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notation-thesis.tex
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% Mathematical functions
% DELETED!
\renewcommand{\Pr}[1]{{\mathbb{P}\left(#1\right) }}
% DELETED!
% DELETED!
% DELETED!
% DELETED!
% DELETED!
% DELETED!
\newcommand{\sufstats}[1]{s\left(#1\right)}
\renewcommand{\exp}[1]{\mbox{exp}\left\{#1\right\}}
\renewcommand{\log}[1]{\mbox{log}\left\{#1\right\}}
\newcommand{\transpose}[1]{{#1}^\mathbf{t}}
\renewcommand{\t}[1]{\transpose{#1}}
\newcommand{\s}[1]{\sufstats{#1}}
\newcommand{\SUFF}{\mathcal{S}}
\newcommand{\Suff}{\mathbf{S}}
\newcommand{\suff}{\mathbf{s}}
\renewcommand{\beta}{\theta}
\newcommand{\weight}{\mathbf{w}}
\newcommand{\Weight}{\mathbf{W}}
% Objects
% DELETED!
% DELETED!
\newcommand{\Graph}{\mathbf{G}}
\newcommand{\graph}{\mathbf{g}}
\newcommand{\GRAPH}{\mathcal{G}}
\newcommand{\Adjmat}{Y}
\newcommand{\adjmat}{y}
\newcommand{\ADJMAT}{\mathcal{Y}}
\newcommand{\INDEPVAR}{\mathcal{X}}
\newcommand{\Indepvar}{X}
\newcommand{\indepvar}{x}
\newcommand{\normconst}{\kappa\left(\params, \Indepvar\right)}
\graphicspath{{./figures/}{.}{./terms/}}
%% NEED THIS FOR CANCY TEX
\usepackage{pstricks}
% Colors
\definecolor{USCCardinal}{HTML}{990000} % 153 0 0 in RGB
\definecolor{USCGold}{HTML}{FFCC00}
\definecolor{USCGray}{HTML}{CCCCCC}
% \bibliography{bibliography.bib}
\def\ergmito{ERGM\textit{ito}}
\def\ergmitos{\ergmito{}\textit{s}}
% Mathematical functions
\newcommand{\isone}[1]{{\boldsymbol{1}\left( #1 \right)}}
\renewcommand{\Pr}[1]{{\mathbb{P}\left(#1\right) }}
\newcommand{\f}[1]{{f\left(#1\right) }}
\newcommand{\Prcond}[2]{{\mathbb{P}\left(#1\vphantom{#2}\;\right|\left.\vphantom{#1}#2\right)}}
\newcommand{\fcond}[2]{{f\left(#1|#2\right) }}
\newcommand{\Expected}[1]{{\mathbb{E}\left\{#1\right\}}}
\newcommand{\ExpectedCond}[2]{{\mathbb{E}\left\{#1\vphantom{#2}\right|\left.\vphantom{#1}#2\right\}}}
\renewcommand{\exp}[1]{\mbox{exp}\left\{#1\right\}}
\newcommand{\Likelihood}[2]{\text{L}\left(#1 \left|\vphantom{#1}#2\right.\right)}
\newcommand{\loglik}[1]{l\left(#1\right)}
% Mathematical Annotation -------------------------------
% Modify this so that it matches the P01 convention overall
% Tree
\newcommand{\phylo}{\Lambda{}} % The actual tree
\newcommand{\aphylo}{D{}} % The annotated phylogenetic tree
\newcommand{\aphyloObs}{\tilde \aphylo{}} % The observed annotated phylogenetic tree
\newcommand{\parent}[1]{\mathbf{p}\left(#1\right)}
\newcommand{\offspring}[1]{\mathbf{O}\left(#1\right)}
\newcommand{\nodes}{\mathcal{N}{}}
\newcommand{\edges}{\mathcal{E}{}}
\newcommand{\class}[1]{C_{#1}{}}
% Annotations
\newcommand{\Ann}{\mathbf{X}{}} % Matrix of "real" annotations
\newcommand{\ann}[1]{x_{#1}{}} % single element of "real" annotations
\newcommand{\constraints}{\mathcal{C}{}} % Taxon constraints
% Obs Annotations
\newcommand{\AnnObs}{\mathbf{Z}{}}%{Z{}} \mathbf{X}^{obs}{}
\newcommand{\annObs}[1]{z_{#1}{}}%{z{}} x_{#1}^{obs
% Pred. Annotations
\newcommand{\AnnPred}{\hat X{}}
\newcommand{\annPred}[1]{\hat x_{#1}}
% Leaf nodes
\newcommand{\Leaf}{L{}}
% Shortest path
\newcommand{\Geodesic}{\text{T}{}}
\newcommand{\geodesic}{\tau{}}
\newcommand{\Params}{\Omega{}}
\newcommand{\params}{\omega{}}
% Parameters
\newcommand{\gain}{\mu_{01}{}}
\newcommand{\loss}{\mu_{10}{}}
\newcommand{\misszero}{\psi_{01}{}}
\newcommand{\missone}{\psi_{10}{}}
\newcommand{\proot}{\pi}