[R] Contrast anova multi factor

Thierry Onkelinx thierry.onkelinx at inbo.be
Sun Apr 26 17:30:32 CEST 2015

Dear Mario,

The interpretation is the same: the average at the reference situation
which is the group that has f1 == "f1 level1" and f2 == "f2 level1".

Best regards,

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2015-04-26 17:12 GMT+02:00 Mario José Marques-Azevedo <mariojmaaz op gmail.com>

> Hi all,
> I am doing anova multi factor and I found different Intercept when model
> has interaction term.
> I have the follow data:
> set.seed(42)
> dt <- data.frame(f1=c(rep("a",5),rep("b",5)),
>                  f2=rep(c("I","II"),5),
>                  y=rnorm(10))
> When I run
> summary.lm(aov(y ~ f1 * f2, data = dt))
> The Intercept term is the mean of first level of f1 and f2. I can confirm
> that with:
> tapply(dt$y, list(dt$f1, dt$f2), mean)
> I know that others terms are difference of levels with Intercept.
> But I do not know what is Intercept when the model do not have interaction
> term:
> summary.lm(aov(y ~f1 + f2, data = dt))
> I know that I can create a specific contrast table, by I would like
> understand the default R output.
> I read contrast sub-chapter on Crawley 2012 (The R book) and in his example
> the Intercept is different when model has or not interaction term, but he
> explain that Intercept is mean of first level of the factors.
> Best regards,
> Mario
> .............................................................
> Mario José Marques-Azevedo
> Ph.D. Candidate in Ecology
> Dept. Plant Biology, Institute of Biology
> University of Campinas - UNICAMP
> Campinas, São Paulo, Brazil
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