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Better way of addressing #35.

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evogytis committed Nov 27, 2017
1 parent 4258ca6 commit 3548a3bcafa650c558ca7058c53f8bf132bfe1af
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@@ -219,7 +219,7 @@ \subsection*{MERS-CoV shows seasonal introductions}
\subsection*{MERS-CoV is poorly suited for human transmission}
Structured coalescent approaches clearly show humans to be a terminal host for MERS-CoV, implying poor transmissibility.
However, we wanted to translate this observation into an estimate of the basic reproductive number $R_{0}$ to provide a more intuitive epidemic behaviour metric.
However, we wanted to translate this observation into an estimate of the basic reproductive number $R_{0}$ to provide an intuitive epidemic behaviour metric that does not require expertise in reading phylogenies.
The parameter $R_{0}$ determines expected number of secondary cases in a single infections as well as the distribution of total cases that result from a single introduction event into the human population (Equation~\ref{clusterLikelihood}, Methods).
We estimate $R_{0}$ along with other relevant parameters via Monte Carlo simulation in two steps.
First, we simulate case counts across multiple outbreaks totaling 2000 cases using Equation \ref{clusterLikelihood} and then we subsample from each case cluster to simulate sequencing of a fraction of cases.

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