Reconstructing transmission trees for communicable diseases using densely sampled genetic data

. Author manuscript; available in PMC: 2016 Apr 1.

Published in final edited form as: Ann Appl Stat. 2016 Mar 25;10(1):395–417. doi: 10.1214/15-aoas898

	Importation (clustered)	Importation (unclustered)	Acquisition
Add	$\frac{(v_{s} - v_{a}) ∣ Y_{ext} (t_{j}^{a}) ∣}{w w^{'} (v_{0} + 1) M_{a}}$	$\frac{v_{s} - v_{a}}{w (1 - w^{'}) (v_{0} + 1) M_{a}}$	$\frac{(v_{s} - v_{a}) (t_{j}^{d} - t_{j}^{a} + 1) C (t_{j}^{c *})}{(1 - w) (v_{0} + 1) M_{a}}$
Remove	$\frac{w w^{'} v_{0} M_{r}}{(v_{s} - v_{a} + 1) ∣ Y_{ext} (t_{j}^{c}) ∣}$	$\frac{w (1 - w^{'}) v_{0} M_{r}}{v_{s} - v_{a} + 1}$	$\frac{v_{0} (1 - w) M_{r}}{(t_{j}^{d} - t_{j}^{a} + 1) (v_{s} - v_{a} + 1) (C (t_{j}^{c}) - 1)}$