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Table 8 Simulation experiments (4-6) using realistic population allele frequencies from the HapMap phase 3 project

From: A fast least-squares algorithm for population inference

  Simulation 4 q ~ Dir(.2,.2,.05) Simulation 5 q ~ Dir(.2,.2,.5) Simulation 6 q ~ Dir(.05,.05,.01)
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) 2.01 ± 0.05 0.87 ± 0.02 94 ± 12 1.98 ± 0.03 1.16 ± 0.03 93 ± 17 1.96 ± 0.07 0.53 ± 0.02 91 ± 9
AD (ε=1.4e-3) 2.01 ± 0.05 0.87 ± 0.02 82 ± 5 1.98 ± 0.03 1.16 ± 0.03 86 ± 13 1.96 ± 0.07 0.53 ± 0.02 82 ± 7
LS1 (ε=1.4e-3) 2.09 ± 0.05 1.70 ± 0.05 31 ± 7 2.06 ± 0.03 1.60 ± 0.04 34 ± 5 2.04 ± 0.07 2.00 ± 0.04 27 ± 7
LSα (ε=1.4e-3) 2.05 ± 0.05 1.17 ± 0.03 17 ± 3 2.02 ± 0.04 1.34 ± 0.04 24 ± 4 1.99 ± 0.07 1.09 ± 0.03 14 ± 3