[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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