Case tree plots

Case tree plots depict the emergence and growth of clusters of disease over time. Each case is represented by a colored node. Nodes that share an epidemiological link are connected by an edge. The color of the node varies based on the node attribute chosen by the plot creator; 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.

Node placement along the x-axis corresponds with the date of illness onset for the 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 zero 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 one. Cases that do not belong to a cluster are not represented on the plot.

To produce a case tree plot, users provide a line list with, at minimum: unique case identifiers, the date of illness 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.

\label{tab:linelist}

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 plot generator will estimate the chain of transmission based on the onset dates. Cases labeled as belonging to the same cluster that have an onset date within one standard deviation of the mean generation time are assumed to be linked.