Hello, and thank you in advance.
I would like to capture the expected survival from a coxph model for
subjects in an observational study with recurrent events, but the
survexp statement is failing due to memory. I am using R version
2.13.1 (2011-07-08) on Windows XP.
My objective is to plot the fitted survival with the Kaplan-Meier
plot. Below is the code with output and [unfortunately] errors. Is
there something wrong in my use of cluster in generating the
proportional hazards model, or is there some syntax to pass it into
survexp?
Mike
> dim(dev)
[1] 899876 25
> mod1 <- coxph(Surv(begin.cp, end.cp, event)
+ ~ age.sex
+ + plan_type
+ + uw_load
+ + cluster(mbr_key)
+ ,data=dev
+ )
>
> summary(mod1)
Call:
coxph(formula = Surv(begin.cp, end.cp, event) ~ age.sex + plan_type +
uw_load + cluster(mbr_key), data = dev)
n= 899876, number of events= 753324
coef exp(coef) se(coef) robust se z
Pr(>|z|)
age.sex19-34_MALE -0.821944 0.439576 0.005529 0.023298 -35.280 <
2e-16 ***
age.sex35-49_FEMALE 0.058776 1.060537 0.004201 0.018477 3.181
0.00147 **
age.sex35-49_MALE -0.515590 0.597148 0.004634 0.019986 -25.798 <
2e-16 ***
age.sex50-64_FEMALE 0.190940 1.210386 0.004350 0.020415 9.353 <
2e-16 ***
age.sex50-64_MALE -0.127514 0.880281 0.004487 0.021431 -5.950
2.68e-09 ***
age.sexCHILD_CHILD -0.327522 0.720707 0.004238 0.017066 -19.192 <
2e-16 ***
plan_typeLOW -0.165735 0.847270 0.002443 0.011080 -14.958 <
2e-16 ***
uw_load1-50 0.215122 1.240014 0.006437 0.029189 7.370
1.71e-13 ***
uw_load101-250 0.551042 1.735060 0.003993 0.018779 29.344 <
2e-16 ***
uw_load251+ 0.981660 2.668884 0.003172 0.017490 56.126 <
2e-16 ***
uw_load51-100 0.413464 1.512046 0.006216 0.027877 14.832 <
2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
exp(coef) exp(-coef) lower .95 upper .95
age.sex19-34_MALE 0.4396 2.2749 0.4200 0.4601
age.sex35-49_FEMALE 1.0605 0.9429 1.0228 1.0996
age.sex35-49_MALE 0.5971 1.6746 0.5742 0.6210
age.sex50-64_FEMALE 1.2104 0.8262 1.1629 1.2598
age.sex50-64_MALE 0.8803 1.1360 0.8441 0.9180
age.sexCHILD_CHILD 0.7207 1.3875 0.6970 0.7452
plan_typeLOW 0.8473 1.1803 0.8291 0.8659
uw_load1-50 1.2400 0.8064 1.1711 1.3130
uw_load101-250 1.7351 0.5763 1.6724 1.8001
uw_load251+ 2.6689 0.3747 2.5789 2.7620
uw_load51-100 1.5120 0.6614 1.4316 1.5970
Concordance= 0.643 (se = 0 )
Rsquare= 0.205 (max possible= 1 )
Likelihood ratio test= 206724 on 11 df, p=0
Wald test = 9207 on 11 df, p=0
Score (logrank) test = 246358 on 11 df, p=0, Robust = 4574 p=0
(Note: the likelihood ratio and score tests assume independence of
observations within a cluster, the Wald and robust score tests do
not).
> dev.fit <- survexp( ~ 1, ratetable=mod1, data=dev)
Error in survexp.cfit(cbind(as.numeric(X), R), Y, conditional,
FALSE, :
cannot allocate memory block of size 15.2 Gb
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