> anova(gnm(UNFILLED ~ GENO + LOC + REP%in%LOC + GENO:LOC, data=data4))

Analysis of Deviance Table

Model: gaussian, link: identity

Response: UNFILLED

Terms added sequentially (first to last)


Df Deviance Resid. Df Resid. Dev
NULL 239 69197
GENO 9 35569 230 33629
LOC 7 11928 223 21701
LOC:REP 8 570 215 21130
GENO:LOC 63 15883 152 5248

> anova(gnm(UNFILLED ~ GENO + LOC + REP%in%LOC + GENO:LOC, family=poisson, link=log, data=data4))
Analysis of Deviance Table

Model: poisson, link: log

Response: UNFILLED

Terms added sequentially (first to last)


Df Deviance Resid. Df Resid. Dev
NULL 239 1664.77
GENO 9 900.78 230 763.99
LOC 7 296.11 223 467.89
LOC:REP 8 13.02 215 454.87
GENO:LOC 63 335.65 152 119.22

> anova(lm(UNFILLED ~ GENO + LOC + REP%in%LOC + GENO:LOC, data=data4))
Analysis of Variance Table

Response: UNFILLED
Df Sum Sq Mean Sq F value Pr(>F)
GENO 9 35569 3952.1 114.4760 < 2e-16 ***
LOC 7 11928 1704.0 49.3575 < 2e-16 ***
LOC:REP 8 570 71.3 2.0657 0.04249 *
GENO:LOC 63 15883 252.1 7.3026 < 2e-16 ***
Residuals 152 5248 34.5
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1


> bilinear1

Call:
gnm(formula = yield.scaled ~ year + treatment + Mult(year, treatment), data = wheat)

Coefficients:
(Intercept) year.L year.Q year.C year^4
393.30315 -0.80314 5.55009 NA 26.60407
year^5 year^6 year^7 year^8 year^9
-2.86687 -20.84145 -35.43304 -98.69652 10.18497
treatment[T.tSM0] treatment[T.TsM0] treatment[T.tsM0] treatment[T.TSm0] treatment[T.tSm0]
-20.69849 -22.95520 -70.30045 -93.56754 -96.39381
treatment[T.Tsm0] treatment[T.tsm0] treatment[T.TSMn] treatment[T.tSMn] treatment[T.TsMn]
-133.45274 -149.49009 53.19506 31.18199 35.25716
treatment[T.tsMn] treatment[T.TSmn] treatment[T.tSmn] treatment[T.Tsmn] treatment[T.tsmn]
32.12958 22.05685 11.57345 10.19872 -2.25118
treatment[T.TSMN] treatment[T.tSMN] treatment[T.TsMN] treatment[T.tsMN] treatment[T.TSmN]
36.38558 26.89342 42.83224 20.23313 39.08567
treatment[T.tSmN] treatment[T.TsmN] treatment[T.tsmN] Mult(., treatment).year1988 Mult(., treatment).year1989
17.29724 30.32213 22.25405 -61.06564 49.32402
Mult(., treatment).year1990 Mult(., treatment).year1991 Mult(., treatment).year1992 Mult(., treatment).year1993 Mult(., treatment).year1994
-55.04009 8.82212 8.18722 -3.34667 -10.53285
Mult(., treatment).year1995 Mult(., treatment).year1996 Mult(., treatment).year1997 Mult(year, .).treatmentTSM0 Mult(year, .).treatmenttSM0
66.69367 72.71498 -75.75336 -0.04431 0.10194
Mult(year, .).treatmentTsM0 Mult(year, .).treatmenttsM0 Mult(year, .).treatmentTSm0 Mult(year, .).treatmenttSm0 Mult(year, .).treatmentTsm0
0.37683 0.71754 0.22600 0.29088 0.37670
Mult(year, .).treatmenttsm0 Mult(year, .).treatmentTSMn Mult(year, .).treatmenttSMn Mult(year, .).treatmentTsMn Mult(year, .).treatmenttsMn
0.46877 -0.75725 -0.46597 -0.79787 -0.55649
Mult(year, .).treatmentTSmn Mult(year, .).treatmenttSmn Mult(year, .).treatmentTsmn Mult(year, .).treatmenttsmn Mult(year, .).treatmentTSMN
-0.22894 -0.26740 -0.42399 0.06097 -1.14563
Mult(year, .).treatmenttSMN Mult(year, .).treatmentTsMN Mult(year, .).treatmenttsMN Mult(year, .).treatmentTSmN Mult(year, .).treatmenttSmN
-0.77004 -1.02695 -0.79638 -0.59191 -0.53061
Mult(year, .).treatmentTsmN Mult(year, .).treatmenttsmN
-0.65282 -0.28747

Deviance: 128382.7
Pearson chi-squared: 128382.7
Residual df: 176
> bilinear1<-a
> bilinear1 <- update(mainEffects, . ~ . + Mult(year, treatment),
+ start = c(coef(mainEffects), svdStart[, 1]))
Running main iterations..
Done
> bilinear1

Call:
gnm(formula = yield.scaled ~ year + treatment + Mult(year, treatment), data = wheat, start = c(coef(mainEffects), svdStart[, 1]))

Coefficients:
(Intercept) year.L year.Q year.C year^4
393.3031 -0.8031 5.5501 NA 26.6041
year^5 year^6 year^7 year^8 year^9
-2.8669 -20.8415 -35.4330 -98.6965 10.1850
treatment[T.tSM0] treatment[T.TsM0] treatment[T.tsM0] treatment[T.TSm0] treatment[T.tSm0]
-20.6984 -22.9551 -70.3002 -93.5674 -96.3937
treatment[T.Tsm0] treatment[T.tsm0] treatment[T.TSMn] treatment[T.tSMn] treatment[T.TsMn]
-133.4526 -149.4899 53.1948 31.1818 35.2569
treatment[T.tsMn] treatment[T.TSmn] treatment[T.tSmn] treatment[T.Tsmn] treatment[T.tsmn]
32.1294 22.0568 11.5734 10.1986 -2.2511
treatment[T.TSMN] treatment[T.tSMN] treatment[T.TsMN] treatment[T.tsMN] treatment[T.TSmN]
36.3852 26.8932 42.8319 20.2329 39.0855
treatment[T.tSmN] treatment[T.TsmN] treatment[T.tsmN] Mult(., treatment).year1988 Mult(., treatment).year1989
17.2971 30.3219 22.2540 -7.6253 6.1590
Mult(., treatment).year1990 Mult(., treatment).year1991 Mult(., treatment).year1992 Mult(., treatment).year1993 Mult(., treatment).year1994
-6.8729 1.1016 1.0223 -0.4179 -1.3153
Mult(., treatment).year1995 Mult(., treatment).year1996 Mult(., treatment).year1997 Mult(year, .).treatmentTSM0 Mult(year, .).treatmenttSM0
8.3280 9.0799 -9.4594 -0.3549 0.8164
Mult(year, .).treatmentTsM0 Mult(year, .).treatmenttsM0 Mult(year, .).treatmentTSm0 Mult(year, .).treatmenttSm0 Mult(year, .).treatmentTsm0
3.0178 5.7463 1.8099 2.3295 3.0167
Mult(year, .).treatmenttsm0 Mult(year, .).treatmentTSMn Mult(year, .).treatmenttSMn Mult(year, .).treatmentTsMn Mult(year, .).treatmenttsMn
3.7540 -6.0643 -3.7317 -6.3896 -4.4565
Mult(year, .).treatmentTSmn Mult(year, .).treatmenttSmn Mult(year, .).treatmentTsmn Mult(year, .).treatmenttsmn Mult(year, .).treatmentTSMN
-1.8334 -2.1414 -3.3955 0.4883 -9.1746
Mult(year, .).treatmenttSMN Mult(year, .).treatmentTsMN Mult(year, .).treatmenttsMN Mult(year, .).treatmentTSmN Mult(year, .).treatmenttSmN
-6.1668 -8.2242 -6.3777 -4.7402 -4.2493
Mult(year, .).treatmentTsmN Mult(year, .).treatmenttsmN
-5.2280 -2.3021

Deviance: 128382.7
Pearson chi-squared: 128382.7
Residual df: 176