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

[John Sorkin]

Daniel,
I want to use the contrast library because I want to be able to specify any arbitrary post-hoc contrast, e.g. Given a 3x2 table describing smoking (never, former, current) by sex (male,female), I can use a post-hoc contrast to compare the fraction of female former smokers to the fraction of male former smokers, or the fraction of male former smokers to the fraction of male current smokers, etc. To the best of my knowledge, post-hoc contrasts are the most flexible, and easiest way to specify arbitrary pre-specified comparisons.
John

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
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)

>>> Daniel Malter <daniel at umd.edu> 10/28/2011 4:02 PM >>>
Is there a specific reason why you insist on using the contrast library? If
not:

# 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)

#Create contrasts

row<-factor(row)
column<-factor(column)
contrasts(row)<-contr.treatment(levels(row))
contrasts(column)<-contr.treatment(levels(column))

# Works for Terps

fit.terp<-glm(counts ~ row + column + row*column,
family=poisson(link="log"))
summary(fit.terp)

HTH,

Daniel Malter
University of Maryland, College Park





John Sorkin 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
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
> 
> Confidentiality Statement:
> This email message, including any attachments, is for ...{{dropped:31}}