DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

Villandré, Luc; Labbe, Aurélie; Brenner, Bluma; Roger, Michel; Stephens, David A

doi:10.1186/s12859-018-2347-3

BMC Bioinformatics

Table 1 Summary statistics for adjusted Rand indices (ARI) for cluster membership estimates obtained from chains run on 50 datasets under different simulation scenarios

From: DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

Topology used	Alpha mean	Estimator	Min.	Max.	10th perc.	Median	90th perc.	Mean	SD	SE
GapProcedure	-	-	0.012	0.719	0.030	0.385	0.654	0.361	0.227	0.005
Bootstrap-70	-	-	0.074	0.882	0.256	0.483	0.771	0.504	0.221	0.004
ML topology	10	MAP	0.000	0.935	0.686	0.820	0.900	0.769	0.210	0.004
		Linkage-0.7	0.000	0.946	0.711	0.853	0.920	0.793	0.213	0.004
		Linkage-0.8	0.000	0.971	0.707	0.838	0.912	0.793	0.213	0.004
		Linkage-0.9	0.000	0.962	0.710	0.822	0.893	0.771	0.206	0.004
		Linkage-1	0.089	0.710	0.359	0.494	0.631	0.484	0.129	0.003
	1	MAP	0.098	0.862	0.328	0.619	0.833	0.601	0.199	0.004
		Linkage-0.7	0.012	0.939	0.381	0.725	0.861	0.653	0.218	0.004
		Linkage-0.8	0.011	0.959	0.394	0.760	0.865	0.680	0.207	0.004
		Linkage-0.9	0.053	0.937	0.466	0.776	0.885	0.712	0.191	0.004
		Linkage-1	0.159	0.716	0.397	0.470	0.646	0.491	0.103	0.002
	100	MAP	0.123	0.931	0.594	0.848	0.917	0.790	0.196	0.004
		Linkage-0.7	0.123	0.973	0.346	0.859	0.931	0.791	0.215	0.004
		Linkage-0.8	0.123	0.971	0.348	0.852	0.920	0.785	0.211	0.004
		Linkage-0.9	0.123	0.980	0.378	0.820	0.896	0.761	0.202	0.004
		Linkage-1	0.123	0.802	0.351	0.514	0.652	0.504	0.133	0.003
MAP topology	10	MAP	0.000	0.935	0.714	0.839	0.923	0.798	0.180	0.004
		Linkage-0.7	0.000	0.950	0.727	0.858	0.919	0.818	0.172	0.004
		Linkage-0.8	0.000	0.953	0.791	0.846	0.919	0.823	0.165	0.003
		Linkage-0.9	0.000	0.947	0.751	0.824	0.891	0.798	0.156	0.003
		Linkage-1	0.000	0.686	0.318	0.449	0.598	0.454	0.117	0.002
	1	MAP	0.011	0.870	0.329	0.623	0.832	0.598	0.203	0.004
		Linkage-0.7	0.162	0.930	0.321	0.738	0.848	0.649	0.212	0.004
		Linkage-0.8	0.170	0.931	0.384	0.746	0.872	0.671	0.201	0.004
		Linkage-0.9	0.175	0.911	0.437	0.764	0.852	0.693	0.178	0.004
		Linkage-1	0.341	0.745	0.396	0.516	0.660	0.524	0.093	0.002
	100	MAP	0.123	0.947	0.761	0.854	0.914	0.816	0.171	0.003
		Linkage-0.7	0.123	0.976	0.793	0.867	0.923	0.830	0.170	0.003
		Linkage-0.8	0.123	0.970	0.789	0.857	0.914	0.825	0.169	0.003
		Linkage-0.9	0.123	0.965	0.703	0.819	0.901	0.789	0.164	0.003
		Linkage-1	0.123	0.672	0.298	0.459	0.619	0.457	0.122	0.002

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