IIona- I think you may be misinterpreting the t-test.
In model 1, consider the speciesH coefficient. A test that speciesH = 0, essentially asks: Is speciesH the same as speciesB? The test statistic for this hypothesis is the t-value reported in the table. (t-value= -4.2, p-value=0.0001) In model 2, the corresponding coefficient, t-value, and p-value do not correspond to the same hypothesis test from model 1. If your goal is to test the overall species effect, then the test you want is: model0<-lme(sprouts~moisture,random=~time|ID,method="ML") model1<-lme(sprouts~species+moisture,random=~time|ID,method="ML") model2<-lme(sprouts~species*moisture,random=~time|ID,method="ML") anova(model0,model2) #TEST OF SPECIES EFFECT IN MODEL WITH INTERACTION anova(model0,model1) #TEST OF SPECIES EFFECT IN MODEL WITHOUT INTERACTION And as an added bonus, (which should probably be done before the test of Species Effect) anova(model1,model2) #TEST OF INTERACTION. That is, do I really need the more complex model? Hope that helps. -tgs On Tue, Jun 29, 2010 at 5:09 AM, Ilona Leyer <ile...@yahoo.de> wrote: > Dear all, > In a greenhouse experiment we tested performance of 4 different species > (B,H,P,R) under 3 different water levels in 10 replications. As response > variable e.g. the number of emerging sprouts were measured on three dates. A > simple Anova considering every measurement date separately shows a higly > significant effect of species and moisture (and partly the interaction of > both). The mixed-effects model with species and moisture shows a highly > significant effect of species and moisture as well. However, when I included > the interaction the t-values of the species dropped strongly and the SE > increase and the results for the species are not significant anymore. For me > this does not seem plausible. Has anybody an idea, how this can be > interpreted and if I have done a mistake in calculating the data? > > Thanks in advance for any help! > Ilona > > > model1<-lme(sprouts~species+moisture,random=~time|ID) > model2<-lme(sprouts~species*moisture,random=~time|ID) > > > Fixed effects: sprouts ~ species + moisture > Value Std.Error DF t-value p-value > (Intercept) 7.971267 1.330500 240 5.991180 0.0000 > speciesH -6.459344 1.536329 114 -4.204400 0.0001 > speciesP -10.063604 1.536329 114 -6.550421 0.0000 > speciesR -5.051894 1.536329 114 -3.288288 0.0013 > moisturemoist 2.228835 1.330500 114 1.675185 0.0966 > moisturewaterlogged 17.111149 1.330500 114 12.860688 0.0000 > > > Fixed effects: sprouts ~ species * moisture > Value Std.Error DF t-value p-value > (Intercept) 4.831965 1.750970 240 2.759594 0.0062 > speciesH -4.464197 2.476245 108 -1.802809 0.0742 > speciesP -3.986787 2.476245 108 -1.610013 0.1103 > speciesR -0.809376 2.476245 108 -0.326856 0.7444 > moisturemoist 3.505506 2.476245 108 1.415654 0.1598 > moisturewaterlogged 24.766934 2.476245 108 10.001811 0.0000 > speciesH:moisturemoist -0.457291 3.501939 108 -0.130582 0.8963 > speciesP:moisturemoist -2.458125 3.501939 108 -0.701932 0.4842 > speciesR:moisturemoist -2.555356 3.501939 108 -0.729697 0.4672 > speciesH:moisturewaterlogged -5.597498 3.501939 108 -1.598400 0.1129 > speciesP:moisturewaterlogged -15.538272 3.501939 108 -4.437048 0.0000 > speciesR:moisturewaterlogged -10.206874 3.501939 108 -2.914635 0.0043 > > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
