that's diversity/phyto, zoop or phyto twice in the formula. On Thu, Jun 3, 2010 at 3:00 AM, Joris Meys <jorism...@gmail.com> wrote:
> 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 > -- 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]]
______________________________________________ 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.
