Complications of entangled chains can affect inference.

<p>ML estimates of and and corresponding 90% confidence regions are when all clusters are treated as chains, and for two approaches to assigning constituent chain sizes for clusters with more than one primary case (details provided in the text). For visual comparison, the contour corresponding to the chain size analysis from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002993#pcbi-1002993-g001" target="_blank">figure 1</a> is replicated.