Hi Steve, The short answer is that there is typically no reason to check (beyond looking to see what contrasts have been defined for the factors in the model; see ?contrasts) because the rules are pretty simple. 1) the design matrix is orthogonal on the row-basis (i.e., the columns sum to zero) when using contr.sum, contr.helmert, or manually set contrasts in which the contrasts sum to zero. 2) if the design matrix is orthogonal and cell sizes are equal, the model matrix will also be orthogonal.
However, you can of course check, as in the following example: dat <- data.frame(y=rnorm(100), x=factor(rep(c("a", "a", "b", "c"), 25))) m <- lm(y ~ x, data=dat) ## model matrix orthoganal on row-basis? apply(model.matrix(m)[,grep("x", colnames(model.matrix(m)))], 2, sum) ## No, sum is non-zero ## design matrix orthoganal on row-basis? apply(contrasts(dat$x), 2, sum) ## No, sum is non-zero ## change contrasts contrasts(dat$x) <- contr.sum(n=3) m2 <- lm(y ~ x, data=dat) ## model matrix orthoganal on row-basis? apply(model.matrix(m2)[,grep("x", colnames(model.matrix(m2)))], 2, sum) ## No, sum is non-zero (because of unbalenced cell sizes) ## model matrix orthoganal on row-basis? apply(contrasts(dat$x), 2, sum) ## Yes, sum is zero. HTH, Ista On Fri, Dec 3, 2010 at 8:47 AM, S Ellison <s.elli...@lgc.co.uk> wrote: > > A common point made in discussion of contrasts, type I, II, III SS etc > is that for sensible comparisons one should use contrasts that are > 'orthogonal in the row-basis of the model matrix' (to quote from > http://finzi.psych.upenn.edu/R/Rhelp02/archive/111550.html) > > Question: How would one check, in R, that this is so for a particular > fitted linear model object? > > Steve Ellison > > > > ******************************************************************* > This email and any attachments are confidential. Any u...{{dropped:18}} ______________________________________________ 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.