> r2g<-echidna(es0.file="fm.es0", + fixed=h5~1+Rep, + random=c(G1~Fam,G2~Fam+Plot), + residual=~units, + batch.G=T, + trace=T) Program runs for 2 more G-structure at one time. ------ run 1 -- random effects: Fam Running Echidna for analysis: h5 Sun Feb 7 15:45:15 2021 Iteration LogL eSigma NEDF 1 1 -2667.81 5289 551 2 2 -2667.71 5340 551 3 3 -2667.71 5333 551 Sun Feb 7 15:45:15 2021 LogL Converged
run 2 -- random effects: Fam Plot Running Echidna for analysis: h5 Sun Feb 7 15:45:16 2021 Iteration LogL eSigma NEDF 1 1 -2671.03 5274 551 2 2 -2668.12 5298 551 3 3 -2668.09 5329 551 4 4 -2667.73 5332 551 5 5 -2667.73 5332 551 Sun Feb 7 15:45:16 2021 LogL Converged
结果查看:
> nr2g<-b2s(r2g) > m1=nr2g$G1 > m2=nr2g$G2 > Var(m1) Term Sigma SE Z.ratio 1 Residual 5333.10 337.20 15.815836 2 Fam 441.96 187.28 2.359889 > Var(m2) Term Sigma SE Z.ratio 1 Residual 5.3320e+03 3.3694e+02 15.824776 2 Plot 5.0493e-02 3.1907e-03 15.825054 3 Fam 4.4301e+02 1.8661e+02 2.373989 > model.comp(m1,m2,LRT=T) Model comparison results as following:
parNO LogL AIC BIC AIC.State BIC.State m1 2 -2667.71 5339.42 5348.05 better better m2 3 -2667.73 5341.46 5354.39 ===================================== Likelihood ratio test (LRT) results: note:left model before "/" is full model,right is reduced.
Likelihood ratio test(s) assuming nested random models.(See Self & Liang, 1987)
> r2r<-echidna(es0.file="MET.es0", + fixed=yield~1+Loc, + random=~Genotype:Loc, + residual=c(R1~sat(Loc):ar1(Col):ar1(Row),R2~sat(Loc):units), + batch.R=T, + met=T) Program runs for 2 more R-structure at one time. ------ run 1 -- residual effects: sat(Loc):ar1(Col):ar1(Row) Running Echidna for analysis: yield
> model.comp(m1,m2,LRT=T) Model comparison results as forllowing: parNO LogL AIC BIC AIC.State BIC.State m2 7 -1238.60 2491.19 2522.31 better m1 19 -1204.05 2446.10 2530.57 better ===================================== Likelihood ratio test (LRT) results: note:left model before "/" is full model,right is reduced.
Likelihood ratio test(s) assuming nested random models.(See Self & Liang, 1987)