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.
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