may add either a \texttt{\_404.Rmd} or \texttt{\_404.md} file to your project root and use code and/or Markdown syntax.

\hypertarget{metadata-for-sharing}{%
\section{Metadata for sharing}\label{metadata-for-sharing}}

Bookdown HTML books will provide HTML metadata for social sharing on platforms like Twitter, Facebook, and LinkedIn, using information you provide in the \texttt{index.Rmd} YAML. To setup, set the \texttt{url} for your book and the path to your \texttt{cover-image} file. Your book's \texttt{title} and \texttt{description} are also used.

This \texttt{bs4\_book} provides enhanced metadata for social sharing, so that each chapter shared will have a unique description, auto-generated based on the content.

Specify your book's source repository on GitHub as the \texttt{repo} in the \texttt{\_output.yml} file, which allows users to view each chapter's source file or suggest an edit. Read more about the features of this output format here:

\url{https://pkgs.rstudio.com/bookdown/reference/bs4_book.html}

Or use:

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{?bookdown}\SpecialCharTok{::}\NormalTok{bs4\_book}
\end{Highlighting}
\end{Shaded}


\bibliography{book.bib,packages.bib}



\end{document}