us(4 !=ABACBA0CBA)constrains all parameters corresponding to A to be equal, similarly for B and C. The 7th parameter would be left unconstrained. This sequence applied to an unstructured 4 x 4 matrix would make it banded, that is
us(site .3 .1 .4 .1 .1 .3 !=0A0AA0 !GPUPUUP).gendefines a structure for the genotype by site interaction effects in a MET in which the genotypes are independent random effects within sites but are correlated across sites with equal covariance.
fa2(site 4*0.9 0 3*0.1 4*0.2 !G4PZ3P4P !=00000000VVVV )defines a 2 factor Factor Analytic model for 4 sites with equal variance. The first loading in the second factor is constrained equal to 0 for identifiability. P places restrictions on the magnitude of the loadings and the variances to be positive.
xfa2(site !=VVVV0 !4P4PZ3P !INIT 4*0.2 4*1.2 0 .1 .2 .3 )defines a 2 factor Factor analytic model in which the specific variances are all equal.
21:28 29with !VCC 1 is equivalent to
21 29//22 30//23 31//24 32//25 33//26 34//27 35//28 36with !VCC 8
xfa1(dTrial).giv1(Family) xfa1(dTrial !USE xfa1(dTrial)).giv2(Line)