On Tue, 5 Oct 2004, Wu, Tongtong wrote:
Hi,
I am taking a survival class. Recently I need to do the Nelson-Aalen estimtor in R. I searched through the R help manual and internet, but could not find such a R function. I tried another way by calculating the Kaplan-Meier estimator and take -log(S). However, the function only provides the summary of KM estimator but no estimated values. Could you please help me with this? I would highly appreciate your great help!
Taking -log(KM) does not give the Nelson-Aalen estimator, though it does give another consistent estimator of the cumulative hazard function.
The easiest way to get the Nelson-Aalen estimator is
basehaz(coxph(Surv(time,status)~1,data=aml))
because the (Breslow) hazard estimator for a Cox model reduces to the Nelson-Aalen estimator when there are no covariates.
You can also compute it from information returned by survfit().
fit <- survfit(Surv(time, status) ~ 1, data = aml) str(fit)
List of 12 $ n : int 23 $ time : num [1:18] 5 8 9 12 13 16 18 23 27 28 ... $ n.risk : num [1:18] 23 21 19 18 17 15 14 13 11 10 ... $ n.event : num [1:18] 2 2 1 1 1 0 1 2 1 0 ... $ surv : num [1:18] 0.913 0.826 0.783 0.739 0.696 ... $ type : chr "right" $ std.err : num [1:18] 0.0643 0.0957 0.1099 0.1239 0.1379 ... $ upper : num [1:18] 1.000 0.996 0.971 0.942 0.912 ... $ lower : num [1:18] 0.805 0.685 0.631 0.580 0.531 ... $ conf.type: chr "log" $ conf.int : num 0.95 $ call : language survfit(formula = Surv(time, status) ~ 1, data = aml) - attr(*, "class")= chr "survfit"
so cumsum(fit$n.event/fit$n.risk) is the Nelson-Aalen estimator for the times given by fit$times.
If you want -log(S), then -log(fit$surv) will give it to you.
-thomas
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