ranef: Extract the modes of the random effects

In famuvie/breedR: Statistical Methods for Forest Genetic Resources Analysts

Description

Extract the conditional modes of the random effects from a fitted model object. For linear mixed models the conditional modes of the random effects are also the conditional means.

Usage

## S3 method for class 'remlf90'
ranef(object, ...)

Arguments

object	a fitted models with random effects of class remlf90.
...	not used

Details

This method is modeled a bit after ranef. However, it is independent and does not inherit from it. In particular, it always returns the conditional variance (argument condVar in lme4).

Value

An object of class ranef.breedR composed of a list of vectors or matrices (multitrait case), one for each random effect. The length of the vectors are the number of levels of the corresponding random effect.

Each random effect has an attribute called "se" which is a vector with the standard errors.

Additionally, depending of the nature of the random effect, there may be further attributes. The pedigree will be given for genetic random effects and the spatial prediction grid for the spatial random effects

Note

To produce a (list of) “caterpillar plots” of the random effects apply plot to the result of a call to ranef.

Examples

res <- remlf90(phe_X ~ bl,
               genetic = list(model = 'add_animal',
                              pedigree = globulus[, 1:3],
                              id = 'self'),
               data = globulus)
str(rr <- ranef(res))
plot(rr)

famuvie/breedR documentation built on Sept. 6, 2021, 4:50 a.m.