StageWise enables selection with multi-trait indices, including restricted indices with one or more traits constrained to have zero response. Another feature is directional dominance, including for polyploids, to account for inbreeding depression in outbred crops. As the name suggests, one of the core features is a fully efficient, two-stage analysis for multiple environments, in which the full variance–covariance matrix of the Stage 1 genotype means is used in Stage 2. R package StageWise was developed to go beyond the capabilities of most specialized software for genomic prediction, without requiring the programming skills needed for more general-purpose software for mixed models. Plant breeders interested in genomic selection often face challenges to fully utilizing multi-trait, multi-environment datasets. R/StageWise enables fully efficient, two-stage analysis of multi-environment, multi-trait datasets for genomic selection, including support for dominance heterosis and polyploidy.
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