?C, ?contrasts, ?options (section on contrasts), ?contr.sum Hope that helps,
-- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Adam Green > Sent: Tuesday, August 12, 2008 12:56 PM > To: r-help@r-project.org > Subject: [R] Changing design matrix in glm > > I'm sure this is an easy thing to do, but I can't seem to get > it right. My first question is: Is there a way to set the > intercept of a glm to be an overall average of the response > variable, as opposed to the coefficient for a particular term. > > For example, let's say there are 2 variables (1 and 2) with > levels A, B, C and D, E, F, respectively. The default glm > output provides an intercept term that is the coefficient for > A*D and seperate terms for B, C, F, B*F, and C*F. My issue > is that I don't always have estimates for certain > interactions. When I try to predict values for new data > using the coefficients from the model, predict.glm assumes > the NAs are 0 and, therefore, those coefficients have the > same estimate as the intercept plus other main effects for > which there are data. So, if there's an easy way to do that, > that would be great. If not... > > ...I could do it by changing the design matrix. I've played > with glm.fit and model.matrix to create the design matrices, > but I'm having trouble using them in glm. I created a matrix > and populated it, but when I use the saved glm.fit as the > "method" argument in glm, I get: > 'Error in switch(method, model.frame = return(mf), glm.fit = > 1, stop("invalid 'method': ", :switch: EXPR must return a > length 1 vector" > > EX > glm.fit(x=model.matrix(Y ~ X+Z), y=c(1,...,1)) glm(Y ~ X+Z, > family='binomial', method=glm.fit) > > So, I guess my question is: How do I include the design > matrix so that the glm function uses it instead of the > default design matrix? > > Thanks, > Adam Green > [[alternative HTML version deleted]] > > ______________________________________________ > 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. > ______________________________________________ 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.
