# [R] (coxph, se) Obtaining standard errors of coefficients from coxph to store

joris.dewolf at cropdesign.com joris.dewolf at cropdesign.com
Mon Aug 27 09:36:51 CEST 2007

```
David,

It would be helpful to give an example of what you would like to extract.

I guess you know how to extract elements from vectors and lists.
However, sometimes the objects returned by functions can be rather complex
(output of coxph() is...)
A general method to capture printed output is via capture.output(). Maybe
not fast, but if you have no other solution...

Joris

> a <- rnorm(10,1,1)
> b <- rnorm(10,1,1)
> mod <- lm(a~b)
> smod <- summary(mod)
> smod

Call:
lm(formula = a ~ b)

Residuals:
Min      1Q  Median      3Q     Max
-1.7482 -0.5991  0.1211  0.8341  1.4975

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept)   1.6210     0.5332   3.040   0.0161 *
b            -0.7667     0.5037  -1.522   0.1664
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.142 on 8 degrees of freedom
Multiple R-Squared: 0.2246,     Adjusted R-squared: 0.1277
F-statistic: 2.317 on 1 and 8 DF,  p-value: 0.1664

> output <- capture.output(print(smod))
> output
[1] ""
[2] "Call:"
[3] "lm(formula = a ~ b)"
[4] ""
[5] "Residuals:"
[6] "    Min      1Q  Median      3Q     Max "
[7] "-1.7482 -0.5991  0.1211  0.8341  1.4975 "
[8] ""
[9] "Coefficients:"
[10] "            Estimate Std. Error t value Pr(>|t|)  "
[11] "(Intercept)   1.6210     0.5332   3.040   0.0161 *"
[12] "b            -0.7667     0.5037  -1.522   0.1664  "
[13] "---"
[14] "Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 "
[15] ""
[16] "Residual standard error: 1.142 on 8 degrees of freedom"
[17] "Multiple R-Squared: 0.2246,\tAdjusted R-squared: 0.1277 "
[18] "F-statistic: 2.317 on 1 and 8 DF,  p-value: 0.1664 "
[19] ""

"David Lloyd"
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Subject
[R] (coxph,  se) Obtaining standard
16/08/2007 11:31          errors of coefficients from coxph
to store

Hi all,

I'm wanting to be able to find and store the z-score of coxph below: -

modz=coxph(Surv(TSURV,STATUS)~RAGE+DAGE+REG_WTIME_M+CLD_ISCH+POLY_VS,
data=kidneyT,method="breslow")

I know summary(modz) will give me this, but how do i extract the
standard error or z-score values in a similar way to obtaining the
coefficients by coef(modz) ? I think it must be something to do with
modz\$var but I'm having a complete mental blank.

I need this info so I can write a function to use within a bootstrap so
I can record the number of times (proportion) each variable in the Cox
PH model is actually significant over all the bootstrap resamples.

Any assistance is greatly appreciated

DL

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