On May 12, 2011, at 2:19 PM, David Winsemius wrote:
On May 12, 2011, at 12:40 PM, Brian McLoone wrote:
Dear List,
Is there an automated way to use the survival package to generate
survival
rate estimates and their standard errors? To be clear, *not *the
survivorship estimates (which are cumulative), but the survival
*rate *
estimates...
Not entirely clear, but from context I suspect you mean
instantaneous hazard?
(Survival is not a rate but rather a proportion. Mortality can be a
rate. The instantaneous hazard is the decrement in survival per unit
time divided by the survival to that time.)
So at each death the non-parametric estimate would divide current
deaths (often 1 but ties are possible) by time since last death and
then divide by proportion surviving.
Or if you have a semi-parametric estimated function for survival
(such as might be output from `basehaz` which calls `survfit`) take:
-delta_survival/delta_time/survival
tdata <- data.frame(time =c(1,1,1,2,2,2,3,3,3,4,4,4),
status=rep(c(1,0,2),4), n =c(12,3,2,6,2,4,2,0,2,3,3,5))
fit <- survfit(Surv(time, time, status, type='interval') ~1,
data=tdata, weight=n)
> T <- c(0, fit$time)
I was doing something else in this session and realized that using 'T'
was _not_ a good choice here.
> T == TRUE
[1] FALSE TRUE FALSE FALSE FALSE
I (almost) always spell out TRUE but not everyone does. Better to use
'sT' or <almost anything else>.
(But don't use: c, df, C, F, pi, rm, t, qt, pt, rt, dt,, df, rf,
qf, ... )
> rm(T)
> T == TRUE
[1] TRUE
--
David.
> S <- c(1, fit$surv)
> (-diff(S)/diff(T) )/fit$surv
[1] 0.8602308 0.8247746 0.4044324 1.2115931
I don't know if Therneau's opinion about estimating smoothed hazards
has changed:
http://finzi.psych.upenn.edu/Rhelp10/2009-March/193104.html
There is also a muhaz package which may generate standard errors for
its estimates but I have read elsewhere that is does not do Cox
models.
http://finzi.psych.upenn.edu/R/library/muhaz/html/00Index.html
--
David Winsemius, MD
West Hartford, CT
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David Winsemius, MD
West Hartford, CT
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
