Table 7 Simulation experiments (1-3) using realistic population allele frequencies from the HapMap phase 3 project

From: A fast least-squares algorithm for population inference

	Simulation 1 q ~ Dir(1,1,1)			Simulation 2 q ~ Dir(.5,.5,.5)			Simulation 3 q ~ Dir(.1,.1,.1)
Original
Admixture
Least-squares (α=1)
Least-squares with α
	RMSE (%) ± Std. Dev.		Time (s.) ± Std. Dev.	RMSE (%) ± Std. Dev.		Time (s.) ± Std. Dev.	RMSE (%) ± Std. Dev.		Time (s.) ± Std. Dev.
	P	Q	Time (s.) ± Std. Dev.	P	Q	Time (s.) ± Std. Dev.	P	Q	Time (s.) ± Std. Dev.
AD (ε=1e-4)	2.50 ± 0.04	2.19 ± 0.11	105 ± 13	1.99 ± 0.02	1.44 ± 0.04	88 ± 9	1.54 ± 0.01	0.76 ± 0.02	86 ± 7
AD (ε=1.4e-3)	2.50 ± 0.04	2.19 ± 0.11	98 ± 13	1.99 ± 0.02	1.44 ± 0.04	87 ± 11	1.54 ± 0.01	0.76 ± 0.02	83 ± 9
LS1 (ε=1.4e-3)	2.51 ± 0.03	1.85 ± 0.07	51 ± 6	2.04 ± 0.02	1.43 ± 0.04	37 ± 8	1.63 ± 0.01	1.75 ± 0.05	27 ± 5
LSα (ε=1.4e-3)	2.51 ± 0.03	1.85 ± 0.07	54 ± 8	2.03 ± 0.02	1.53 ± 0.04	28 ± 4	1.57 ± 0.01	1.08 ± 0.02	15 ± 4

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