[R] degrees of freedom in custom contrasts ananlysis

[ronny]

Hi,

I would like to understand why the residual standard error, and the degrees
of freedom are changing when I define custom contrasts, which are not
orthogonal.

For example:
y <- rnorm(40)
x <- factor(rep(1:10,4))
summary(lm(y~x)) #standard model: Residual standard error: 1.103 on 30
degrees of freedom
summary(lm(y~C(x,contr.sum))) #orthogonal contrasts: Residual standard
error: 1.103 on 30 degrees of freedom
summary(lm(y~C(x,c(rep(0.2,5),1,rep(0,4)),1))) #custom contrast: Residual
standard error: 1.049 on 38 degrees of freedom

In addition, is there a way to run the custom contrasts analysis without
equal variance assumption? I expect the degrees of freedom to get lower in
this case, as in ANOVA welch.

Thanks!



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