Table 5.

Prediction R-squared (R²_VAL), square root of the mean-squared prediction error (RMSE) in testing data sets by trait and model, and pair-wise comparisons of prediction accuracies of the models for milk technological properties

Trait2 and model	R2VAL				RMSE	Pair-wise comparisons
	Mean	Minimum	Maximum	SD		PLS	MPLS	Bayes RR	Bayes A	Bayes B
RCT
PLS	0.50	0.41	0.59	0.05	4.14	—	96	100	100	96
MPLS	0.57	0.41	0.65	0.05	3.82	***	—	92	88	92
Bayes RR	0.60	0.48	0.67	0.05	3.70	***	***	—	60	80
Bayes A	0.60	0.47	0.68	0.05	3.67	***	***	NS	—	72
Bayes B	0.63	0.53	0.73	0.06	3.59	***	***	**	*	—
CYCURD
PLS	0.66	0.55	0.76	0.07	1.11	—	84	96	96	92
MPLS	0.68	0.54	0.80	0.07	1.07	***	—	48	80	84
Bayes RR	0.68	0.56	0.78	0.07	1.08	***	NS	—	80	80
Bayes A	0.70	0.59	0.81	0.07	1.04	***	***	***	—	72
Bayes B	0.71	0.57	0.82	0.06	1.03	***	***	***	NS	—
RECPROTEIN
PLS	0.47	0.30	0.63	0.09	1.75	—	100	100	100	100
MPLS	0.60	0.37	0.75	0.10	1.52	***	—	96	96	80
Bayes RR	0.65	0.47	0.79	0.09	1.42	***	***	—	48	44
Bayes A	0.65	0.46	0.80	0.09	1.42	***	***	NS	—	48
Bayes B	0.65	0.47	0.80	0.09	1.44	***	***	NS	NS	—
RECFAT
PLS	0.21	0.07	0.36	0.08	3.31	—	88	80	88	92
MPLS	0.28	0.14	0.42	0.09	3.13	***	—	4	16	52
Bayes RR	0.23	0.07	0.37	0.08	3.24	**	***	—	84	92
Bayes A	0.24	0.08	0.38	0.08	3.22	***	***	**	—	92
Bayes B	0.28	0.14	0.42	0.09	3.13	***	NS	***	***	—

¹PLS = partial least squares regression; MPLS = modified partial least squares regression, Bayes RR = Bayes ridge regression; R²_VAL = coefficient of determination calculated as the square of the correlation between observed and predicted values; Mean, Minimum, Maximum = mean, minimum, and maximum of the R² of 25 replicates; RMSE = mean of the root mean square errors of 25 replicates; the values above the diagonal indicate the percentage of replicates where the model in the column had a higher prediction R²_VAL than the model in the row; the asterisks below the diagonal indicate P-values from paired t-tests comparing the R²_VAL of the model in the column and the model in the row: ***, **, and *: significant differences at the 0.001, 0.01, and 0.05 levels, respectively; NS indicates no significant difference at the 0.05 level.

²RCT = rennet coagulation time, min; CY_CURD = cheese yield, weight of fresh curd as a percentage of the milk processed by weight; REC_PROTEIN = recovery of protein, protein of the curd as a percentage of the protein of the milk processed; REC_FAT = recovery of fat, fat of the curd as a percentage of the fat of the milk processed.