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Table 2 Mean percentage reduction in average loss for the genetic covariance matrix together with the average proportion of replicates for which penalisation increased loss

From: Performance of penalized maximum likelihood in estimation of genetic covariances matrices

Penalty

% reduction in average loss

% replicates with increased loss

 

V∞

V1

CV3

CV5

L5%

V∞

V1

CV3

CV5

L5%

P λ

71.3

60.6

55.9

50.4

68.3

7.3

8.7

14.6

14.6

12.0

P λ 2

72.9

63.7

60.7

58.1

70.2

6.5

7.5

13.0

13.2

10.0

P β b

71.4

62.9

58.1

53.9

69.5

6.4

7.5

13.6

14.0

9.8

P Σ

70.6

60.6

54.9

52.7

64.1

4.6

8.9

15.4

15.5

15.6

P ρ

72.0

62.9

54.4

51.6

70.5

4.0

7.1

9.9

10.2

9.2

  1. Data for q = 5 traits and s = 100 sire families; using different penalties and strategies to determine the tuning factor (V∞: using population values, V1: sampling one additional data set, CV3 and CV5: 3- and 5- fold cross-validation, and L5%: limiting the change in log likelihood)