source |
The known inverse or relationship matrix:
a sparse inverse variance
matrix held in three column co-ordinate form in row major
order. This triplet matrix must have class ginv
from a call to ainverse() , or have attribute INVERSE
set to TRUE . For backwards compatability, a three column
data frame is also accepted. In either case, the source must
have a rowNames attribute.
a sparse relationship
matrix held in three column co-ordinate form (as a matrix) in row major
order. If the attribute INVERSE is not set then
FALSE is assumed; a rowNames
attribute must be set.
a matrix (or Matrix object) with a
dimnames attribute giving the levels of the model term
being defined. This may be a relationship matrix or its inverse; if
an inverse, it must have an attribute INVERSE set to
TRUE .
a numeric vector of the lower triangular elements in row
major order. The vector must have a rowNames attribute, and
if an inverse structure, it must also have an INVERSE
attribute set to TRUE .
|
singG |
Ignored if source has class ginv or attribute
INVERSE =TRUE ; in such cases source must be one
of:
a sparse matrix in coordinate form with class ginv , or
attribute INVERSE =TRUE , or
an object of class matrix or Matrix
with INVERSE =TRUE ), or
a vector assumed to be the lower triangle in row
major order with attribute INVERSE =TRUE .
If source does not have class ginv , or the attribute
INVERSE is FALSE or is not set, and singG is
NULL (the default), then source is assumed a positive
definite relationship matrix and singG is reset to
"PD" . Otherwise, a character string giving the state of the
(to be inverted) source object:
"PD" positive definite (default)
"ND" source is non-singular indefinite (positive
and negative roots). In this case
asreml ignores the indefinite condition and
proceeds
"PSD" source is positive semi-definite. In this case,
asreml proceeds using lagrangian multipliers to process the
matrix. Two cases arise: whether the singularity arises because of
an effect has zero variance or whether it arises as a linear
dependence. An example of the first is when the GRM represents a
dominance matrix, and the list of genotypes includes fully inbred
individuals which by definition have no dominance. An example of
the second is when the list of genotypes includes clones
"NSD" source is singular indefinite (positive, zero and
negative roots). The indefinite condition is ignored
and asreml proceeds using lagrangian multipliers as for
"PSD" matrices
.
|