CDmean score (GBLUP form)

Mean coefficient of determination of the contrasts between each target row and the target mean, for a GBLUP model with \(K = XX'/p\), a general mean as the only fixed effect, and penalty \(\lambda = \sigma_e^2/\sigma_A^2\) (default 1). Larger is better.

Usage

cdmean_score(X, X0, lambda = NULL)

Arguments

X

A numeric matrix of the training set (row: individual; column: marker or PC).

X0

A numeric matrix of the target rows (the test set), with the same columns as X.

lambda

A positive number, the ridge penalty, or NULL (default) for the default of the criterion.

Value

A number.

Details

See criteria for the list of criteria and the package website for one page per criterion.

References

Rincent, R., et al. (2012). Maximizing the reliability of genomic selection by optimizing the calibration set of reference individuals. Genetics, 192, 715-728. <doi:10.1534/genetics.112.141473> Chen, S.-P., Sung, W.-H., & Liao, C.-T. (2024). Constructing training sets for genomic selection to identify superior genotypes in candidate populations. Theoretical and Applied Genetics, 137, 270. <doi:10.1007/s00122-024-04766-y>

Author

Jen-Hsiang Ou

Examples

data(geno)
cdmean_score(geno[1:50, ], geno[51:100, ])
#> [1] 0.6039068