fillData: Filling gaps for a dataset to balance

In lme4breeding: Relationship-Based Mixed-Effects Models

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)

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.

Value

$res

a data frame with traits in long format.

Author(s)

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)



## 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")[,,]

lme4breeding documentation built on April 3, 2025, 6:28 p.m.