Create formula call from character string

问题

I use a best subset selection package to determine the best independent variables from which to build my model (I do have a specific reason for doing this instead of using the best subset object directly). I want to programmatically extract the feature names and use the resulting string to build my model formula. The result would be something like this:

x <- "x1 + x2 + x3"
y <- "Surv(time, event)"

Because I'm building a coxph model, the formula is as follows:

coxph(Surv(time, event) ~ x1 + x2 + x3)

Using these string fields, I tried to construct the formula like so:

form <- y ~ x

This creates an object of class formula but when I call coxph it doesn't evaluate based on the references created form the formula object. I get the following error:

Error in model.frame.default(formula = y ~ x) : object is not a matrix

If I call eval on the objects y and x within the coxph call, I get the following:

Error in model.frame.default(formula = eval(y) ~ eval(x), data = df) :

variable lengths differ (found for 'eval(x)')

I'm not really sure how to proceed. Thanks for your input.

回答1:

Couldn't find a good dupe, so posting comment as an answer.

If you build the full formula as a string, including the ~, you can use as.formula on it, e.g.,

x = "x1 + x2 + x3"
y = "Surv(time, event)"
form = as.formula(paste(y, "~", x))
coxph(form, data = your_data)

For a reproducible example, consider the first example at the bottom of the ?coxph help page:

library(survival)
test1 <- list(time=c(4,3,1,1,2,2,3), 
              status=c(1,1,1,0,1,1,0), 
              x=c(0,2,1,1,1,0,0), 
              sex=c(0,0,0,0,1,1,1)) 
# Fit a stratified model 
coxph(Surv(time, status) ~ x + strata(sex), test1)
# Call:
# coxph(formula = Surv(time, status) ~ x + strata(sex), data = test1)
# 
#    coef exp(coef) se(coef)    z    p
# x 0.802     2.231    0.822 0.98 0.33
# 
# Likelihood ratio test=1.09  on 1 df, p=0.3
# n= 7, number of events= 5 

lhs = "Surv(time, status)"
rhs = "x + strata(sex)"
form = as.formula(paste(lhs, "~", rhs))
form
# Surv(time, status) ~ x + strata(sex)
## formula looks good

coxph(form, test1)
# Call:
# coxph(formula = form, data = test1)
# 
#    coef exp(coef) se(coef)    z    p
# x 0.802     2.231    0.822 0.98 0.33

Same results either way.

来源：https://stackoverflow.com/questions/52413017/create-formula-call-from-character-string

标签

formula

cox-regression