error object not found when calling with(dataset, coxph(formula))

Question

I have a multiply imputed dataset of class mids. I use the with() function to estimate the m different datasets with the coxph() function. However, I'm having trouble using the with() function within my own function.

The code below is a simplified example that reproduces the error: Error in Surv(enter,exit,event) object 'enter' not found

list<-"X1+X2"
var.used<-formula(paste("Surv(enter,exit,event)~",list,sep=""))

with.coxph<-function(form,dataset){
 with(dataset,coxph(form))
}

with.coxph(var.used,data)

When I simply run the function on its own:

with(dataset, coxph(Surv(enter,exit,event)~X1+X2))

It works fine.

I think the problem is related to the environment where with() is called. I found different posts in here, but I can't seem to make it work. I tried assigning the dataset and the formula to the global environment:

with.coxph2<-function(form,dataset){
 assign(".dataset",dataset,envir=.GlobalEnv)
 assign(".form",dataset,envir=.GlobalEnv)
 with(dataset,coxph(form))
 remove(".dataset",dataset,envir=.GlobalEnv)
 remove(".form",dataset,envir=.GlobalEnv)
}

with.coxph2(var.used,data)

but this produced the same error.

EDIT

I have attempted to fix the problem as described below. When i simply run the function with out the with() statement it works perfectly.

makeModel<-function(resp, explan, mData) {
 mF <- formula(paste(resp, paste(explan, collapse = "+"), sep = "~"))
 mod <- coxph(mF, data = mData)
 mod$call$formula <- mF
 mod$call$data <- as.symbol(deparse(substitute(mData)))
 mod
}

cp <- makeModel("Surv(start, stop, event)", "X1", complete(data))

# This works fine

However, I still get the same error when I include the with() statement in the equation:

with.coxph<-function(resp, explan, mData) {
 mF <- formula(paste(resp, paste(explan, collapse = "+"), sep = "~"))
 mod <- with(mData,coxph(mF))
 mod$call$formula <- mF
 mod$call$data <- as.symbol(deparse(substitute(mData)))
 mod
}

cp <- with.coxph("Surv(start, stop, event)", "X1", data)

# Error in Surv(enter,exit,event): object 'enter' not found

thothal thothal · Accepted Answer · 2014-12-04T12:05:06

I had similiar issues when using the lm function and I wanted to pass the formula and/or data argument to it. Tha's what I am doing now to circumvent that:

makeModel <- function(resp, explan, mData) {
   mF <- formula(paste(resp, paste(explan, collapse = "+"), sep = "~"))
   mod <- coxph(mF, data = mData)
   mod$call$formula <- mF
   mod$call$data <- as.symbol(deparse(substitute(mData)))
   mod
}

makeModelBad <- function(resp, explan, mData) {
   mF <- formula(paste(resp, paste(explan, collapse = "+"), sep = "~"))
   coxph(mF, data = mData)
}

library(survival)
example(coxph) # to load the data

(cp <- makeModel("Surv(start, stop, event)", "x", test2))
# Call:
# coxph(formula = Surv(start, stop, event) ~ x, data = test2)
#
#
#      coef exp(coef) se(coef)       z    p
# x -0.0211     0.979    0.795 -0.0265 0.98
#
# Likelihood ratio test=0  on 1 df, p=0.979  n= 10, number of events= 7 

cp.bad <- makeModelBad("Surv(start, stop, event)", "x", test2)

Explanation

In order to use the models created inside a function, I had to explicitely change the respective slots, because mData is not known outside the function and a call to update for example will fail:

update(cp, . ~ 1) # works
update(cp.bad, . ~ 1) # does not work
# Error in terms.formula(formula, special, data = data) : 
# object 'mData' not found

The change to the formula slot, is more eye candy to show the formula in the print of the object.

error object not found when calling with(dataset, coxph(formula))

EDIT

1 Answers