estimateV.asreml {asremlPlus}  R Documentation 
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 ASRemlR 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 sigmaparameterized
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 sigmaparameterized.
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 mor 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 passsing 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 ASRemlR User Guide Version 4 (Butler et al., 2018).
Value
A matrix
containing the estimated variance matrix.
Author(s)
Chris Brien
References
Butler, D. G., Cullis, B. R., Gilmour, A. R., Gogel, B. J. and
Thompson, R. (2018). ASRemlR Reference Manual Version 4.
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)
[Package
asremlPlus version 4.232
Index]