Matvec Users’ Guide

11.2. PENALIZED QUASI-LIKELIHOOD 83
dam wt_6wk fd_int
13c 0.275847 -0.172521
13r -0.319031 0.506760
16b -0.319031 0.506760
REML estimates can be obtained with:
this.parameter("EPSILON",1.e-8);
M.link("normal",3);
est=M.vce_aireml(30,1.e-8);
vc=est(*,1);
cov=est(*,2:est.ncol());
se=cov.diag(0).sqrt();
"\nVariance Estimates and Standard Errors\n"
[vc se]
M.info("mouse3.info","out");
"Log Like",M.residual_log_like()
The M.link("normal",3) is needed by M.vce aireml(), 3 is for the 3 residual variance components in a
2-trait residual covariance matrix. The EPSILON was set to larger value for numerical stability. The code:
vc=est(*,1);
cov=est(*,2:est.ncol());
se=cov.diag(0).sqrt();
"\nVariance Estimates and
[vc se]
Standard Errors\n"
calculates asymptotic standard errors and prints the estimated variance components along with their standard
errors. The abbreviated output:
Original
Residual Log Likelihood:-2200.19
Iteration 1.0 Res Log Like -2200.08 Change 0.114878
Iteration 2.0 Res Log Like -2200.06 Change 0.0188999
Iteration 3.0 Res Log Like -2200.06 Change 0.000345039
Iteration 4.0 Res Log Like -2200.06 Change 3.24196e-05
Iteration 5.0 Res Log Like -2200.06 Change 4.6876e-06
Iteration 6.0 Res Log Like -2200.06 Change 8.18218e-07
Iteration 7.0 Res Log Like -2200.06 Change 1.57462e-07
Iteration 8.0 Res Log Like -2200.06 Change 3.17959e-08
Iteration 9.0 Res Log Like -2200.06 Change 6.70434e-09
Iteration 9 Converged
. . . . . . . . . . . . . . .
Variance Estimates and
Standard Errors
4.05386 2.68904
-0.4364 2.80002
0.412177 1.81148
-0.0398331 2.12659
5.60885 6.16926
1.36832 2.29069
-0.432407 3.66772
1.58627 2.28487