104 lines
3.2 KiB
Plaintext
104 lines
3.2 KiB
Plaintext
|
|
||
|
|
R Under development (unstable) (2019-10-26 r77334) -- "Unsuffered Consequences"
|
||
|
|
Copyright (C) 2019 The R Foundation for Statistical Computing
|
||
|
|
Platform: x86_64-pc-linux-gnu (64-bit)
|
||
|
|
|
||
|
|
R is free software and comes with ABSOLUTELY NO WARRANTY.
|
||
|
|
You are welcome to redistribute it under certain conditions.
|
||
|
|
Type 'license()' or 'licence()' for distribution details.
|
||
|
|
|
||
|
|
R is a collaborative project with many contributors.
|
||
|
|
Type 'contributors()' for more information and
|
||
|
|
'citation()' on how to cite R or R packages in publications.
|
||
|
|
|
||
|
|
Type 'demo()' for some demos, 'help()' for on-line help, or
|
||
|
|
'help.start()' for an HTML browser interface to help.
|
||
|
|
Type 'q()' to quit R.
|
||
|
|
|
||
|
|
> options(na.action=na.exclude) # preserve missings
|
||
|
|
> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
|
||
|
|
> library(survival)
|
||
|
|
>
|
||
|
|
> # Tests using the rats data
|
||
|
|
> #
|
||
|
|
> # (Female rats, from Mantel et al, Cancer Research 37,
|
||
|
|
> # 3863-3868, November 77)
|
||
|
|
>
|
||
|
|
> rfit <- coxph(Surv(time,status) ~ rx + frailty(litter), rats,
|
||
|
|
+ method='breslow', subset= (sex=='f'))
|
||
|
|
> rfit
|
||
|
|
Call:
|
||
|
|
coxph(formula = Surv(time, status) ~ rx + frailty(litter), data = rats,
|
||
|
|
subset = (sex == "f"), method = "breslow")
|
||
|
|
|
||
|
|
coef se(coef) se2 Chisq DF p
|
||
|
|
rx 0.906 0.323 0.319 7.882 1.0 0.005
|
||
|
|
frailty(litter) 16.888 13.8 0.253
|
||
|
|
|
||
|
|
Iterations: 6 outer, 25 Newton-Raphson
|
||
|
|
Variance of random effect= 0.474 I-likelihood = -181.1
|
||
|
|
Degrees of freedom for terms= 1.0 13.9
|
||
|
|
Likelihood ratio test=36.3 on 14.8 df, p=0.001
|
||
|
|
n= 150, number of events= 40
|
||
|
|
>
|
||
|
|
> rfit$iter
|
||
|
|
[1] 6 25
|
||
|
|
> rfit$df
|
||
|
|
[1] 0.975943 13.854864
|
||
|
|
> rfit$history[[1]]
|
||
|
|
$theta
|
||
|
|
[1] 0.4742849
|
||
|
|
|
||
|
|
$done
|
||
|
|
c.loglik
|
||
|
|
TRUE
|
||
|
|
|
||
|
|
$history
|
||
|
|
theta loglik c.loglik
|
||
|
|
[1,] 0.0000000 -181.8451 -181.8451
|
||
|
|
[2,] 1.0000000 -168.3683 -181.5458
|
||
|
|
[3,] 0.5000000 -173.3117 -181.0788
|
||
|
|
[4,] 0.3090061 -175.9446 -181.1490
|
||
|
|
[5,] 0.4645720 -173.7590 -181.0775
|
||
|
|
[6,] 0.4736210 -173.6431 -181.0773
|
||
|
|
|
||
|
|
$c.loglik
|
||
|
|
[1] -181.0773
|
||
|
|
|
||
|
|
>
|
||
|
|
> rfit1 <- coxph(Surv(time,status) ~ rx + frailty(litter, theta=1), rats,
|
||
|
|
+ method='breslow', subset=(sex=="f"))
|
||
|
|
> rfit1
|
||
|
|
Call:
|
||
|
|
coxph(formula = Surv(time, status) ~ rx + frailty(litter, theta = 1),
|
||
|
|
data = rats, subset = (sex == "f"), method = "breslow")
|
||
|
|
|
||
|
|
coef se(coef) se2 Chisq DF p
|
||
|
|
rx 0.918 0.327 0.321 7.851 1.0 0.0051
|
||
|
|
frailty(litter, theta = 1 27.245 22.7 0.2324
|
||
|
|
|
||
|
|
Iterations: 1 outer, 6 Newton-Raphson
|
||
|
|
Variance of random effect= 1 I-likelihood = -181.5
|
||
|
|
Degrees of freedom for terms= 1.0 22.7
|
||
|
|
Likelihood ratio test=50.7 on 23.7 df, p=0.001
|
||
|
|
n= 150, number of events= 40
|
||
|
|
>
|
||
|
|
> rfit2 <- coxph(Surv(time,status) ~ frailty(litter), rats, subset=(sex=='f'))
|
||
|
|
> rfit2
|
||
|
|
Call:
|
||
|
|
coxph(formula = Surv(time, status) ~ frailty(litter), data = rats,
|
||
|
|
subset = (sex == "f"))
|
||
|
|
|
||
|
|
coef se(coef) se2 Chisq DF p
|
||
|
|
frailty(litter) 18 14.6 0.24
|
||
|
|
|
||
|
|
Iterations: 6 outer, 22 Newton-Raphson
|
||
|
|
Variance of random effect= 0.504 I-likelihood = -184.8
|
||
|
|
Degrees of freedom for terms= 14.6
|
||
|
|
Likelihood ratio test=30 on 14.6 df, p=0.01
|
||
|
|
n= 150, number of events= 40
|
||
|
|
>
|
||
|
|
> proc.time()
|
||
|
|
user system elapsed
|
||
|
|
0.755 0.045 0.793
|