sbrier {ipred} | R Documentation |
Model fit for survival data: the integrated Brier score for censored observations.
sbrier(obj, pred, btime=c(0, max(obj[,1])))
obj |
an object of class |
pred |
predicted values. Either a probability or a list of
|
btime |
numeric vector of times, the integrated Brier score is
computed if this is of |
There is no obvious criterion of model fit for censored data. The Brier score for censoring as well as it's integrated version were suggested by Graf et al (1999).
The (integrated) Brier score with attribute time
is returned.
Erika Graf, Claudia Schmoor, Willi Sauerbrei and Martin Schumacher (1999), Assessment and comparison of prognostic classification schemes for survival data. Statistics in Medicine 18(17-18), 2529–2545.
data(DLBCL) smod <- Surv(DLBCL$time, DLBCL$cens) KM <- survfit(smod ~ 1) # integrated Brier score up to max(DLBCL$time) sbrier(smod, KM) # integrated Brier score up to time=50 sbrier(smod, KM, btime=c(0, 50)) # Brier score for time=50 sbrier(smod, KM, btime=50) # a "real" model: one single survival tree with Intern. Prognostic Index # and mean gene expression in the first cluster as predictors mod <- bagging(Surv(time, cens) ~ MGEc.1 + IPI, data=DLBCL, nbagg=1) # this is a list of survfit objects (==KM-curves), one for each observation # in DLBCL pred <- predict(mod, newdata=DLBCL) # integrated Brier score up to max(time) sbrier(smod, pred) # Brier score at time=50 sbrier(smod, pred, btime=50) # artificial examples and illustrations cleans <- function(x) { attr(x, "time") <- NULL; names(x) <- NULL; x } n <- 100 time <- rpois(n, 20) cens <- rep(1, n) # checks, Graf et al. page 2536, no censoring at all! # no information: \pi(t) = 0.5 a <- sbrier(Surv(time, cens), rep(0.5, n), time[50]) stopifnot(all.equal(cleans(a),0.25)) # some information: \pi(t) = S(t) n <- 100 time <- 1:100 mod <- survfit(Surv(time, cens) ~ 1) a <- sbrier(Surv(time, cens), rep(list(mod), n)) mymin <- mod$surv * (1 - mod$surv) stopifnot(all.equal(cleans(a),sum(mymin)/max(time))) # independent of ordering rand <- sample(1:100) b <- sbrier(Surv(time, cens)[rand], rep(list(mod), n)[rand]) stopifnot(all.equal(cleans(a), cleans(b))) # 2 groups at different risk time <- c(1:10, 21:30) strata <- c(rep(1, 10), rep(2, 10)) cens <- rep(1, length(time)) # no information about the groups a <- sbrier(Surv(time, cens), survfit(Surv(time, cens) ~ 1)) b <- sbrier(Surv(time, cens), rep(list(survfit(Surv(time, cens) ~1)), 20)) stopifnot(all.equal(a, b)) # risk groups known mod <- survfit(Surv(time, cens) ~ strata) b <- sbrier(Surv(time, cens), c(rep(list(mod[1]), 10), rep(list(mod[2]), 10))) stopifnot(a > b)