Table 3.

Best XGB model parameters for each dataset obtained via grid search cross-validation

Data seta	Subset of features	Learning rate	Individual tree depth	Data sample
Sim 5	0.01	0.05	2	0.05
Sim 50	0.40	0.10	2	0.90
Sim rand	0.30	0.05	6	0.80
Sim real	0.80	0.20	2	0.10
Real data	0.60	0.30	6	0.90

^aSim 5 = simulated data with a 5% missing rate for all SNPs; Sim 50 = simulated data with a 50% missing rate for all SNPs; Sim rand = simulated data with a random error rate in the range of 5 to 50%; Sim real = simulated data with a random error rate in the range of 5 to 10% for 5 SNPs and 10 to 50% for 10 SNPs; real data = data from the Finnish Rainbow Trout Breeding Program