lme4breeding (version 1.0.60)

fillData: Filling gaps for a dataset to balance

Description

fillData creates a balanced dataset in the long format to be used with the lmebreed solver for multi-trait models.

Usage

fillData(data, toBalanceSplit=NULL, toBalanceFill=NULL)

Value

$res

a data frame with traits in long format.

Arguments

data

a data frame with traits in wide format.

toBalanceSplit

variable to split the dataset for balancing.

toBalanceFill

variable of the factor to balance across the levels of the toBalanceSplit variable.

Author

Giovanny Covarrubias-Pazaran

References

Giovanny Covarrubias-Pazaran (2024). lme4breeding: enabling genetic evaluation in the age of genomic data. To be submitted to Bioinformatics.

Douglas Bates, Martin Maechler, Ben Bolker, Steve Walker (2015). Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software, 67(1), 1-48.

See Also

The function for the lmebreed solver.

Examples

DT <- DT_example
A <- A_example
DT2 <- fillData(DT , toBalanceSplit="Env", toBalanceFill="Name" )
head(DT2)

# \donttest{

## Compound simmetry (CS) model
ans2 <- lmebreed(Yield~Env+ (0+Env|Name),
                 relmat = list(Name=A),
                 rotation = TRUE,
                 data=DT2)
vc <- VarCorr(ans2); print(vc,comp=c("Variance"))

BLUP <- ranef(ans2, condVar=TRUE)$Name
SEs <- attr(BLUP, which="postVar")[,,]

# }