[R] Contrasts with an interaction. How does one specify the dummy variables for the interaction

[Max Kuhn]

This is failing because it is a saturated model and the contrast
package tries to do a t-test (instead of a z test). I can add code to
do this, but it will take a few days.

Max

On Fri, Oct 28, 2011 at 2:16 PM, John Sorkin
<JSorkin at grecc.umaryland.edu> wrote:
> Forgive my resending this post. To data I have received only one response (thank you Bert Gunter), and I still do not have an answer to my question.
> Respectfully,
> John
>
>
> Windows XP
> R 2.12.1
> contrast package.
>
>
> I am trying to understand how to create contrasts for a model that contatains an interaction. I can get contrasts to work for a model without interaction, but not after adding the interaction. Please see code below. The last two contrast statements show the problem. I would appreciate someone letting me know what is wrong with the syntax of my contrast statements.
> Thank you,
> John
>
>
> library(contrast)
>
> # Create 2x2 contingency table.
> counts=c(50,50,30,70)
> row <-    gl(2,2,4)
> column <- gl(2,1,4)
> mydata <- data.frame(row,column,counts)
> print(mydata)
>
> # Show levels of 2x2 table
> levels(mydata$row)
> levels(mydata$column)
>
>
> # Models, no interaction, and interaction
> fitglm0 <- glm(counts ~ row + column,              family=poisson(link="log"))
> fitglm  <- glm(counts ~ row + column + row*column, family=poisson(link="log"))
>
> # Contrasts for model without interaction works fine!
> anova(fitglm0)
> summary(fitglm0)
> con0<-contrast(fitglm0,list(row="1",column="1"))
> print(con0,X=TRUE)
>
> # Contrast for model with interaction does not work.
> anova(fitglm)
> summary(fitglm)
> con<-contrast(fitglm,list(row="1",column="1")
> print(con,X=TRUE)
>
> # Nor does this work.
> con<-contrast(fitglm,list(row="1",column="1",row:column=c("0","0")))
> print(con,X=TRUE)
>
>
>
>
> John David Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
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