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$group) <- group.dumcodes summary(lm(y ~ group, data=D)) -Ista On Thu, Feb 4, 2010 at 6:02 PM, Martin Ivanov <tra...@abv.bg> wrote: > Dear R users, > > This is probably a very stupid question, nevertheless I obviously am not > qualified enough > to cope with it. I do not understand what the coefficients are that are > output by running > summary.lm on an aov object. I thought they should be the differential > effects for the levels of the factor and the overall mean, but they are > obviously not, as illustrated by the following simple example: > > x <- c(1:15); y <- factor(c(rep("a", 5), rep("b", 10))) >> tapply(X=x, INDEX=y, FUN=mean) > a b > 3.0 10.5 > >> mean(x) > [1] 8 > >> a <- aov(x ~ y) >> summary.lm(a)$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 > > ______________________________________________ > 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. > -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org ______________________________________________ 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.