Code & data – A note on the conditioning of the H^-1 matrix used in single-step GBLUP

Pedigree, genotype, and phenotype data were simulated on ten populations and twenty generations. Some pedigree, genotype, and phenotype data were set to missing. Data were analysed using the single-step GBLUP method forming the inverse of the pedigree-genomic relationship matrix (H^-1). Different components of H^-1 (H^-1 itself, A^-1 (together with A_22^-1), G^-1, and G^-1 - A_22^-1) were weighted by α ranging from 0.8 to 1.2. Responses regarding the regression of phenotypes on genomic breeding values and the correlation between phenotypes and genomic breeding values were recorded and averaged over the ten populations. All the processes are presented in Jupyter Notebooks (also available in HTML and Rmd) written in R programming language.