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15
Examples
294
3.74 0.97 0.019 0.941
!PATH 2
4 0 FA1 !GP
# Factor Analytic 1
.5 .5 .01 .1
4.95 4.63 0.037 0.941
!PATH 3
4 0 US
# Unstructured
5.073
3.545
3.914
0.1274
0.08909 0.02865
0.07277 0.05090 0.001829 1.019
!PATH
lit
Table 15.15: Variance models fitted for each part of the ASReml job in the analysis
of the genetic example
term
sire
dam
litter
error
matrix
!PATH 1
!PATH 2
!PATH 3
Σs
Σd
Σl
Σe
DIAG
CORGH
DIAG
US
FA1
CORGH
FA1
US
US
US
US
US
In !PATH 1, the error variance model is taken to be unstructured, but the starting
values are set to zero. This instructs ASReml to obtain starting values from the
sample covariance matrix of the data. For incomplete data the matrix so obtained
may not, in general be positive definite. Care should be taken when using this
option for incomplete multivariate data. The command to run !PATH 1 is
asreml -nrw64 mt 1
The Loglikelihood from this run is −20000 − 1444.93. When the job runs, the
message
Non positive definite G matrix:
order 3
0 singularities 1 negative pivots;
appears to the screen. This refers to the 3 × 3 dam matrix which is estimated as