[R] ظ: cch() and coxph() for case-cohort

From: Jin Wang <jinwang25_at_gmail.com>
Date: Mon, 16 Jun 2008 13:03:29 -0500


I tried to compare if cch() and coxph() can generate same result for same case cohort data

Use the standard data in cch(): nwtco

Since in cch contains the cohort size=4028, while ccoh.data size =1154 after selection, but coxph does not contain info of cohort size=4028.

The rough estimate between coxph() and cch() is same, but the lower and upper CI and P-value are a little different. Can we exactly use coxph() to repeat cch() using with appropriate configuration in coxph()? Is SAS a better way(PHREG,CASECOH.SAS) to implement time-dependent case-cohort?

> summary(fit2.ccP)

Call:
coxph(formula = Surv(edrel, rel) ~ stage + histol + age + offset(-100 *

    (1 - subcohort)) + cluster(seqno), data = ccoh.data)

  n= 1154

           coef exp(coef) se(coef) robust se    z       p
stageII  0.7363      2.09   0.1213    0.1699 4.33 1.5e-05
stageIII 0.5976      1.82   0.1233    0.1753 3.41 6.5e-04
stageIV  1.3921      4.02   0.1339    0.2081 6.69 2.2e-11
histolUH 1.5059      4.51   0.0911    0.1644 9.16 0.0e+00
age      0.0432      1.04   0.0146    0.0243 1.78 7.6e-02

         exp(coef) exp(-coef) lower .95 upper .95
stageII       2.09      0.479     1.497      2.91
stageIII      1.82      0.550     1.289      2.56
stageIV       4.02      0.249     2.676      6.05
histolUH      4.51      0.222     3.267      6.22
age           1.04      0.958     0.996      1.09

Rsquare= 0.273 (max possible= 1 )

Likelihood ratio test= 368  on 5 df,   p=0
Wald test            = 134  on 5 df,   p=0
Score (logrank) test = 490  on 5 df,   p=0,   Robust = 165  p=0

  (Note: the likelihood ratio and score tests assume independence of
     observations within a cluster, the Wald and robust score tests do not).


> summary(fit.ccSP)
Case-cohort analysis,x$method, SelfPrentice  with subcohort of 668 from cohort of 4028

Call: cch(formula = Surv(edrel, rel) ~ stage + histol + age, data = ccoh.data,

    subcoh = ~subcohort, id = ~seqno, cohort.size = 4028, method = "SelfPren")

Coefficients:

          Coef HR (95% CI) p

stageII  0.736 2.088 1.491 2.925 0.000
stageIII 0.597 1.818 1.285 2.571 0.001
stageIV  1.392 4.021 2.670 6.057 0.000
histolUH 1.506 4.507 3.274 6.203 0.000
age      0.043 1.044 0.996 1.095 0.069


2008/6/12, Terry Therneau <therneau_at_mayo.edu>:
> Jin Wang had an error. My original note specified a variable that was 1 for
> subjects NOT in the subcohort, so the correct coxph call is
>
> coxph(Surv(edrel, rel) ~ stage + histol + age +
> offset(-100*(subcohort==0)) + cluster(seqno), data =ccoh.data)
>
> This gives the same coefficients as the cch example, along with the
> infinitesimal jackknife or "robust" variance estimate.
>
> Terry Therneau
>
>
>



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