Presentation Version

Latex/Presentation/presentation.tex

@@ -27,6 +27,7 @@
 \input{../assets/preambles/BibPreamble.tex}
 \input{../assets/preambles/GeneralPreamble.tex}
 
+\addbibresource{/home/will/research/ClinicalTrialsPaper/Latex/assets/preambles/References.bib}
 
 %----------------------------------------------------------------------------------------
 %    TITLE PAGE
@@ -445,19 +446,20 @@ Washington State University \\ % Your institution for the title page
 
     Thus the required adjustment set depends on the effects of interest.
 
-    For the total effect these are controls for:
+    For the total effect:
     \begin{itemize}
         \item Proceed with Phase III
         \item Condition
         \item Population
     \end{itemize}
 
-    For the direct effect these are controls for:
+    For the direct effect:
     \begin{itemize}
         \item Proceed with Phase III
         \item Condition
         \item Population (optional)
-        \item Enrollment
+        \item Enrollment Status
+        \item Elapsed Duration
     \end{itemize}
 
 \end{frame}
@@ -736,24 +738,53 @@ Washington State University \\ % Your institution for the title page
 \begin{frame}
     \frametitle{Total Effects Model}
     %TODO: describe X\beta
+    \begin{itemize}
+        \item asinh(brands with identical ingredients)
+        \item asinh(brands in USP-DC category)
+        \item asinh(high sdi DALY estimate)
+        \item asinh(high-medium sdi DALY estimate)
+        \item asinh(medium sdi DALY estimate)
+        \item asinh(low-medium sdi DALY estimate)
+        \item asinh(low sdi DALY estimate)
+    \end{itemize}
+    Units of observation: Snapshots
 \end{frame}
 %-------------------------------
 \begin{frame}
     \frametitle{Direct Effects Model}
     %TODO: describe X\beta
+    \begin{itemize}
+        \item elapsed duration 
+        \item enrollment status
+        \item asinh(brands with identical ingredients)
+        \item asinh(brands in USP-DC category)
+        \item asinh(high sdi DALY estimate)
+        \item asinh(high-medium sdi DALY estimate)
+        \item asinh(medium sdi DALY estimate)
+        \item asinh(low-medium sdi DALY estimate)
+        \item asinh(low sdi DALY estimate)
+    \end{itemize}
+    Units of Observation: Snapshot
 \end{frame}
 
 %-------------------------------
 \begin{frame}
     \frametitle{Analysis}
 
-    Review:
+    For each effect, we will look at:
     \begin{itemize}
-        \item Hyperparameters
-        \item Parameters of Interest
+        \item Distribution of Parameters of Interest
         \item Distrbution of Predicted Differences (Hypothetical Causal Intervention)
     \end{itemize}
 
+    \vspace{12pt}
+
+    The interventions are:
+    \begin{itemize}
+        \item Adding a single brand to the generic market competitors
+        \item Adding a single brand to the USP DC market competitors
+    \end{itemize}
+
 \end{frame}
 %-------------------------------
 \begin{frame}
@@ -767,29 +798,30 @@ Washington State University \\ % Your institution for the title page
 %--------------------------------
 %-------------------------------
 \begin{frame}
-    \frametitle{Priors - Mu}
+    \frametitle{Data Summaries}
     \begin{figure}
-%        \includegraphics[height=0.8\textheight]{../assets/img/Images/}
-        \label{FIG:Prior:Mu}
-        \caption{Prior - Mu}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/HistTrialDurations_Faceted.png}
     \end{figure}
 \end{frame}
 %-------------------------------
 \begin{frame}
-    \frametitle{Priors - Sigma}
+    \frametitle{Data Summaries}
     \begin{figure}
-%        \includegraphics[height=0.8\textheight]{../assets/img/Images/}
-        \label{FIG:Prior:Sigma}
-        \caption{Prior - Sigma}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/HistSnapshots.png}
     \end{figure}
 \end{frame}
 %-------------------------------
 \begin{frame}
-    \frametitle{Priors - $p$}
+    \frametitle{Data Summaries}
     \begin{figure}
-%        \includegraphics[height=0.8\textheight]{../assets/img/Images/}
-        \label{FIG:Prior:p}
-        \caption{Prior - $p$}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/SnapshotsVsDurationVsTermination.png}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Data Summaries}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/CategoryCounts.png}
     \end{figure}
 \end{frame}
 %--------------------------------
@@ -803,29 +835,96 @@ Washington State University \\ % Your institution for the title page
 %        - Distributions
 % - Review Posterior Prediction for interventions
 %--------------------------------
+%%-------------------------------
+%\begin{frame}
+%    \frametitle{Priors - Mu}
+%    \begin{figure}
+%%        \includegraphics[height=0.8\textheight]{../assets/img/Images/}
+%        \label{FIG:Prior:Mu}
+%        \caption{Prior - Mu}
+%    \end{figure}
+%\end{frame}
+%%-------------------------------
+%\begin{frame}
+%    \frametitle{Priors - Sigma}
+%    \begin{figure}
+%%        \includegraphics[height=0.8\textheight]{../assets/img/Images/}
+%        \label{FIG:Prior:Sigma}
+%        \caption{Prior - Sigma}
+%    \end{figure}
+%\end{frame}
 %-------------------------------
 \begin{frame}
-    \frametitle{Results}
-    Because Bayesian estimation is typically done numerically, we will first 
-    validate convergence.
-
-    Then we will take a look at preliminary results.
-
-    Sampling details
-
-    %TODO: Update
-    \begin{itemize}
-        \item 4 chains
-        \item 2,500 warm-up, 2,500 sampling runs
-        \item seed = 11021585
-    \end{itemize}
+    \frametitle{Priors - $p$}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/TotalEffects/prior_p.png}
+        \label{FIG:Prior:p}
+        \caption{Prior prediction - $p$}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Posteriors - $\beta$ Competing Brands}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/TotalEffects/Parameters/1&2_generics_and_uspdc.png}
+        \label{FIG:Posterior:beta-brands-total}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Predictive Posteriors - $p$ - no intervention}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/TotalEffects/posterior_p.png}
+        \label{FIG:Prior:p}
+        \caption{Posterior prediction - $p$}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Posteriors - $p$ with intervention (generics)}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/TotalEffects/default_p_generic_intervention_interv.png}
+        \label{FIG:Prior:p-intervention_total}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Distribution of Differences - Generics Intervention}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/TotalEffects/default_p_generic_intervention_distdiff.png}
+        \label{FIG:Prior:p-intervention_total}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Distribution of Differences - Generics Intervention | By group}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/TotalEffects/p_generic_intervention_histdiff_by_group.png}
+        \label{FIG:Prior:p-intervention_total}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Posteriors - $p$ with intervention (USP DC)}
+    \begin{figure}
+%        \includegraphics[height=0.8\textheight]{../assets/img/Images/}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/TotalEffects/p_uspdc_intervention_distdiff_styled.png}
+        \label{FIG:Prior:p-intervention_total}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Posteriors - $p$ with intervention (USP DC) by group}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/TotalEffects/p_uspdc_intervention_distdiff_by_group.png}
+        \label{FIG:Prior:p-intervention_total}
+    \end{figure}
 \end{frame}
 %-------------------------------
 \begin{frame}
     \frametitle{Questions?}
 
 \end{frame}
-%-------------------------------
 %--------------------------------
 \subsubsection{Direct Effects}
 % - Review Parameter Values
@@ -839,14 +938,62 @@ Washington State University \\ % Your institution for the title page
 %--------------------------------
 %-------------------------------
 \begin{frame}
-    \frametitle{Convergence}
-    Sampling details
-    %TODO: UPDATE
-    \begin{itemize}
-        \item 6 chains
-        \item 2,500 warm-up, 2,500 sampling runs
-        \item seed = 11021585
-    \end{itemize}
+    \frametitle{Posteriors - $\beta$ Competing Brands}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/DirectEffects/Parameters/2+3_generic_and_uspdc.png}
+        \label{FIG:Posterior:beta-brands-total}
+        \caption{Posterior prediction - $\beta$}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Predictive Posteriors - $p$ - no intervention}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/DirectEffects/posterior_p.png}
+        \label{FIG:Prior:p}
+        \caption{Posterior prediction - $p$}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Posteriors - $p$ with intervention (generics)}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/DirectEffects/default_p_generic_intervention_interv.png}
+        \label{FIG:Prior:p-intervention_total}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Distribution of Differences - Generics Intervention}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/DirectEffects/default_p_generic_intervention_distdiff.png}
+        \label{FIG:Prior:p-intervention_total}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Distribution of Differences - Generics Intervention | By group}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/DirectEffects/p_generic_intervention_histdiff_by_group.png}
+        \label{FIG:Prior:p-intervention_total}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Posteriors - $p$ with intervention (USP DC)}
+    \begin{figure}
+%        \includegraphics[height=0.8\textheight]{../assets/img/Images/}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/DirectEffects/p_uspdc_intervention_distdiff_styled.png}
+        \label{FIG:Prior:p-intervention_total}
+    \end{figure}
+\end{frame}
+%-------------------------------
+\begin{frame}
+    \frametitle{Posteriors - $p$ with intervention (USP DC) by group}
+    \begin{figure}
+        \includegraphics[height=0.8\textheight]{/home/will/research/ClinicalTrialsPaper/Latex/Presentation/Images/DirectEffects/p_uspdc_intervention_histdiff_by_group.png}
+        \label{FIG:Prior:p-intervention_total}
+    \end{figure}
 \end{frame}
 %-------------------------------
 \begin{frame}
@@ -865,13 +1012,27 @@ Washington State University \\ % Your institution for the title page
     \begin{enumerate}
         \item Match more trials to ICD-10 codes and Formularies
         \item Add more formularies
-        \item Remove disease categories that don't exist in the data from the priors
+        \item Remove disease categories that don't exist in the data.
         \item Imputing Enrollment
+        \item Add covariance terms to $\beta$.
     \end{enumerate}
+
+    Suggestions?
 \end{frame}
 %-------------------------------
 \begin{frame}
     \frametitle{Summary}
+
+    Results Summary
+    \begin{enumerate}
+        \item A trial's response to adding a competitor drug depends on:
+            \begin{itemize}
+                \item Whether the drug is a generic or not
+                \item The disease category that applies to the trial
+            \end{itemize}
+            The effects suggest that the enrollment pathway had a strong regulating effect.
+        \item
+    \end{enumerate}
 \end{frame}
 %-------------------------------
 \begin{frame}
@@ -885,75 +1046,49 @@ Washington State University \\ % Your institution for the title page
 %-------------------------------------------------------------------------------------
 %----------------------------------
 %%%%%%%%%%%%%%%%%%%% Convergence Tests
-\subsection{Convergence}
+%\subsection{Convergence}
 %----------------------------------
 %-------------------------------
-\begin{frame}
-    \frametitle{Warnings}
-    %TODO: UPDATE
-
-    \begin{itemize}
-        \item There were no diverging transitions.
-        \item There were 15,000 transitions that exceeded max treedepth. 
-            Sampling efficiency is poor.
-        \item All chains had low Bayesian Fraction of Missing Information. 
-            Some areas of the distribution were poorly explored.
-        \item R-hat = $1.23$, ideal is around 1, chains did not mix well.
-        \item Bulk and Tail Effective Sample sizes were low, 
-            suggesting mean and variance/quantile estimates will be unreliable.
-    \end{itemize}
-    \cite{mc-stan}
-\end{frame}
-%-------------------------------
-\begin{frame}
-    \frametitle{Convergence: Mu}
-    \begin{figure}
-        %TODO: UPDATE
-        %\includegraphics[height=0.9\textheight]{../assets/img/2023-04-11_mu_points.png}
-        \label{FIG:caption}
-        \caption{Hyperparameter Points Plots: Mu}
-    \end{figure}
-\end{frame}
-%-------------------------------
-\begin{frame}
-    \frametitle{Convergence: Sigma}
-    \begin{figure}
-        %TODO: UPDATE
-        %\includegraphics[height=0.9\textheight]{../assets/img/2023-04-11_mu_points.png}
-        \label{FIG:caption}
-        \caption{Hyperparameter Points Plots: Sigma}
-    \end{figure}
-\end{frame}
-%-------------------------------
-\begin{frame}[allowframebreaks]
-    \frametitle{Bibliography}
-    \printbibliography
-\end{frame}
-%-------------------------------
-\end{document} 
-%=========================================
 %\begin{frame}
-%    \frametitle{MarginalRevenue}
+%    \frametitle{Warnings}
+%    %TODO: UPDATE
+%
+%    \begin{itemize}
+%        \item There were no diverging transitions.
+%        \item There were 15,000 transitions that exceeded max treedepth. 
+%            Sampling efficiency is poor.
+%        \item All chains had low Bayesian Fraction of Missing Information. 
+%            Some areas of the distribution were poorly explored.
+%        \item R-hat = $1.23$, ideal is around 1, chains did not mix well.
+%        \item Bulk and Tail Effective Sample sizes were low, 
+%            suggesting mean and variance/quantile estimates will be unreliable.
+%    \end{itemize}
+%    \cite{mc-stan}
+%\end{frame}
+%%-------------------------------
+%\begin{frame}
+%    \frametitle{Convergence: Mu}
 %    \begin{figure}
-%        \tikzfig{../Assets/owned/ch8_MarginalRevenue}
-%        \includegraphics[height=\textheight]{../Assets/copyrighted/KrugmanObsterfeldMeliz_fig8-7.jpg}
-%        \label{FIG:costs}
-%        \caption{Average Cost Curve as firms enter.}
+%        %TODO: UPDATE
+%        %\includegraphics[height=0.9\textheight]{../assets/img/2023-04-11_mu_points.png}
+%        \label{FIG:caption}
+%        \caption{Hyperparameter Points Plots: Mu}
 %    \end{figure}
 %\end{frame}
-%-------------------------------
+%%-------------------------------
 %\begin{frame}
-%    \frametitle{Columns}
-%     \begin{columns}
-%        \begin{column}{0.5\textwidth}
-%        \end{column}
-%        \begin{column}{0.5\textwidth}
-%               \begin{figure}
-%                   \tikzfig{../Assets/owned/ch7_EstablishedAdvantageExample2}
-%                   \label{FIG:costs}
-%                   \caption{Setting the Stage}
-%               \end{figure}
-%        \end{column}
-%     \end{columns}
+%    \frametitle{Convergence: Sigma}
+%    \begin{figure}
+%        %TODO: UPDATE
+%        %\includegraphics[height=0.9\textheight]{../assets/img/2023-04-11_mu_points.png}
+%        \label{FIG:caption}
+%        \caption{Hyperparameter Points Plots: Sigma}
+%    \end{figure}
 %\end{frame}
-% %---------------------------------------------------------------
+%%-------------------------------
+\begin{frame}[allowframebreaks]
+    \frametitle{Bibliography}
+    \printbibliography
+\end{frame}
+%-------------------------------
+\end{document} 

Latex/assets/preambles/BibPreamble.tex

@@ -5,6 +5,5 @@
 
 %%% Setup Bibliography
 \usepackage[backend=biber,autocite=inline]{biblatex}
-\addbibresource{./assets/preambles/References.bib}
 
 

Latex/assets/preambles/GeneralPreamble.tex

@@ -10,8 +10,6 @@
 
 %Setup the-
 \usepackage{graphicx}
-\graphicspath{assets/img/}
-
 
 
 %quotes