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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 P Q P Q
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