clinical_report.tex

\documentclass{article}\usepackage[]{graphicx}\usepackage[]{xcolor}
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\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
\newcommand{\hlsng}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
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\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
\let\hlipl\hlkwb

\usepackage{framed}
\makeatletter
\newenvironment{kframe}{%
 \def\at@end@of@kframe{}%
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\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX

\usepackage{alltt}
\usepackage{geometry}
\usepackage{graphicx}
\usepackage{hyperref}
\usepackage{booktabs} % Required for xtable aesthetics

\title{Phase III Clinical Trial Analysis}
\author{Bioinformatics Division}
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\begin{document}
\maketitle

\section{Statistical Analysis Protocol}

We investigate the efficacy of Treatment A vs. Placebo. The analysis is performed using R version 4.5.1.

% Global Chunk Options
% echo=TRUE: Show R code in the document (transparency)
% warning=FALSE: Suppress warning messages in final PDF
% dev='pdf': Generate high-quality vector graphics


\section{Data Ingestion and Summary}

\begin{kframe}
\begin{alltt}
\hlcom{# Simulate Clinical Data}
\hlkwd{set.seed}\hldef{(}\hlnum{2024}\hldef{)}
\hldef{n} \hlkwb{<-} \hlnum{50}
\hldef{df} \hlkwb{<-} \hlkwd{data.frame}\hldef{(}
  \hlkwc{id} \hldef{=} \hlnum{1}\hlopt{:}\hldef{(}\hlnum{2}\hlopt{*}\hldef{n),}
  \hlkwc{group} \hldef{=} \hlkwd{factor}\hldef{(}\hlkwd{rep}\hldef{(}\hlkwd{c}\hldef{(}\hlsng{"Placebo"}\hldef{,} \hlsng{"Treatment"}\hldef{),} \hlkwc{each}\hldef{=n)),}
  \hlkwc{recovery_days} \hldef{=} \hlkwd{c}\hldef{(}\hlkwd{rnorm}\hldef{(n,} \hlkwc{mean}\hldef{=}\hlnum{14}\hldef{,} \hlkwc{sd}\hldef{=}\hlnum{3}\hldef{),} \hlkwd{rnorm}\hldef{(n,} \hlkwc{mean}\hldef{=}\hlnum{10}\hldef{,} \hlkwc{sd}\hldef{=}\hlnum{2.5}\hldef{))}
\hldef{)}

\hlcom{# Descriptive Statistics Table}
\hldef{summary_stats} \hlkwb{<-} \hlkwd{aggregate}\hldef{(recovery_days} \hlopt{~} \hldef{group,} \hlkwc{data}\hldef{=df,} \hlkwc{FUN}\hldef{=}\hlkwa{function}\hldef{(}\hlkwc{x}\hldef{)} \hlkwd{c}\hldef{(}\hlkwc{Mean}\hldef{=}\hlkwd{mean}\hldef{(x),} \hlkwc{SD}\hldef{=}\hlkwd{sd}\hldef{(x)))}
\hldef{summary_stats} \hlkwb{<-} \hlkwd{do.call}\hldef{(data.frame, summary_stats)} \hlcom{# Flatten structure}

\hlcom{# Print as LaTeX table using xtable}
\hlkwd{print}\hldef{(}\hlkwd{xtable}\hldef{(summary_stats,} \hlkwc{caption}\hldef{=}\hlsng{"Descriptive Statistics by Group"}\hldef{),}
      \hlkwc{booktabs}\hldef{=}\hlnum{TRUE}\hldef{,} \hlkwc{include.rownames}\hldef{=}\hlnum{FALSE}\hldef{)}
\end{alltt}
\end{kframe}% latex table generated in R 4.5.1 by xtable 1.8-4 package
% Sat Nov 22 21:54:49 2025
\begin{table}[ht]
\centering
\begin{tabular}{lrr}
  \toprule
group & recovery\_days.Mean & recovery\_days.SD \\ 
  \midrule
Placebo & 13.77 & 3.19 \\ 
  Treatment & 9.76 & 2.48 \\ 
   \bottomrule
\end{tabular}
\caption{Descriptive Statistics by Group} 
\end{table}


The table above is generated dynamically. If the underlying dataset \texttt{df} changes, the table updates automatically without manual re-formatting.

\section{Hypothesis Testing and Visualization}

We perform an independent t-test to compare the groups.



The t-test yields a p-value of < 0.001.
This indicates a statistically significant difference.

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{ggplot}\hldef{(df,} \hlkwd{aes}\hldef{(}\hlkwc{x}\hldef{=group,} \hlkwc{y}\hldef{=recovery_days,} \hlkwc{fill}\hldef{=group))} \hlopt{+}
  \hlkwd{geom_boxplot}\hldef{(}\hlkwc{alpha}\hldef{=}\hlnum{0.7}\hldef{)} \hlopt{+}
  \hlkwd{geom_jitter}\hldef{(}\hlkwc{width}\hldef{=}\hlnum{0.2}\hldef{,} \hlkwc{alpha}\hldef{=}\hlnum{0.5}\hldef{)} \hlopt{+}
  \hlkwd{theme_minimal}\hldef{()} \hlopt{+}
  \hlkwd{labs}\hldef{(}\hlkwc{y}\hldef{=}\hlsng{"Days to Recovery"}\hldef{,} \hlkwc{x}\hldef{=}\hlsng{"Study Group"}\hldef{)} \hlopt{+}
  \hlkwd{scale_fill_brewer}\hldef{(}\hlkwc{palette}\hldef{=}\hlsng{"Pastel1"}\hldef{)}
\end{alltt}
\end{kframe}\begin{figure}
\includegraphics[width=\maxwidth]{figure/boxplot-1} \caption[Distribution of Recovery Days by Treatment Group]{Distribution of Recovery Days by Treatment Group}\label{fig:boxplot}
\end{figure}

\end{knitrout}

\end{document}