R help - May 2007 - Predicted Cox survival curves - factor coding problems..

The combination of survfit, coxph, and factors is getting confused.  It is
not smart enough to match a new data frame that contains a numeric for sitenew
to a fit that contained that variable as a factor.  (Perhaps it should be smart
enough to at least die gracefully -- but it's not).

   The simple solution is to not use factors.
   
site1 <- 1*(coxsnps$sitenew==1)
site2 <- 1*(coxsnps$sitenew==2)
test1 <- coxph(Surv(time, censor) ~ snp1 + sex + site1 + site2 + gene +
	  eth.self + strata(edu), data= coxsnps)
	  
	 output

profile1 <- data.frame(snp1=c(0,1), site2=c(0,0), sex=c(0,0),  
	               site1=c(0,0), site2=c(0,0), geno=c(0,0) eth.self=c(0,0))
plot(survfit(test1, newdata=profile1))

 Note that you do not have to explicitly make "edu" a factor.  Since
it is
included in a strata statement, the coxph routine must treat it as discrete
groups.



	Terry Therneau

On Mon, 7 May 2007, Terry Therneau wrote:
>  The combination of survfit, coxph, and factors is getting confused.  It is
> not smart enough to match a new data frame that contains a numeric for
sitenew
> to a fit that contained that variable as a factor.  (Perhaps it should be
smart
> enough to at least die gracefully -- but it's not).
The 'standard' model-fitting functions in R do make an attempt to match 
the new data to that used for fitting, or die gracefully.  Perhaps Thomas 
could look into adding this to survift and coxph (see 
http://developer.r-project.org/model-fitting-functions.txt).

>   The simple solution is to not use factors.
>
> site1 <- 1*(coxsnps$sitenew==1)
> site2 <- 1*(coxsnps$sitenew==2)
> test1 <- coxph(Surv(time, censor) ~ snp1 + sex + site1 + site2 + gene +
> 	  eth.self + strata(edu), data= coxsnps)
>
> 	 output
>
> profile1 <- data.frame(snp1=c(0,1), site2=c(0,0), sex=c(0,0),
> 	               site1=c(0,0), site2=c(0,0), geno=c(0,0) eth.self=c(0,0))
> plot(survfit(test1, newdata=profile1))
>
> Note that you do not have to explicitly make "edu" a factor. 
Since it is
> included in a strata statement, the coxph routine must treat it as discrete
> groups.
>
> 	Terry Therneau
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
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