added initial background information on clinical trials

ClinicalTrialsEstimation

@@ -1 +1 @@
-Subproject commit 09d0faa84c30f0735b0a16a3159afd2d816e9296
+Subproject commit a7e1f71e124bc8f27621373ba6b66234f091834f

Latex/Presentation/presentation.tex

@@ -35,7 +35,7 @@
 %	TITLE PAGE
 %----------------------------------------------------------------------------------------
 
-\title[short title]{Long title} 
+\title[Clinical Trials]{Pharmaceutial competitors and their effect on clinical trial completion} 
 
 \author{Will King} % Your name
 \institute[WSU] % Your institution as it will appear on the bottom of every slide, may be shorthand to save space
@@ -56,47 +56,274 @@ Washington State University \\ % Your institution for the title page
 \end{frame}
 
 
+%-------------------------------
+\begin{frame}
+    \frametitle{Introduction}
+
+\end{frame}
+%-------------------------------
 \begin{frame}[allowframebreaks] %Allow frame breaks
 \frametitle{Overview} % Table of contents slide, comment this out to remove it
 \tableofcontents 
 \end{frame}
+%-------------------------------
 
 %-------------------------------------------------------------------------------------
-%%%%%%%%%%%%%%%%%%%% Developing the Model%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%% Introduction and Background %%%%%%%%%%%%%%%%%%%%%%%%
-\section{Money: Supply and Demand}
+\section{Background}
+% TOC
+% - Background on drug process
+% - Literature on clinical trials
+% - My questions
 %-------------------------------------------------------------------------------------
+
 %-------------------------------
 \begin{frame}
-    \frametitle{What is Money?}
+    \frametitle{Clinical Trials and Drug develoment}
-    \begin{block}{Money}
+    % add info about trials
-        A commodity that is:
+    % - Requirements (pre registered design [2007], updated "regularly" on clinicaltrials.gov)
+    % - Phases (1,2,3,4, mixed)
+    % - Safety and Ethicas (oversight boards, restrictions on payments)
+    % - Approval processes (biologics vs small-molecule)
+    % add info about drugs
+
+    The FDA requires clinical trials before approving new drug compounds
+    \begin{itemize}
+	    \item Pre-registered design
+	    \item Updated regularly on clinicaltrials.gov
+	    \item Often requires an oversight board.
+	    \item Goal is to prove efficacy and safety of a compound/dosage/route.
+	    \item A new drug candidate (NDC) must complete 3 phases of clinical trials before approval.
+	    \item Phases are reviewed with FDA.
+	    \item Not all clinical trials are for new drugs.
+    \end{itemize}
+\end{frame}
+%-----------------------------
+\begin{frame}
+    \frametitle{Literature}
     \begin{itemize}
-            \item Medium of exchange: A generally accepted means of payment.
+        \item Ekaterina
-            \item Store of value: A method to transfer value from now into the future.
+        \item Adams
+        \item 
     \end{itemize}
-    \end{block}
 
-    What types of money exist?
+\end{frame}
+%-----------------------------
+\begin{frame}
+    \frametitle{Questions of Interest}
+
+	\begin{itemize}
+		\item How do the competitors on the market affect clinical trial completion?
+		\item How is this effect moderated by the enrollment of participants?
+	\end{itemize}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Audience Questions}
+
+	\center{What can I clarify?}
+\end{frame}
+%-------------------------------
+%-------------------------------------------------------------------------------------
+%%%%%%%%%%%%%%%%%%%% Causality and Data %%%%%%%%%%%%%%%%%%%%%%%%
+\section{Causal Story and Data}
+% TOC
+% - Causal Story (no subsection)
+%    - Clinical trials: targets specific drug/condition combination.
+%    - Enrollment process: patients counsel with providers
+%    - Trials terminate if unsafe, ineffective, unprofitable, or cannot enroll patients
+%    - Ethical concerns exist throughout.
+%    - This is complicated by the fact that the experiment reveals information over time.
+% - Formalization
+% - Data Sources
+%-------------------------------------------------------------------------------------
+
+%-------------------------------
+\begin{frame}[shrink=10] %evil option is helpful here.
+    \frametitle{How do clinical trials proceed?}
+	\begin{columns}[T]
+	\begin{column}{0.5\textwidth}
+    What does a complete trial look like.
+	\begin{enumerate}
+		\item Study sponsor comes up with design
+		\item Apply for NCT ID from ClinicalTrials.gov
+		\item Begin enrolling participants
+		\item Update ClinicalTrials.gov to recruit
+		\item Close Enrollment
+		\item Update ClinicalTrials.gov as not recruiting*
+		\item Reach primary objectives
+		\item Update ClinicalTrials.gov as complete
+		\item Reach secondary objectives
+		\item Update ClinicalTrials.gov with more information
+	\end{enumerate}
+	\end{column}
+	\begin{column}{0.5\textwidth}
+    What does an incomplete trial look like?
+	\begin{enumerate}
+		\item Study sponsor comes up with design
+		\item Apply for NCT ID from ClinicalTrials.gov
+		\item Begin enrolling participants
+		\item Update ClinicalTrials.gov to advertise
+		\item Run into issues: 
 			\begin{itemize}
-        \item M0: Currency
+				\item Safety
-        \item \textbf{M1: M0 + Checking/bank deposits}
+				\item Efficacy
+				\item Profitability
+				\item Feasiblity (enrollment, PI leaves, etc.)
 			\end{itemize}
+		\item Close Enrollment*
+		\item Decide to terminate clinical trial.
+		\item Update ClinicalTrials.gov as terminated.
+	\end{enumerate}
+	\end{column}
+	\end{columns}
 \end{frame}
 %-------------------------------
 \begin{frame}
-    \frametitle{Money Demand}
+    \frametitle{ClinicalTrials.gov}
+	Thus ClinicalTrials.gov becomes an (append only) repository of 
+	the ``current'' status of clincal trials.
+
 
-    Nominal Money Demand
+	As it is designed to help faciltate enrollment in clinical trials, 
-    \begin{align}
+	the record includes important information such as 
-        M^d = P \cdot L(R,Y)
-    \end{align}
 
 	\begin{itemize}
-        \item $Y \uparrow \Rightarrow L(R,Y) \uparrow$
+		\item drugs
-        \item $R \downarrow \Rightarrow L(R,Y) \uparrow$
+		\item study arms
+		\item conditions
+		\item expected and final enrollment figures
+		\item current status
 	\end{itemize}
 
+	ClinicalTrials.gov also reports the ``history'' from previous
+	updates.
+\end{frame}
+
+%-------------------------------
+\begin{frame}
+    \frametitle{Questions?}
+
+\end{frame}
+%-------------------------------
+%--------------------------------
+%%%%%%%%%%%%%%%%%%%% Causal Formalization
+\subsection{Formalization}
+% - Introduce basic triangle
+%    - discuss total vs direct effects
+%    - 
+% - Add confounders and controls
+% - Introduce backdoor criterion
+%--------------------------------
+
+
+%-------------------------------
+\begin{frame}
+    \frametitle{Questions?}
+
+\end{frame}
+%-------------------------------
+%--------------------------------
+%%%%%%%%%%%%%%%%%%%% Data sources
+\subsection{Data Sources}
+% TOC
+% - Main Data Sources
+%    - ClinicalTrials.gov and AACT
+%    - IHME Burden of Disease
+%    - Marketing Data
+%    - MeSH, RxNorm/RxNav
+% - How did I Link Data Sources
+% - Data Sizes
+%--------------------------------
+
+%-------------------------------
+\begin{frame}
+    \frametitle{Questions?}
+
+\end{frame}
+%-------------------------------
+%-------------------------------------------------------------------------------------
+%%%%%%%%%%%%%%%%%%%% Analysis %%%%%%%%%%%%%%%%%%%%%%%%
+\section{Analysis}
+% TOC
+% - Review questions and datasets to use for each
+% - 
+% - 
+%-------------------------------------------------------------------------------------
+
+%-------------------------------
+\begin{frame}
+    \frametitle{Questions?}
+
+\end{frame}
+%--------------------------------
+%%%%%%%%%%%%%%%%%%%% Econometric Model
+\subsection{Econometric Model}
+% - Present model per effect
+% - 
+% - 
+%--------------------------------
+
+%-------------------------------
+\begin{frame}
+    \frametitle{Questions?}
+
+\end{frame}
+%--------------------------------
+%%%%%%%%%%%%%%%%%%%% Results
+\subsection{Results}
+%--------------------------------
+%--------------------------------
+\subsubsection{Total Effect}
+% - Review Parameter Values
+%    - hyperparameters
+%        - Table of MLE
+%        - Distributions
+%    - betas
+%        - Table of MLE
+%        - Distributions
+% - Review Posterior Prediction for interventions
+%--------------------------------
+%-------------------------------
+\begin{frame}
+    \frametitle{Questions?}
+
 \end{frame}
+%-------------------------------
+%--------------------------------
+\subsubsection{Direct Effects}
+% - Review Parameter Values
+%    - hyperparameters
+%        - Table of MLE
+%        - Distributions
+%    - betas
+%        - Table of MLE
+%        - Distributions
+% - Review Posterior Prediction for interventions
+%--------------------------------
+
+%-------------------------------
+\begin{frame}
+    \frametitle{Questions?}
+
+\end{frame}
+%-------------------------------
+%-------------------------------------------------------------------------------------
+%%%%%%%%%%%%%%%%%%%% Conclusion %%%%%%%%%%%%%%%%%%%%%%%%
+\section{Conclusion}
+%-------------------------------------------------------------------------------------
+
+%-------------------------------
+\begin{frame}
+    \frametitle{Final Questions}
+
+	\center{\huge{Time is yours to ask any remaining questions.}}
+\end{frame}
+%-------------------------------------------------------------------------------------
+%%%%%%%%%%%%%%%%%%%% Appendicies %%%%%%%%%%%%%%%%%%%%%%%%
+\section{Appendices}
+%-------------------------------------------------------------------------------------
+
 %-------------------------------
 \begin{frame}
     \frametitle{Equilibrium in the Money Market}
@@ -111,11 +338,6 @@ Washington State University \\ % Your institution for the title page
     \end{figure}
 \end{frame}
 %-------------------------------
-\begin{frame}
-    \frametitle{Questions?}
-
-\end{frame}
-%-------------------------------
 \end{document} 
 %=========================================
 %\begin{frame}

Latex/assets/preambles/BibPreamble.tex

@@ -4,7 +4,7 @@
 
 
 %%% Setup Bibliography
-\usepackage[backend=biber,style=apa,autocite=inline]{biblatex}
+\usepackage[backend=biber,autocite=inline]{biblatex}
 \addbibresource{./assets/preambles/References.bib}