Finished introduction, added new background section.

Latex/Paper/Main.tex

@@ -51,6 +51,8 @@ completion of clinical trials\\ \small{Preliminary Draft}}
 % \section{Literature Review}\label{SEC:LiteratureReview}
 % %---------------------------------------------------------------
 % \subfile{sections/05_LitReview}
+\section{Clincal Trial Background}\label{SEC:ClinicalTrials}
+\subfile{sections/12_clinical_trial_background}
 
 %---------------------------------------------------------------
 \section{Causal Story and Data}\label{SEC:Data}

Latex/Paper/sections/11_intro_and_lit.tex

@@ -176,7 +176,7 @@ or other studies prove that the trial requires a protocol change.
 
 This paper proposes the first model to separate the causal effects of 
 market conditions (a strategic concern) from the effects of 
-participant enrollment (an operational concern). 
+participant enrollment (an operational concern) on Phase III Clinical trials. 
 This will allow me to answer the questions:
 \begin{itemize}
     \item What is the marginal effect on trial completion of an additional 
@@ -193,7 +193,7 @@ Finally I'll review the results and conclusion in sections
 \ref{SEC:Results}
 and
 \ref{SEC:Conclusion}
-respectively
+respectively.
 
 % \subsection{Market incentives and drug development}
 % %%%%%%%%% What do we know about drug development incentives?

Latex/Paper/sections/12_clinical_trial_background.tex

@@ -0,0 +1,116 @@
+\documentclass[../Main.tex]{subfiles}
+\graphicspath{{\subfix{Assets/img/}}}
+
+\begin{document}
+
+% Clinical Trials Background Outline
+% - ClinicalTrials.gov
+% - Clincial trial progression
+% - 
+% - 
+% - 
+% - 
+% - 
+%   - 
+%   - 
+
+To understand how my administrative clinical trial is obtained, 
+let's take a look at how trial investigators record data on 
+\url{ClinicalTrials.gov} operate.
+Figure \ref{Fig:Stages} illuistrates the process I describe below.
+During the Pre-Trial period the trial investigators will design the trial, 
+choose primary and secondary objectives, 
+and decide on how many participants they need to enroll. 
+Once they have decided on these details, they post the trial to \url{ClinicalTrials.com}
+and decide on a date to begin enrolling trial participants.
+If the investigators decide to not continue with the trial before enrolling any participants,
+the trial is marked as ``Withdrawn''. 
+On the other hand, if they begin enrolling participants, there are two methods to do so.
+The first is to enter a general ``Recruiting'' state, where patients attempt to enroll.
+The second is to enter an "Enrollment by invitation only" state.
+After a trial has enrolled their participants, they wil typically move to an 
+"Active, not recruiting" state to inform potential participants that they are
+not recruiting. 
+Finally, when the investigators have obtained enough data to achieve their primary
+objective, the clinical trial will be closed, and marked as ``Completed'' in
+\url{ClinicalTrials.gov}
+If the trial is closed before achieving the primary objective, the trial is 
+marked as ``Terminated'' on
+\url{ClinicalTrials.gov}.
+
+
+\begin{figure}[H] %use [H] to fix the figure here.
+    \includegraphics[width=\textwidth]{../assets/img/ClinicalTrialStagesAndStatuses}
+    \par \small 
+        Diamonds represent decision points while
+	Squares represent states of the clinical trial and Rhombuses represend data obtained by the trial.
+    \caption[Clinical Trial Stages and Progression]{Clinical Trial Stages and Progression}
+    \label{Fig:Stages}
+\end{figure}
+
+Note the information we obtain about the trial from the final status: 
+``Withdrawn'', ``Terminated'', or ``Completed''.
+Although \cite{khm} describes a clinical failure due to safety or efficacy as a 
+\textit{scientific} failure, it is better described as a compound failure.
+Discovering that a compound doesn't work as hoped is not a failure but the whole
+purpose of the clinical trials process. 
+On the other hand, when a trial terminates early due to reasons 
+other than safety or efficacy concerns, the trial operator does not learn
+if the drug is effective or safe. 
+This is a true failure in that we did not learn if the drug was effective or not.
+Unfortunately, although termination documentation typically includes a 
+description of a reason for the clinical trial termination, this doesn't necessarily
+list all the reasons contributing to the trial termination and may not exist for a given trial.
+
+% SHOULD I EXPLAIN THE CLINICAL TRIALS DATA, i.e. AACT and SCRAPING EFFORT YET?
+% For this reason we use administrative data, the records of clinical trial states, to track how trials proceed.
+% There is also the issue of confounding between different 
+
+
+
+% \begin{enumerate}
+%     \item The compound demonstrates sufficient safety and efficacy, and proceeds in the appoval process. 
+%         \label{Item:EndSuccess}
+%     \item The compound fails to demonstrate sufficient safety and efficacy, and the approval process halts. 
+%         \label{Item:EndFail}
+%     \item The trial is terminated before it can acheive one of the first two 
+%         outcomes, for reasons unrelated to safety and efficacy concerns. 
+%         \label{Item:Terminate}
+% \end{enumerate}
+% 
+% 
+% \begin{table}
+%     \caption{Potential States of Knowledge from a clinical trial}\label{tab:StatesOfKnowledge}
+%     \begin{center}
+%         \begin{tabular}{p{0.15\textwidth} p{0.2\textwidth}||p{0.25\textwidth}|p{0.25\textwidth}|}
+%         \cline{3-4}
+%             \multicolumn{2}{c|}{Drug-Indication Match}  & safe and efficacious & not safe or not efficatious \\
+%         \hline
+%         \hline
+%             \multirow{2}{0.15\textwidth}{Operations} & Success & Known good & Known bad \\
+%         \cline{2-4}
+%             & Failure & \multicolumn{2}{c|}{Unkown} \\
+%         \cline{2-4}
+%         \end{tabular}
+%     \end{center}
+% \end{table}
+% 
+% 
+% \begin{table}
+%     \caption{Clinical Trial end states}\label{tab:ClinicalTrialEndStates}
+%     \begin{center}
+%         \begin{tabular}{p{0.15\textwidth} p{0.2\textwidth}||p{0.25\textwidth}|p{0.25\textwidth}|}
+%         \cline{3-4}
+%             \multicolumn{2}{c|}{Drug-Indication Match}  & safe and efficacious & not safe or not efficatious \\
+%         \hline
+%         \hline
+%             \multirow{2}{0.15\textwidth}{Operations} & Success & Completion & Completion or Termination \\
+%         \cline{2-4}
+%             & Failure & \multicolumn{2}{c|}{Termination} \\
+%         \cline{2-4}
+%         \end{tabular}
+%     \end{center}
+% \end{table}
+
+
+\end{document}