Table 3 UM imputation error for the KE DH-lines by changing a single imputing parameter with ne = 1,000 for BEAGLE 5.0 / 5.1 and ne = 300 for BEAGLE 4.1
Parameterdefaultrange testedbestoverall impact
BEAGLE 5.0 / 5.1default (3.09%)
ne1,000,0001 - 1,000,0001,000 (0.0877%)Figure 5 and S46
err0.01 (5.0) / 0.00098 (5.1)0.001 - 0.000010.00005 (0.0877%)Figure S47 and S48
window4010 - 1,000200 (0.0868%)Figure S49 and S50
burnin62 - 25default (0.0877%)Figure S51 and S52
iterations122 - 25default (0.0877%)Figure S53 and S54
phase-segment (5.0)41 - 10050 (0.0873%)Figure S55
phase-states28050 - 1,000default (0.0877%)Figure S56 and S57
imp-states1,600100 - 5,000250 (0.0873%)Figure S58 and S59
imp-segment62 - 10050 (0.0874%)Figure S60 and S61
imp-step (5.1)0.10.001 - 200.05 (0.0876%)Figure S62
imp-nsteps (5.1)71 - 5050 (0.875%)Figure S63
cluster0.0050.1 - 0.000010.00005 (0.0868%)Figure S64 and S65
BEAGLE 4.1default (6.59%)
ne1,000,0001 - 1,000,000300 (0.0958%)Figure S66
niterations50 - 25Figure S68
modelscale0.80.5 - 52 (0.0886%)Figure S67
BEAGLE 4.0default (5.15%)
buildwindow1,2001 - 2,500100 (0.799%)Figure S69
singlescale0.80.5 - 51.5 (0.188%)Figure S70
nsamples41 - 252 (4.36%)Figure S71
burnin-its52 - 50default (5.15%)Figure S72
phase-its52 - 5025 (5.071%)Figure S73
impute-its52 - 5050 (0.189%)Figure S74