estimateV.asreml {asremlPlus}

Forms the estimated variance, random or residual matrix for the observations from the variance parameter estimates.

Description

Forms the estimated variance (V), random (G) or (R) matrix for the observations, a square symmetric matrix of order equal to the number of observations. The estimates of the variance parameters and the information about the random and residual models for which they were estimated are obtained from the asreml object. This function is not available in ASReml-R version 3.

Usage

## S3 method for class 'asreml'
estimateV(asreml.obj, which.matrix = "V", 
          extra.matrix = NULL, ignore.terms = NULL, fixed.spline.terms = NULL, 
          bound.exclusions = c("F","B","S","C"), ...)

Arguments

asreml.obj

An asreml object from a call to asreml in which the data argument has been set.

which.matrix

A character giving the matrix that is to be formed. It must be one of "V", to produce the variance matrix V = G + R, "G" to produce the matrix G, corresponding to the random formula, or "R" to produce the matrix R, corresponding to the residual formula.

extra.matrix

A matrix of order equal to the number of observations that is to be added to the matrix specified by which.matrix, the latter based on the information in asreml.obj. It is assumed that the sigma-parameterized values of the variance parameter estimates, such as is given in the varcomp component of summary.asreml, have been used in calculating extra.matrix; the values in the vparameters component of G.param and R.param may be either gamma- or sigma-parameterized. The argument extra.matrix can be used in conjunction with ignore.terms as a workaround to include components of the variance matrix for variance functions that have not been implemented in estimateV.

ignore.terms

A character giving terms from either the random or residual models that are to be ignored in that their contributions to the variance is not to be included in the estimated matrix. The term names are those given in the vparameters component of the asreml object or the varcomp component produced by summary.asreml, but only up to the first exclamation mark (!). This can be used in conjunction with estimateV.asreml as a workaround to include components of the variance matrix for variance functions that have not been implemented in estimateV.

fixed.spline.terms

A character vector giving one or more spline terms in the random model that are regarded as fixed and so are to be ignored because they are not regarded as contributing to the variance. The term names are those given in the vparameters component of the asreml object or the varcomp component produced by summary.asreml, but only up to the first exclamation mark (!).

bound.exclusions

A character specifying one or more bound codes that will result in a variance parameter in the random model being excluded from contributing to the variance. If set to NULL then none will be excluded.

...

Provision for passing arguments to functions called internally - not used at present.

Details

The information about the variance parameters in the fitted mixed model are obtained from the G.param and R.param components of the asreml object. The function can deal with the following variance functions in either the random or residual models: id, diag, us, ar1, ar2, ar3, sar,sar2, ma1, ma2, arma, exp, gau, cor, corb and corg. All of these functions, except us, can be combined with either v or h. It will also cope with the following functions in the random model: at, str, spl, dev, grp, fa and rr. Additionally, it can deal with the function dsum in the residual model. For further information see the ASReml-R User Guide Version 4 (Butler et al., 2023).

Value

A matrix containing the estimated variance matrix. It has an attribute missing.termmatrix (use attr(x, which = "missing.termmatrix") to access the atrribute). It will be NULL, unless the design matrix could not be obtained for one or more model terms. If is is not NULL, it will be a list of terms that could not be produced for inclusion in the variance matrix estimate, and NA will be returned for the estimated variance matrix.

Author(s)

Chris Brien

References

Butler, D. G., Cullis, B. R., Gilmour, A. R., Gogel, B. J. and Thompson, R. (2023). ASReml-R Reference Manual Version 4.2. VSN International Ltd, https://asreml.kb.vsni.co.uk/.

See Also

asreml, simulate.asreml, variofaces.asreml.

Examples

## Not run: 
data(Wheat.dat)
current.asr <- asreml(yield ~ Rep + WithinColPairs + Variety, 
                      random = ~ Row + Column + units,
                      residual = ~ ar1(Row):ar1(Column), 
                      data=Wheat.dat)
# Form variance matrix based on estimated variance parameters
V <- estimateV(current.asr)


## End(Not run)