CODEWITHSUNDEEP
rfunctionextracttext-extractioninformation-extraction
anxoestevez
anxoestevez

Reputation: 188

How to extract attributes from cox.zph R function

I need to extract the p attribute of a specific row in the output of cox.zph function in R.

To put you in question, I describe my problem as follows, step by step with an example:

require('survival')

# I create the simplest test data set

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 

coxmodel <- coxph(Surv(time, status) ~ x + strata(sex), test1)

And then, I use cox.zph function:

zph <- cox.zph(coxmodel)

With the following output:

    rho chisq    p
x 0.354 0.322 0.57

I tried to get p attribute value (in this case, 0.57) by using attributes(zph) but p doesn't appear in order to do something like zph$p. I also used plyr package with no results.

Does anyone could help me? Thanks.

Upvotes: 3

Views: 1160

Answers (1)

January
January

Reputation: 17120

Here it is:

zph$table[ , "p" ]

The you can access the members of the zph object using $, since it is a list:

names( zph )
# returns:
# [1] "table"     "x"         "y"         "var"       "call"      "transform"

Then look up zph$table and presto.

In R, usually the different "slots" of an object are accessible through $ (S3 OO framework) or @ (S4 OO framework).

Upvotes: 4

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