Jeff Newmiller wrote/hat geschrieben on/am 17.03.2020 05:39:
The coxph function appears to rely on finding the name of the data argument in
the environment in which the formula was created. The lm function does not have
this problem.
Oh, and df is the name of the F distribution density function, which explains why the
error complained about a "closure".
new<-as.data.frame(list(t=1:4,d=rep(1,4),s=c(1,0,0,1)))
library(survival)
mine<-function(ff,df){
fit<-coxph(as.formula(ff),data=df)
survfit(fit,df)
}
mine("Surv(t,d)~s",new)
Therefore a workaround could be to use the character string for the
formula as argument and apply as.formula() within the function.
mine2 <-function(fstr,df){
fit<-coxph(as.formula(fstr),data=df)
out<-survfit(fit,df)
out
}
mine2("Surv(t,d)~s",new)
Heinz
On March 16, 2020 7:23:26 PM PDT, John Kolassa <kola...@stat.rutgers.edu> wrote:
I ran across an issue that looks like variable scoping in survfit is
not acting as I would expect. Here's a minimal example:
new<-as.data.frame(list(t=1:4,d=rep(1,4),s=c(1,0,0,1)))
library(survival)
mine<-function(ff,df){
fit<-coxph(ff,data=df)
out<-survfit(fit,df)
}
mine(as.formula("Surv(t,d)~s"),new)
I would expect this to fit the proportional hazards regression model
using formula Surv(t,d)~s, using data set new, and then calculate a
separate fitted survival curve for each member of the data set.
Instead I get an error
Error in eval(predvars, data, env) :
invalid 'envir' argument of type 'closure'
The code runs without error if I modify it by copying the data set new
to the local variable within the function mine before running:
new<-as.data.frame(list(t=1:4,d=rep(1,4),s=c(1,0,0,1)))
library(survival)
mine<-function(ff,df){
fit<-coxph(ff,data=df)
out<-survfit(fit,df)
}
df<-new
mine(as.formula("Surv(t,d)~s"),new)
which leads me to believe that there's some variable scoping error.
Can anyone point out what I'm doing wrong? Thanks, John
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