That's what one would expect with type III sum of squares. You have Phyto twice in your model, but only as a nested factor. To compare the full model with a model without diversity of zoop, you have either the combination diversity/phyto, zoop/phyto or phyto twice in the formula. That's aliasing.
Depending on how you stand on type III sum of squares, you could call that a "bug". Personally, I'd just not use them. https://stat.ethz.ch/pipermail/r-help/2001-October/015984.html Cheers Joris On Thu, Jun 3, 2010 at 2:13 AM, Anita Narwani <anitanarw...@gmail.com>wrote: > Hello, > > I have been trying to get an ANOVA table for a linear model containing a > single nested factor, two fixed factors and a covariate: > > carbonmean<-lm(C.Mean~ Mean.richness + Diversity + Zoop + Diversity/Phyto > + > Zoop*Diversity/Phyto) > > > > where, *Mean.richness* is a covariate*, Zoop* is a categorical variable > (the > species), *Diversity* is a categorical variable (Low or High), and > *Phyto*(community composition) is also categorical but is nested > within the level > of *Diversity*. Quinn & Keough's statistics text recommends using Type III > SS for a nested ANOVA with a covariate. > > I get the following output using the Type I SS ANOVA: > > > > Analysis of Variance Table > Response: C.Mean > Df Sum Sq > Mean > Sq F value Pr(>F) > Mean.richness 1 56385326 56385326 > 23.5855 3.239e-05 *** > Diversity 1 14476593 > 14476593 > 6.0554 0.019634 * > Zoop 1 13002135 > 13002135 > 5.4387 0.026365 * > Diversity:Phyto 6 126089387 21014898 > 8.7904 1.257e-05 *** > Diversity:Zoop 1 263036 > 263036 > 0.1100 0.742347 > Diversity:Zoop:Phyto 6 61710145 10285024 > 4.3021 > 0.002879 ** > Residuals 31 74110911 > 2390675 > > I have tried using both the drop1() command and the Anova() command in the > car package. > > When I use the Anova command I get the following error message: > > >Anova(carbonmean,type="III") > > Error in linear.hypothesis.lm(mod, hyp.matrix, summary.model = sumry,: One > or more terms aliased in model. > > > > I am not sure why this is aliased. There are no missing cells, and the > cells > are balanced (aside from for the covariate). Each Phyto by Zoop cross is > replicated 3 times, and there are four Phyto levels within each level of > Diversity. When I remove the nested factor (Phyto), I am able to get the > Type III SS output. > > > > Then when I use drop1(carbonmean,.~.,Test=F) I get the following output: > > > drop1(carbonmean,.~.,Test="F") > > Single term deletions > > > > Model: > > C.Mean ~ Mean.richness + Diversity + Zoop + Diversity/Phyto + Zoop * > Diversity/Phyto > > Df Sum of Sq > RSS AIC > > <none> 74110911 718 > > Mean.richness 1 49790403 123901314 > 741 > > Diversity 0 0 > 74110911 718 > > Zoop 0 0 > 74110911 718 > > Diversity:Phyto 6 118553466 192664376 > 752 > > Diversity:Zoop 0 -1.49e-08 74110911 > 718 > > Diversity:Zoop:Phyto 6 61710145 135821055 > 735 > > > > There are zero degrees of freedom for Diversity, Zoop and their > interaction, > and zero sums of sq for Diversity and Zoop. This cannot be correct, however > when I do the model simplification by dropping terms from the models > manually and comparing them using anova(), I get virtually the same > results. > > > > I would appreciate any suggestions for things to try or pointers as to what > I may be doing incorrectly. > > > > Thank you. > > Anita Narwani. > > [[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. > > -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[alternative HTML version deleted]]
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