atm: Selected-level diagonal covariance structure

In sommer: Solving Mixed Model Equations in R

Selected-level diagonal covariance structure

Description

Selected-level diagonal covariance structure. The returned dimensionless covariance shape is intended for use inside vsm, which supplies the single overall variance scale.

Usage

atm(x, levs, values = NULL, fixed = NULL)

Arguments

x	Variable defining all available levels.
levs	Character names or numeric positions of the levels retained in this covariance factor.
values	Optional positive starting variances for the selected levels.
fixed	Logical vector of length length(levs)-1 controlling the selected variance ratios.

Details

atm is a selected-level version of dsm. The design is restricted to levs; observations outside those levels receive zeros for this factor. The first selected level is the scale reference and the remaining selected levels are positive variance ratios. This representation is most naturally used for random effects; residual factors must still assign exactly one covariance-product coordinate to every observation.

Value

A list containing the incidence/design matrix in Z and a compiled CovarianceFactor v2 descriptor in covFactor, for use inside vsm.

See Also

dsm, vsm, mmes.

Examples

## Not run: 
vsm(atm(environment, c("E1","E3")), ism(genotype))

## End(Not run)

sommer documentation built on Oct. 25, 2026, 5:06 p.m.