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popgen_notes.tex
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% make clean all
% make site deploy
%\documentclass[12pt,titlepage]{article}
\documentclass{tufte-book}
\usepackage{url}
%\usepackage[authoryear]{natbib}
\bibliographystyle{genetics}
\usepackage{amsfonts}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{graphicx}
\usepackage{rotating}
\usepackage{wasysym}
\usepackage{array}
%\usepackage[normalem]{ulem} %%MArs/Venus symbols
%\usepackage{marginnote}
\usepackage{color,booktabs}
%\usepackage{fullpage}
\usepackage{nicefrac}
\usepackage{csvsimple}
%\usepackage[hypertexnames=false]{hyperref}
\hypersetup{colorlinks=true, urlcolor=black, citecolor=black, linkcolor=black,linkbordercolor=black}
%\usepackage[normalem]{ulem}
%\usepackage{tcolorbox}
\newcommand{\ec}[1]{{\em \color{blue} #1}}
\newcommand{\gc}[1]{{\color{green} #1}} %\color{black} #1}} %
\newcommand{\sa}[1]{{\color{black} #1}}
\newcommand{\plr}[1]{{\em \color{green} (#1)}}
\newcommand{\E}{\mathbb{E}}
\renewcommand{\P}{\mathbb{P}}
\newcommand{\half}{\tfrac{1}{2}}
%FOR compiling on xelatex
\renewcommand\allcapsspacing[1]{{\addfontfeature{LetterSpace=15}#1}}
%%comment out this line for overleaf
\renewcommand\smallcapsspacing[1]{{\addfontfeature{LetterSpace=10}#1}} %%comment out this line for overleaf
\usepackage[colorinlistoftodos ,disable]{todonotes} % ,disable ,disable
%\usepackage[colorlinks=true, allcolors=black]{hyperref}
\newcommand{\wbar}{\overline{w}}
% New commands added by Simon:
\newcommand{\fis}{F_{\mathrm{IS}}}
\newcommand{\fit}{F_{\mathrm{IT}}}
\newcommand{\fst}{F_{\mathrm{ST}}}
\newcommand{\Wbar}{\overline{W}}
\newcommand{\dNdS}{\nicefrac{d_N}{d_S}}
%\newcommand{\graham}[1]{\todo[size=\scriptsize, color=red!50]{#1}}
%Image from the Biodiversity Heritage Library. Contributed by [Holding Institution]. | www.biodiversitylibrary.org
%Image from the Biodiversity Heritage Library. Contributed by [Holding
%Institution]. licensed under CC BY 2.0
\usepackage{caption}
\newcommand{\BHLCC}[4]{\newline \noindent \tiny{#1 Image from the \href{#2}{Biodiversity
Heritage Library}. Contributed by #3. Licensed under CC
BY-#4. \par}} %\caption*{
\newcommand{\BHLNKC}[3]{\newline \noindent \tiny{#1 Image from the \href{#2}{Biodiversity
Heritage Library}. Contributed by #3. No known copyright restrictions.}}
\newcommand{\BHLNC}[3]{\newline \noindent \tiny{#1 Image from the \href{#2}{Biodiversity Heritage Library}. Contributed by #3. Not in copyright.}}
\newcommand{\IANC}[3]{\newline \noindent \tiny{#1 Image from the \href{#2}{Internet Archive}. Contributed by #3. No known copyright restrictions.}}
\newcommand{\gitcode}[1]{Code \href{#1}{here}.}
\newcommand{\PLOSccBY}{{licensed under CC BY 4.0}}
\newcommand{\graham}[1]{\todo[size=\scriptsize, color=red!50]{#1}}
\newcommand{\erin}[1]{\todo[size=\scriptsize, color=blue!50]{#1}}
%\newcounter{Question}[section]
%\setcounter{Question}{1}
\newcounter{question}[chapter] %[section] %%modified from https://www.sharelatex.com/learn/Counters
\newenvironment{question}[1][]{\refstepcounter{question}\par\medskip
\textbf{Question~\thequestion. #1} \rmfamily}{\medskip}
%\newenvironment{question}[1][]{\refstepcounter{question}\par \begin{tcolorbox}
% \medskip \textbf{Question~\thequestion. #1}\rmfamily}{\medskip} \end{tcolorbox}
\setcounter{secnumdepth}{2}
%\newenvironment{question}[1][]{\refstepcounter{question}\par\medskip
% \textbf{Question~\thequestion. #1} \rmfamily}{\medskip}
% Prints the month name (e.g., January) and the year (e.g., 2008)
\newcommand{\monthyear}{%
\ifcase\month\or January\or February\or March\or April\or May\or June\or
July\or August\or September\or October\or November\or
December\fi\space\number\year
}
\definecolor{rev1}{rgb}{1, 0, 0}
\begin{document}
\title{Population and\newline Quantitative \newline Genetics}
\author{Graham Coop}
% \small $^1$ Department of Evolution and Ecology \& Center for Population Biology,\\
% \small University of California, Davis.\\
% \small To whom correspondence should be addressed: \texttt{[email protected]}\\
% \small This work is licensed under a Creative Commons Attribution 3.0 Unported License.\\
% \small http://creativecommons.org/licenses/by/3.0/ \\
% \small i.e. you are free to reuse and remix this work, but please include an attribution to the original.
\date{}
\maketitle
\newpage
\begin{fullwidth}
~\vfill
\thispagestyle{empty}
\setlength{\parindent}{0pt}
\setlength{\parskip}{\baselineskip}
%Copyright \copyright\ \the\year\
Author: \thanklessauthor\\
\small Author address: Department of Evolution and Ecology \& Center for Population Biology,\\
\small University of California, Davis.\\
\small To whom correspondence should be addressed: \texttt{[email protected]}\\
\small This work is licensed under a Creative Commons Attribution 3.0 Unported License.\\
\small http://creativecommons.org/licenses/by/3.0/ \\
\small i.e. you are free to reuse and remix this work, but please include an attribution to the original.
\par Typeset using \LaTeX~and the \smallcaps{tufte-latex} book style.
\par The \LaTeX~code and R code for this book are kept here
https://github.com/cooplab/popgen-notes/ and again are under a Creative Commons Attribution 3.0 Unported License.
\par\textit{Updated on \monthyear}
\end{fullwidth}
\newpage
\tableofcontents
\newpage
\include{Chapters/intro}
\include{Chapters/chapter-01}
\include{Chapters/genetic_drift}
%\include{chapter-03}
\include{Chapters/Pheno_var}
\include{Chapters/Response_to_sel}
\include{Chapters/One_locus_selection}
\include{Chapters/Genetic_drift_selection}
%\include{chapter-07}
\include{Chapters/Linked_selection}
\include{Chapters/multi_locus_sel}
\bibliography{popgen_notes}
\end{document}