[R] formula error inside function

[David Winsemius]

On Jan 25, 2012, at 2:02 AM, moli wrote:

> I want use survfit() and basehaz() inside a function, but it doesn't  
> work.
> Could you take a look at this problem. Thanks for your help.  
> Following is my
> codes:
>
> library(survival)
> n <- 50      # total sample size
> nclust <- 5  # number of clusters
> clusters <- rep(1:nclust,each=n/nclust)
> beta0 <- c(1,2)
> set.seed(13)
> #generate phmm data set
> Z <- cbind(Z1=sample(0:1,n,replace=TRUE),
>       Z2=sample(0:1,n,replace=TRUE),
>       Z3=sample(0:1,n,replace=TRUE))
> b <-
> cbind(rep(rnorm(nclust),each=n/nclust),rep(rnorm(nclust),each=n/ 
> nclust))
> Wb <- matrix(0,n,2)
> for( j in 1:2) Wb[,j] <- Z[,j]*b[,j]
> Wb <- apply(Wb,1,sum)
> T <- -log(runif(n,0,1))*exp(-Z[,c('Z1','Z2')]%*%beta0-Wb)
> C <- runif(n,0,1)
> time <- ifelse(T<C,T,C)
> event <- ifelse(T<=C,1,0)
> mean(event)
> phmmd <- data.frame(Z)
> phmmd$cluster <- clusters
> phmmd$time <- time
> phmmd$event <- event
>
> fmla <- as.formula("Surv(time, event) ~ Z1 + Z2")
>
> BaseFun <- function(x){

You should adopt a practice of using more meaningful parameter names.  
In this case "x" happens to be one of the parameter names for coxph.  
So I suguggest something like:

> BaseFun <- function(frm){


> start.coxph <- coxph(x, phmmd)

Then try changing that line to

start.coxph <- coxph(frm, phmmd, x=TRUE,y=TRUE)

It turns out that unless I included x=TRUE and y=TRUE, (as suggested  
by an error essage I encountered during debugging) that the right  
information was not available inside your function. Personally I would  
have passed the data to the functions as well but that doesn't seem to  
have been necessary (or sufficient to solve the problem).

-- 
David.

>
> print(

> )
>
> betahat <- start.coxph$coefficient
> print(betahat)
> print(333)
> print(survfit(start.coxph))
> m <- basehaz(start.coxph)
> print(m)
> }
> BaseFun(fmla)
>
>
>
> Error in formula.default(object, env = baseenv()) : invalid formula
>
>
> But the following function works:
> coxph(fmla, phmmd)
>
> --
> View this message in context: http://r.789695.n4.nabble.com/formula-error-inside-function-tp4326549p4326549.html
> Sent from the R help mailing list archive at Nabble.com.
>
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David Winsemius, MD
West Hartford, CT