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.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
