[R] Issue when using a coxph + summary function in R while using a pspline-transformed covariate

Dumortier, Thomas
Thu, 01 Aug 2013 08:02:34 -0000

Hello
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I have an issue with obtaining a confidence interval from a coxph object in R
while using a spline-transformed covariate.

This is a time to event analysis using coxph() from the survival package.
In the model below, COVA is a continuous covariate. COVA is time-dependent hence
the counting process notation. COVA is transformed via pspline, COVB (FALSE or
TRUE) is a fixed covariate.
My goal is to get the confidence interval for COVB. With this purpose, I use the
summary(?,conf.int=.95) function.
I have pasted the code and the console below.

The estimation works well.
The summary function returns the desired confidence interval in the console, but
it returns a NULL object (psp.sum is returned NULL, see below the code and the
console)

Note that if I do not use pspline, it works !!!!!
So it seems that the use of pspline is not compatible with the summary function.

This is a problem because I would like to do some simulation and need to
retrieve the confidence interval from psp.sum.

Can you kindly help?

Rgds
Tom

CODE
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psp<-coxph(Surv(DAY2,DAY2P1,EVTF)~COVB+pspline(COVA, df = 0, caic =
T),data=dsn4,method='breslow')
psp
psp.sum<-summary(psp,conf.int=.95)
psp.sum
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CONSOLE

1> psp<-coxph(Surv(DAY2,DAY2P1,EVTF)~COVB+pspline(COVA, df = 0, caic =
T),data=dsn4,method='breslow')
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1> psp
Call:
coxph(formula = Surv(DAY2, DAY2P1, EVTF) ~ COVB + pspline(COVA,
????df = 0, caic = T), data = dsn4, method = "breslow")
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??????????????????? ??????coef?? se(coef) se2??? Chisq DF?? p?????
COVBTRUE????????????????? -1.625 0.4223?? 0.4198 14.80 1.00 1.2e-04
pspline(COVA, df = 0, caic -0.341 0.0761?? 0.0761 20.04 1.00 7.6e-06
pspline(COVA, df = 0, caic???????????????????????? 1.95 0.83 1.3e-01
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Iterations: 10 outer, 29 Newton-Raphson
???? Theta= 0.98
Degrees of freedom for terms= 1.0 1.8
Likelihood ratio test=22.3? on 2.81 df, p=4.52e-05? n= 16933
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1> psp.sum<-summary(psp,conf.int=.95)
Call:
coxph(formula = Surv(DAY2, DAY2P1, EVTF) ~ COVB + pspline(COVA,
????df = 0, caic = T), data = dsn4, method = "breslow")
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? n= 16933, number of events= 35
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????????????????????????? coef?? se(coef) se2??? Chisq DF?? p?????
COVBTRUE????????????????? -1.625 0.4223?? 0.4198 14.80 1.00 1.2e-04
pspline(COVA, df = 0, caic -0.341 0.0761?? 0.0761 20.04 1.00 7.6e-06
pspline(COVA, df = 0, caic???????????????????????? 1.95 0.83 1.3e-01
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????????? exp(coef) exp(-coef) lower .95 upper .95
COVBTRUE??? 0.19690?????? 5.08? 8.61e-02??? 0.4506
ps(COVA)3??? 0.59903?????? 1.67? 3.48e-01??? 1.0301
ps(COVA)4??? 0.35872?????? 2.79? 1.36e-01??? 0.9470
ps(COVA)5??? 0.21394?????? 4.67? 5.82e-02??? 0.7857
ps(COVA)6??? 0.12594?????? 7.94? 2.69e-02??? 0.5898
ps(COVA)7??? 0.07290????? 13.72? 1.31e-02??? 0.4051
ps(COVA)8??? 0.04275????? 23.39? 6.84e-03??? 0.2673
ps(COVA)9??? 0.02647????? 37.78? 3.89e-03??? 0.1802
ps(COVA)10?? 0.01785????? 56.04? 2.45e-03??? 0.1301
ps(COVA)11?? 0.01310????? 76.32? 1.68e-03??? 0.1024
ps(COVA)12?? 0.01019????? 98.11? 1.19e-03??? 0.0870
ps(COVA)13?? 0.00810???? 123.39? 8.32e-04??? 0.0790
ps(COVA)14?? 0.00645???? 154.95? 5.43e-04??? 0.0767
ps(COVA)15?? 0.00512???? 195.45? 3.26e-04??? 0.0803
ps(COVA)16?? 0.00405???? 246.92? 1.80e-04??? 0.0913
ps(COVA)17?? 0.00320???? 312.04? 9.11e-05??? 0.1127
ps(COVA)18?? 0.00254???? 394.32? 4.29e-05??? 0.1499
ps(COVA)19?? 0.00201???? 498.30? 1.89e-05??? 0.2133
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Iterations: 10 outer, 29 Newton-Raphson
???? Theta= 0.98
Degrees of freedom for terms= 1.0 1.8
Concordance= 0.673? (se = 0.05 )
Rsquare= 0.001?? (max possible= 0.026 )
Likelihood ratio test= 22.3? on 2.81 df,?? p=4.52e-05
Wald test??????????? = 24.6? on 2.81 df,?? p=1.48e-05
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1> psp.sum
NULL
1>
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