latex

[medewitt]

\documentclass[11pt, letterpaper]{article}

% === Page Layout ===
% Configured to 0.5-inch margins, standard for NIH and DOD grant proposals.
\usepackage[margin=0.5in]{geometry}

% === Mathematics ===
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{mathtools}
\usepackage{bm} % Standard for bold math vectors/matrices in pdfLaTeX

% === Graphics & Diagrams ===
\usepackage{graphicx}
\usepackage{subcaption}
\usepackage{tikz}
\usetikzlibrary{shapes.geometric, arrows.meta, positioning, fit, calc}
% Note: Use the path below to map reproducible SVGs/assets from https://bioart.niaid.nih.gov/
\graphicspath{{./assets/}}

% === Tables ===
\usepackage{booktabs}
\usepackage{tabularx}

% === Citations & Cross-Referencing ===
\usepackage[style=nature, backend=biber]{biblatex} % Numerically sorted, highly compact
% \addbibresource{references.bib}

\usepackage[colorlinks=true, linkcolor=blue, citecolor=blue, urlcolor=blue]{hyperref}
\usepackage[nameinlink]{cleveref} % Must be loaded after hyperref

% === Document Metadata ===
\title{{{ title }}}
\author{{{ author }}{% if affiliation %} \ {{ affiliation }}{% endif %}}
\date{{{ today }}}

\begin{document}

\maketitle

\begin{abstract}
Brief summary of the mathematical model, inferential approach, and epidemiological findings.
\end{abstract}

\section{Introduction}
\label{sec:intro}
Introduction to the infectious disease system and the specific transmission dynamics under study.

\section{Methods}
\label{sec:methods}

\subsection{Mechanistic Model}
The underlying transmission dynamics are governed by the following system of ordinary differential equations \cref{eq:system}:

\begin{subequations}
\label{eq:system}
\begin{align}
\frac{dS}{dt} &= -\beta S I \
\frac{dI}{dt} &= \beta S I - \gamma I \
\frac{dR}{dt} &= \gamma I
\end{align}
\end{subequations}

\subsection{Conceptual Diagram}
% Example TikZ scaffolding for compartmental diagrams.
% Replace node contents with \includegraphics{} calls to NIAID BioArt assets for reproducible high-fidelity figures.
\begin{figure}[htbp]
\centering
\begin{tikzpicture}[
node distance=3cm,
compartment/.style={draw, rectangle, minimum width=2cm, minimum height=1cm, align=center},
flow/.style={->, >=Stealth, thick}
]
\node[compartment] (S) {Susceptible};
\node[compartment, right=of S] (I) {Infected};
\node[compartment, right=of I] (R) {Recovered};

    \draw[flow] (S) -- node[above] {$\beta$} (I);
    \draw[flow] (I) -- node[above] {$\gamma$} (R);
\end{tikzpicture}
\caption{Compartmental flow diagram representing the modeled disease states.}
\label{fig:diagram}

\end{figure}

\section{Results}
\label{sec:results}
Results summary referencing \cref{tab:params} and the structural model in \cref{fig:diagram}.

\begin{table}[htbp]
\centering
\caption{Prior distributions and fixed parameter values utilized in the Bayesian inference engine.}
\label{tab:params}
\begin{tabular}{llr}
\toprule
Parameter & Description & Value / Prior \
\midrule
$\beta$ & Transmission rate & $\text{LogNormal}(0, 1)$ \
$\gamma$ & Recovery rate & $1/7$ \
\bottomrule
\end{tabular}
\end{table}

% \printbibliography

\end{document}