[R] Changing design matrix in glm

[Greg Snow]

?C, ?contrasts, ?options (section on contrasts), ?contr.sum

Hope that helps,

--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
(801) 408-8111



> -----Original Message-----
> From: r-help-bounces at r-project.org
> [mailto:r-help-bounces at r-project.org] On Behalf Of Adam Green
> Sent: Tuesday, August 12, 2008 12:56 PM
> To: r-help at 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 at 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.
>