Hi,
I am running a cox regression with coxph in R The regression runs fine and reports standard errors on the coefficients too. This is good. But I need to run a number of simulation runs and collect the standard errors. The standard errors are printed when I print the object:but I can find no way of getting them from the coxph.object returned by coxph. There is no mention of them in the coxph.object documentation:
> coxph.result
Call:
coxph(formula = Surv(timeall, event = PatientDeceased) ~ treatment +
AgeAtIndexDate + BMI + cellcount)
coef exp(coef) se(coef) z p
treatmentA 5.057e-01 1.658e+00 2.153e-01 2.349 0.0188
treatmentB 8.014e-02 1.083e+00 2.465e-01 0.325 0.7451
AgeAtIndexDate 4.626e-05 1.000e+00 2.258e-05 2.048 0.0405
BMI -5.023e-03 9.950e-01 1.939e-02 -0.259 0.7956
cellcount 2.113e-02 1.021e+00 9.299e-02 0.227 0.8202
Likelihood ratio test=8.88 on 5 df, p=0.114
n= 137, number of events= 123
Can anyone tell me where to get the standard errors?
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written
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roba6848 •
1 answer
In statistics, the term "standard error" means an estimated standard deviation. A standard deviation is just the square root of a variance, and the variance matrix of the coefficients is documented in the coxph.object help page.
You can extract the standard errors from coxph.result by
SE <- sqrt( diag( coxph.result$var ))
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I am not sure how familiar with R you are and I don't have a computer in front of my to check this, but I think you should just be able to go:
to store results in a variable, then you could go:
to print to the console what type of object it is, then look up indexing/slicing that object on google/stackoverflow. you probably need to make a function to get the specific elements that you want.
EDIT: Sorry I forgot to leave this as a comment not an answer :(