127 lines
4.6 KiB
Plaintext
127 lines
4.6 KiB
Plaintext
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R Under development (unstable) (2018-05-10 r74706) -- "Unsuffered Consequences"
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Copyright (C) 2018 The R Foundation for Statistical Computing
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Platform: x86_64-pc-linux-gnu (64-bit)
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R is free software and comes with ABSOLUTELY NO WARRANTY.
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You are welcome to redistribute it under certain conditions.
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Type 'license()' or 'licence()' for distribution details.
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R is a collaborative project with many contributors.
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Type 'contributors()' for more information and
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'citation()' on how to cite R or R packages in publications.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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'help.start()' for an HTML browser interface to help.
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Type 'q()' to quit R.
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> options(na.action=na.exclude) # preserve missings
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> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
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> library(survival)
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>
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> #
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> # Here is a test case with multiple smoothing terms
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> #
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>
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> fit0 <- coxph(Surv(time, status) ~ ph.ecog + age, lung)
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> fit1 <- coxph(Surv(time, status) ~ ph.ecog + pspline(age,3), lung)
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> fit2 <- coxph(Surv(time, status) ~ ph.ecog + pspline(age,4), lung)
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> fit3 <- coxph(Surv(time, status) ~ ph.ecog + pspline(age,8), lung)
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>
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>
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>
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> fit4 <- coxph(Surv(time, status) ~ ph.ecog + pspline(wt.loss,3), lung)
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>
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> fit5 <-coxph(Surv(time, status) ~ ph.ecog + pspline(age,3) +
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+ pspline(wt.loss,3), lung)
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>
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> fit1
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Call:
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coxph(formula = Surv(time, status) ~ ph.ecog + pspline(age, 3),
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data = lung)
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coef se(coef) se2 Chisq DF p
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ph.ecog 0.44802 0.11707 0.11678 14.64453 1.00 0.00013
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pspline(age, 3), linear 0.01126 0.00928 0.00928 1.47231 1.00 0.22498
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pspline(age, 3), nonlin 2.07924 2.08 0.37143
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Iterations: 4 outer, 12 Newton-Raphson
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Theta= 0.861
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Degrees of freedom for terms= 1.0 3.1
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Likelihood ratio test=21.9 on 4.08 df, p=2e-04
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n= 227, number of events= 164
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(1 observation deleted due to missingness)
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> fit2
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Call:
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coxph(formula = Surv(time, status) ~ ph.ecog + pspline(age, 4),
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data = lung)
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coef se(coef) se2 Chisq DF p
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ph.ecog 0.45047 0.11766 0.11723 14.65751 1.00 0.00013
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pspline(age, 4), linear 0.01117 0.00927 0.00927 1.45195 1.00 0.22822
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pspline(age, 4), nonlin 2.95816 3.08 0.41197
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Iterations: 4 outer, 11 Newton-Raphson
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Theta= 0.797
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Degrees of freedom for terms= 1.0 4.1
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Likelihood ratio test=22.7 on 5.07 df, p=4e-04
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n= 227, number of events= 164
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(1 observation deleted due to missingness)
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> fit3
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Call:
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coxph(formula = Surv(time, status) ~ ph.ecog + pspline(age, 8),
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data = lung)
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coef se(coef) se2 Chisq DF p
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ph.ecog 0.47640 0.12024 0.11925 15.69732 1.00 7.4e-05
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pspline(age, 8), linear 0.01172 0.00923 0.00923 1.61161 1.00 0.20
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pspline(age, 8), nonlin 6.93188 6.99 0.43
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Iterations: 5 outer, 15 Newton-Raphson
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Theta= 0.691
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Degrees of freedom for terms= 1 8
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Likelihood ratio test=27.6 on 8.97 df, p=0.001
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n= 227, number of events= 164
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(1 observation deleted due to missingness)
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> fit4
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Call:
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coxph(formula = Surv(time, status) ~ ph.ecog + pspline(wt.loss,
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3), data = lung)
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coef se(coef) se2 Chisq DF p
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ph.ecog 0.51545 0.12960 0.12737 15.81939 1.00 7e-05
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pspline(wt.loss, 3), line -0.00702 0.00655 0.00655 1.14638 1.00 0.28
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pspline(wt.loss, 3), nonl 2.44612 2.09 0.31
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Iterations: 3 outer, 10 Newton-Raphson
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Theta= 0.776
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Degrees of freedom for terms= 1.0 3.1
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Likelihood ratio test=21.1 on 4.06 df, p=3e-04
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n= 213, number of events= 151
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(15 observations deleted due to missingness)
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> fit5
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Call:
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coxph(formula = Surv(time, status) ~ ph.ecog + pspline(age, 3) +
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pspline(wt.loss, 3), data = lung)
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coef se(coef) se2 Chisq DF p
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ph.ecog 0.47422 0.13495 0.13206 12.34842 1.00 0.00044
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pspline(age, 3), linear 0.01368 0.00976 0.00974 1.96406 1.00 0.16108
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pspline(age, 3), nonlin 1.90116 2.07 0.40284
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pspline(wt.loss, 3), line -0.00717 0.00661 0.00660 1.17529 1.00 0.27832
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pspline(wt.loss, 3), nonl 2.07729 2.03 0.35929
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Iterations: 4 outer, 12 Newton-Raphson
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Theta= 0.85
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Theta= 0.779
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Degrees of freedom for terms= 1.0 3.1 3.0
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Likelihood ratio test=25.2 on 7.06 df, p=7e-04
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n= 213, number of events= 151
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(15 observations deleted due to missingness)
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>
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> rm(fit1, fit2, fit3, fit4, fit5)
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>
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> proc.time()
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user system elapsed
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0.832 0.048 0.877
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