Performance of the No-U-Turn sampler in multi-trait variance component estimation using genomic data

Table 3 Estimated variance components, heritability and correlations in Scenario 1 using the real PIC pig data

Parameter	NUTS (LKJ prior)		NUTS (IW prior)		GS		REML
Parameter	Mean	SE	Mean	SE	Mean	SE	Estimate	SE
Additive (co)variances
\({\sigma }_{a}^{2}(T1)\)	0.03	0.02	0.07	0.02	0.05	0.02	0.04	0.02
\({\sigma }_{a}^{2}(T2)\)	0.23	0.03	0.24	0.03	0.26	0.03	0.25	0.03
\({\sigma }_{a}^{2}(T3)\)	0.24	0.04	0.25	0.04	0.27	0.04	0.26	0.04
\({\sigma }_{a}(T1,T2)\)	0.02	0.01	0.02	0.05	0.02	0.02	0.02	0.02
\({\sigma }_{a}(T1,T3)\)	0.02	0.02	0.03	0.07	0.03	0.02	0.03	0.02
\({\sigma }_{a}(T2,T3)\)	0.03	0.02	0.03	0.02	0.03	0.02	0.03	0.02
Residual (co)variances
\({\sigma }_{e}^{2}(T1)\)	0.97	0.03	0.94	0.03	0.96	0.03	0.96	0.03
\({\sigma }_{e}^{2}(T2)\)	0.62	0.02	0.62	0.02	0.61	0.02	0.61	0.02
\({\sigma }_{e}^{2}(T3)\)	0.75	0.03	0.75	0.03	0.73	0.03	0.73	0.03
\({\sigma }_{e}(T1,T2)\)	0.01	0.02	0.02	0.02	0.01	0.02	0.01	0.02
\({\sigma }_{e}(T1,T3)\)	0.00	0.04	0.00	0.04	0.00	0.03	0.00	0.02
\({\sigma }_{e}(T2,T3)\)	0.02	0.02	0.01	0.05	0.01	0.02	0.01	0.02
Heritabilities
\({h}^{2}(T1)\)	0.03	0.02	0.07	0.02	0.05	0.02	0.04	0.02
\({h}^{2}(T2)\)	0.27	0.03	0.27	0.03	0.30	0.03	0.29	0.03
\({h}^{2}(T3)\)	0.24	0.03	0.25	0.03	0.27	0.03	0.26	0.03
Additive genetic correlations
\({r}_{a}(T1,T2)\)	0.24	0.17	0.12	0.12	0.19	0.14	0.25	0.25
\({r}_{a}(T1,T3)\)	0.27	0.22	0.21	0.15	0.26	0.17	0.37	0.34
\({r}_{a}(T2,T3)\)	0.13	0.09	0.14	0.03	0.12	0.09	0.14	0.10
Residual genetic correlations
\({r}_{e}(T1,T2)\)	0.02	0.02	0.02	0.03	0.02	0.03	0.02	0.03
\({r}_{e}(T1,T3)\)	0.00	0.04	0.00	0.04	0.00	0.05	0.00	0.03
\({r}_{e}(T2,T3)\)	0.02	0.03	0.02	0.03	0.02	0.03	0.02	0.03

NUTS No-U-Turn sampler, LKJ Lewandowski-Kurowicka-Joe, IW inverse-Wishart, GS Gibbs sampling, REML restricted maximum likelihood, SE standard error
\({\sigma }_{a}^{2}\): additive genetic variance, \({\sigma }_{a}\): additive genetic covariance, \({\sigma }_{e}^{2}\): residual variance, \({\sigma }_{e}\): residual covariance, \({h}^{2}\): heritability, \({r}_{a}\): additive genetic correlation, \({r}_{e}\): residual correlation

ISSN: 1297-9686