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
| Â | Simulation 4 q ~ Dir(.2,.2,.05) | Simulation 5 q ~ Dir(.2,.2,.5) | Simulation 6 q ~ Dir(.05,.05,.01) | ||||||
|---|---|---|---|---|---|---|---|---|---|
Original |
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| Â | Â | Â | Â | Â | Â |
Admixture |
|
|
| Â | Â | Â | Â | Â | Â |
Least-squares (α=1) |
|
|
| Â | Â | Â | Â | Â | Â |
Least-squares with α |
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| Â | Â | Â | Â | Â | Â |
RMSE (%) Std. Dev. |  | Time (s.) ± Std. Dev. | RMSE (%) ± Std. Dev. | Time (s.) ± Std. Dev. | RMSE (%) ± Std. Dev. | Time (s.) ± Std. Dev. | |||
| Â | 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 |
