Survival Rate Estimates
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 > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT