FA

XFA

y ~ site !r geno.xfa(site,2) 0 0 1 geno.xfa(site,2) 2 geno xfa(site,2) 0 XFA2 !GP 10*0.1 # Psi (Specific variances, assuming 10 sites) 10*0.3 # First loadings 10*0.1 # Second loadingsIn ASReml 3 if no loadings are fixed (i.e. !GP), ASReml will rotate the loadings to orthogonality, and hold the leading loadings of lower factors fixed. They are however updated in the orthogonalization process which occurs at the beginning of each iteration (so the final returned values have not been formally rotated). Finding the REML solutions for multifactor Factor Analytic models can be difficult. The first problem is specifying initial values. When using !CONTINUE and progressing XFA(

!WORK 1 !NOGRAPH !continue Title: ALBUSA previous set of analyses using these five models gave LogL values for the models CORUH, XFA1, XFA2, XFA3 and XFA4 respectively of 2782, 2910, 3021, 3109 and 3200 using the strategies listed above in separate runs. Running this job using the integrated strategy produced LogL values of 2783, 2911, 3048, 3153 and 3206. However, for models XFA3 and XFA4, the LogL drifted away again. The XFA display reported in the .res file has been revised. The current output from a small example with 9 environments and 2 factors is %Ontario_{2}tage. #trial,year,region,variety,yield,rep,weight,ems #KFA02BURU,2002,NSW,KIEV-MUTANT,0.873,3,2136.562,0.0010000 trial !A year !I region !A variety !A yield rep * weight !*0.025 ems !CYCLE 11 1 2 3 4 !DOPART $I ALBUS_{2}tage.csv !SKIP 1 !MAXIT 40 !AILOAD 20 !PART 11 !MAXIT 25 yield !wt=weight ~ mu trial !r trial.variety 1 1 1 0 !S2==0.025 trial.variety 2 trial 0 CORUH .1 87*.1 variety !PART 1 2 3 4 yield !wt=weight ~ mu trial !r xfa(trial,$I).var 1 1 1 0 !S2==0.025 xfa(trial,$I).var 2 xfa(trial 0 XFA$I !GP 87*.01 87*.07 87*.07 87*.07 87*.07 variety

DISPLAY of variance partitioning for XFA structure in xfa(Env,2).Geno Lvl |----+----+----+----+----+----+----+----+----+----| TotalVar %expl PsiVar Loadings 1 | 1 | 0.3339 79.7 0.0679 0.5147 0.0335 2 | 1 2 0.1666 100.0 0.0000 0.4003 0.0797 3 | 1 2 | 0.2475 67.8 0.0798 0.3805 0.1514 4 | 1 2 0.1475 100.0 0.0000 0.3625 0.1269 5 | 1 2 0.4496 100.0 0.0000 0.6104 -0.278 6 | 1 2 0.1210 100.0 0.0000 0.2287 0.2622 7 | 1 2 | 0.4106 54.4 0.1872 0.4152 -0.226 8 | 1 2 0.0901 100.0 0.0000 0.0922 0.2857 9 | 1 2 0.1422 100.0 0.0000 0.2819 0.2506 0 |----+----+----+----+----+----+----+----+-- Average 0.2343 89.1 0.0372 0.3651 0.0763In the figure, 1 indicates the proportion of TotalVar explained by the first loading, 2 indicates the proportion explained by first and second (provided it plots right of 1. Consequently, the distance from 2 to the right margin represents PsiVar. %expl reports the percentage of TotalVar explained by all loadings. The last row contains column averages.