deletions | additions       diff --git a/Case tree plots.tex b/Case tree plots.tex  index 7f33780..7315349 100644  --- a/Case tree plots.tex  +++ b/Case tree plots.tex 
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\subsection*{Case tree plots}  The Case tree plots depict clusters of disease over time. Placement along the  x-axis represents time, and corresponds with the date of illness onset for  the y axis case. When the onset date is not known, diagnosis date may be used instead. The y-axis value  represents the case  generation. Nodes at generation 1 are human cases acquired from an animal source. If that infected human passes the disease to two other humans, those two subsequent cases are plotted at generation 2, and connected to the node of origin by edges. Cases that do not belong to a cluster are represented as independent nodes on the plot.The meaning of the color of the node varies based on the node attribute. In many cases, color simply signifies membership to a human to human cluster. However, it could also represent health status (e.g. alive, dead), the sex of the patient, or any other categorical attribute.  The meaning of the color of the node varies based on the node attribute. In many cases, color simply signifies membership to a human to human cluster. However, it could also represent health status (e.g. alive, dead), the sex of the patient, or any other categorical attribute.  To generate a case tree plot, users provide a line listing with, at minimum: unique  case ids, identifiers, the  date of illness onset, onset (or the date the illness was reported, if onset date is not available),  and cluster membership, as seen in table~\ref{tab:linelist}. Any additional relevant  variables like patient age and sex may also be included. \begin{table}  \centering 
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\label{tab:linelist}  \end{table}  Users must also provide the mean and standard deviation of the generation time between cases. Because generation time is not always known in the early days of the outbreak, the incubation period may be a reasonable proxy.  The line listing need not specify the chain of transmission; the case tree plot generator will estimate the chain of transmission based on the onset dates based generation time values. Cases belonging to the same cluster that have an onset date within one standard deviation of the mean generation time are assumed to be linked.