Commit 3d2d7aef authored by Chris Jewell's avatar Chris Jewell
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Added fixed-gamma traces

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......@@ -683,7 +683,7 @@ The algorithm is run on data for the interval [2020-05-19, 2020-08-06].
Here we present results of running the MCMC algorithm for 200000 iterations, thinning by
20 iterations. The object is to demonstrate lack of efficient chain convergence,
particularly with respect to the occult infections and infection and removal rates. The
MCMC settings used are presented in Table \ref{tab:august-settings0}.
MCMC settings used are presented in Table \ref{tab:august-settings}.
\begin{table}[H]
\centering
......@@ -700,8 +700,8 @@ MCMC settings used are presented in Table \ref{tab:august-settings0}.
thin & 20 \\
\hline
\end{tabular}
\caption{MCMC tuning settings for August 6th analysis}
\label{tab:august-settings0}
\caption{\label{tab:august-settings}MCMC tuning settings for August 6th analysis}
\end{table}
......@@ -735,7 +735,7 @@ appraise occult mixing when transition parameters are fixed.
In this section, we run the MCMC algorithm holding all transition parameters $\bm{\theta}
= \left\{ \beta_1, \beta_2, \bm{\xi}, \gamma \right\}$ fixed to values as shown in Table
\ref{tab:fixed-params}. The MCMC settings are as in \ref{tab:august-settings0}.
\ref{tab:fixed-params}. The MCMC settings are as in Table \ref{tab:august-settings}.
\begin{table}[H]
\centering
......@@ -764,11 +764,32 @@ In this section, we run the MCMC algorithm holding all transition parameters $\b
\centering
\includegraphics[width=0.6\columnwidth]{figs/occults_2020-08-06_param_fixed_zoom.png}
\caption{Total number of occult events present in system, parameters fixed -- a closed look, omitting burn-in.}
\label{fig:august-occults-param-fixed}
\label{fig:august-occults-param-fixed-zoom}
\end{figure}
\paragraph{Conclusion}
Fixing transition parameters markedly improves convergence. Next step: fix the removal rate.
Fixing transition parameters markedly improves convergence. Next step: fix the removal
rate.
\subsection{Fixed $\gamma$}
In this section, we fix $\gamma = 0.45$ and estimate the joint posterior over the
partially-observed events, occults, and infection rate parameters. The MCMC settings are
as in Table \ref{tab:august-settings}.
\begin{figure}[H]
\centering
\includegraphics[width=0.6\columnwidth]{figs/occults_2020-08-06_gamma_fixed.png}
\caption{Total number of occult events present in system, $\gamma=0.45$ fixed}
\label{fig:august-occults-gamma-fixed}
\end{figure}
\begin{figure}[H]
\centering
\includegraphics[width=0.6\columnwidth]{figs/occults_2020-08-06_gamma_fixed_zoom.png}
\caption{Total number of occult events present in system, $\gamma=0.45$ fixed, zoomed in}
\label{fig:august-occults-gamma-fixed-zoom}
\end{figure}
\clearpage
......
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