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

[Jin Wang]

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
> 	
>
>