From 963293fc2b489dbfeca283432c7c94cee1405832 Mon Sep 17 00:00:00 2001
From: Will King <will.king.git@youainti.com>
Date: Mon, 13 Jan 2025 21:15:44 -0800
Subject: [PATCH] Added diagnostics appendix, notes in results

---
 Paper/Main.tex                             |  1 +
 Paper/sections/06_Results.tex              |  7 ++--
 Paper/sections/21_appendix_diagnostics.tex | 38 ++++++++++++++++++++++
 3 files changed, 42 insertions(+), 4 deletions(-)
 create mode 100644 Paper/sections/21_appendix_diagnostics.tex

diff --git a/Paper/Main.tex b/Paper/Main.tex
index fed77ef..79b47bf 100644
--- a/Paper/Main.tex
+++ b/Paper/Main.tex
@@ -103,6 +103,7 @@ Section \ref{SEC:Results} discusses the results of the analysis.
 %---------------------------------------------------------------
 \section{Appendicies}
 %---------------------------------------------------------------
+\subfile{sections/21_appendix_diagnostics}
 
 \newpage
 \tableofcontents
diff --git a/Paper/sections/06_Results.tex b/Paper/sections/06_Results.tex
index 5d4b89a..bf4a34e 100644
--- a/Paper/sections/06_Results.tex
+++ b/Paper/sections/06_Results.tex
@@ -190,10 +190,9 @@ result comes from different disease categories.
 \subsection{Secondary Results}
 
 % Examine beta parameters 
-% - 
-% - 
-% - 
-% - 
+% - Little movement except where data is strong, general negative movement. Still really wide 
+% - Note how they all learned (partial pooling) reduction in \beta from ANR?
+% - Need to discuss the 5 different states. Can't remember which one is dropped for the life of me. May need to fix parameterization.
 % - 
 
 \begin{figure}[H]
diff --git a/Paper/sections/21_appendix_diagnostics.tex b/Paper/sections/21_appendix_diagnostics.tex
new file mode 100644
index 0000000..848b484
--- /dev/null
+++ b/Paper/sections/21_appendix_diagnostics.tex
@@ -0,0 +1,38 @@
+\documentclass[../Main.tex]{subfiles}
+\graphicspath{{\subfix{Assets/img/}}}
+
+\begin{document}
+\subsection{Diagnostics}
+Reported low E-BFMI scores (low is considered below $0.2$)
+\todo{Fill these out based on what is in the rendered report.}
+\begin{itemize}
+    \item Chain 1: 0.178
+    \item Chain 2: 0.189
+\end{itemize}
+
+No other reported issues.
+
+\begin{figure}[H]
+    \caption{Diagnostics: Trace Rank Plots - $\mu$}
+    \label{fig:trial_durations}
+    \includegraphics[width=\textwidth]{../assets/img/diagnostics/trace_rank_plot_mu_1-4}
+    \\[\smallskipamount]
+    \includegraphics[width=\textwidth]{../assets/img/diagnostics/trace_rank_plot_mu_5-8}
+    \\[\smallskipamount]
+    \includegraphics[width=\textwidth]{../assets/img/diagnostics/trace_rank_plot_mu_9-12}
+\end{figure}
+Mixing seems to be fine
+
+\begin{figure}[H]
+    \caption{Diagnostics: Trace Rank Plots - $\sigma$}
+    \label{fig:trial_durations}
+    \includegraphics[width=\textwidth]{../assets/img/diagnostics/trace_rank_plot_sigma_1-4}
+    \\[\smallskipamount]
+    \includegraphics[width=\textwidth]{../assets/img/diagnostics/trace_rank_plot_sigma_5-8}
+    \\[\smallskipamount]
+    \includegraphics[width=\textwidth]{../assets/img/diagnostics/trace_rank_plot_sigma_9-12}
+\end{figure}
+Mixing is slower than $\mu$ values, but doesn't seem too problematic in light of
+other deficencies such as low number of observations.
+
+\end{document}