[R] coefs from summary.lm of an aov object

[Ista Zahn]

Hi Martin,
See ?contrasts and associated help pages ?contr.sum, ?contr.treatment
etc. Also note that you can set contrasts "manually":

D <- data.frame(y = rnorm(20), group <- factor(c(rep("A", 5), rep("B",
5), rep("C", 5), rep("D", 5))))

group.dumcodes <- matrix(c(0, 0, 0,
                           1, 0, 0,
                           0, 1, 0,
                           0, 0, 1), ncol=3, byrow=TRUE)

colnames(group.dumcodes) <- c("dum1", "dum2", "dum3")

contrasts(D$group) <- group.dumcodes

summary(lm(y ~ group, data=D))

-Ista


On Thu, Feb 4, 2010 at 6:02 PM, Martin Ivanov <tramni at abv.bg> wrote:
>  Dear R users,
>
> This is probably a very stupid question, nevertheless I obviously am not qualified enough
> to cope with it. I do not understand what the coefficients are that are output by running
> summary.lm on an aov object. I thought they should be the differential effects for the levels of the factor and the overall mean, but they are obviously not, as illustrated by the following simple example:
>
> x <- c(1:15); y <- factor(c(rep("a", 5), rep("b", 10)))
>> tapply(X=x, INDEX=y, FUN=mean)
>   a    b
>  3.0 10.5
>
>> mean(x)
> [1] 8
>
>> a <- aov(x ~ y)
>> summary.lm(a)$coef
>            Estimate Std. Error  t value     Pr(>|t|)
> (Intercept)      3.0   1.192928 2.514821 0.0258555905
> yb               7.5   1.461032 5.133357 0.0001921826
>
>
>> model.tables(a)
> Tables of effects
>
>  y
>     a    b
>    -5  2.5
> rep  5 10.0
>
> Besides, I fit a factor with two levels, "a" and "b", but there is only the "yb" coefficient for the "b" level, no "ya" coefficient for the "a" factor level. I read a lot of materials on anova with R, but I could not find what are these coefficients. I would be grateful if someone gives me some clue. And what is the intercept term? I though it should be the overall mean, but it is obviously not.
>
> Regards and best wishes,
>
> Martin Ivanov
>
> ______________________________________________
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>



-- 
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org