R help - Mar 2010 - Question on passing in parameter to Cox hazard

Hi,

I wanted to do the cox model using a matrix. The following lines illustrate what
I want to do:
--------------------------------
dat <- matrix(rnorm(30), ncol=3,dimnames = list(1:10,letters[1:3]))
Survival <- rexp(10)
Status <- ifelse(runif(10) < .7, 1, 0)
mat <- as.data.frame(cbind(dat,Survival,Status))

cmod <- coxph(Surv(Survival, Status) ~ a+b+c, mat)
---------------------------------
This works fine. However, I need to change the code so that the column headers (
a+b+c )are passed into the coxph function on the fly. What string/object do I
need to generate so the function works? I am trying:

# For example
chead <- "a+b+c"
cmod <- coxph(Surv(Survival, Status) ~ chead, mat)
but this gives an error since I'm passing in a string. Can I change chead to
something so that the code works?
many thanks.


      
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On Mar 9, 2010, at 4:19 PM, Tim Smith wrote:
> Hi,
>
> I wanted to do the cox model using a matrix. The following lines  
> illustrate what I want to do:
> --------------------------------
> dat <- matrix(rnorm(30), ncol=3,dimnames = list(1:10,letters[1:3]))
> Survival <- rexp(10)
> Status <- ifelse(runif(10) < .7, 1, 0)
> mat <- as.data.frame(cbind(dat,Survival,Status))
>
> cmod <- coxph(, mat)
> ---------------------------------
> This works fine. However, I need to change the code so that the  
> column headers ( a+b+c )are passed into the coxph function on the  
> fly. What string/object do I need to generate so the function works?  
> I am trying:
>
> # For example
> chead <- "a+b+c"
?as.formula

Perhaps:
as.formula(paste("Surv(Survival, Status) ~", chead))

Formula arguments are not just character strings. They have additional  
attributes.

 > cmod <- coxph(as.formula(paste("Surv(Survival, Status) ~",
chead)),
mat)
 > cmod
Call:
coxph(formula = as.formula(paste("Surv(Survival, Status) ~",
     chead)), data = mat)


     coef exp(coef) se(coef)      z    p
a -0.286     0.751    0.663 -0.431 0.67
b  0.161     1.174    0.705  0.228 0.82
c -0.330     0.719    1.307 -0.252 0.80

Likelihood ratio test=0.62  on 3 df, p=0.893  n= 10
> cmod <- coxph(Surv(Survival, Status) ~ chead, mat)
> but this gives an error since I'm passing in a string. Can I change  
> chead to something so that the code works?
> many thanks.

David Winsemius, MD
West Hartford, CT