On Mon, 26 Jan 2004, Paul Boutros wrote: > > On Sat, 24 Jan 2004 [EMAIL PROTECTED] wrote: > > > > > I didn't get any response on this before, leading me to believe > > > I've missed > > > something fundamental. Can anybody guide me in the correct > > > direction for more help on this? > > Thanks for your reply: > > > You will need to explain to us why the object you list is `the design > > matrix': have *you* a reference for that? R is doing the conventional > > thing, and I at least have no idea where your example comes from. > > Perhaps I have used the wrong terminology? My understanding of a design > matrix is that it identifies the factors are present for a given experiment.
The design matrix is X in the regression usually represented by y = Xb + e and is called a model matrix in S/R. > Here, I have a two factor experiment, where each factor has two levels. > In the case I gave: > t1 t2 > 1 1 0 > 2 1 1 > 3 0 0 > 4 0 1 > > I had expected this to represent four distinct experiments where > factor one is present in the first two and absent in the second two. You can't have factors that are present/absent. (You can have levels of treatments which are present/absent.) We understand the rows to represent the individuals runs of a single experiment, but what do the columns represent? > > You seem to have coded variables t1 and t2 the opposite ways (the > > reference level is 2 for t1 and 1 for t2), and your model has the fit at > > levels t1=2,t1=1 constrained to pass through the origin. I don't think R > > has a simple syntax for that (although you can fake anything), and I find > > it hard to believe that is actually what you want. > > That wasn't my intention, I want to retain the intercept term and > not constrain it to pass through the origin. So why did you use ~ -1 + (t1+t2) ? That explicitly removes the intercept. > Paul > > > > > > > Paul > > > > > > ================================================= > > > I want to be able to create a design matrix with two factors. > > For instance, if > > > I have: > > > > > > > t1 <- factor(c(1,1,2,2)); > > > > t2 <- factor(c(1,2,1,2)); > > > > design <- model.matrix(~ -1 + (t1+t2)); > > > > design; > > > t11 t12 t22 > > > 1 1 0 0 > > > 2 1 0 1 > > > 3 0 1 0 > > > 4 0 1 1 > > > > > > But the design matrix I want is: > > > t1 t2 > > > 1 1 0 > > > 2 1 1 > > > 3 0 0 > > > 4 0 1 > > > > > > Actually, in general I'm struggling with the syntax for > > formulating a design > > > matrix I can write down on paper. Is there a reference for > > this beyond the R > > > documentation? > > > > Chapter 6 of MASS has the most complete exposition (by Bill > > Venables) that > > I know of, and the White Book (Chambers & Hastie, 1992) goes well beyind > > the R documentation (which uses it as the reference). > > > > -- > > Brian D. Ripley, [EMAIL PROTECTED] > > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > > University of Oxford, Tel: +44 1865 272861 (self) > > 1 South Parks Road, +44 1865 272866 (PA) > > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html