BLUP(trait="yield",family="all",env="all", MAF=0.05,use.check=TRUE,impute="FM",rm.rep=TRUE)The algorithm start from selecting the chosen families and environment that will be used for the best linear unbias predictor (BLUP). The BLUP values are calculates based on the following model: ($Trait = Control + Environment + Genotype$). Where control is a covariate set as fixed effect based on the checks of each set (microenvironment); Environment is a random effect that represents the combination of location and year; and Genotype is the random effect associated to the lines. The BLUP values are the regression coefficients corresponding to the Genotype effect. The BLUP is calculated using the R package lme4 (Bates 2010) using REML.
If checks are used as covariate (use.check=TRUE), then the best linear unbias estimator (BLUE) of the check effects is assigned to each set as a micro-environmental control. Each set had between one and five controls, including the SoyNAM parents and five other cultivars. These genotypes are normalized by environment and the BLUE of each set is calculated. All genotypes in a same set will have the same check effect.
Test=BLUP(trait="yield",family=2:5,env=2:7)
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