From: Joris Meys <jorismeys_at_gmail.com>

Date: Thu, 03 Jun 2010 03:00:57 +0200

Date: Thu, 03 Jun 2010 03:00:57 +0200

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.

https://stat.ethz.ch/pipermail/r-help/2001-October/015984.html

Cheers

Joris

On Thu, Jun 3, 2010 at 2:13 AM, Anita Narwani <anitanarwani_at_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_at_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.Meys_at_Ugent.be ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[alternative HTML version deleted]]Received on Thu 03 Jun 2010 - 01:03:58 GMT______________________________________________ R-help_at_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.

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