quantileKM: Compute arbitrary quantile of a Kaplan-Meier estimate of a...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/quantileKM.R

Description

In survival analysis, often some quantiles (mainly the median) of an estimated survival function are of interest. The survfit function in the 'survival' packages of version < 2.35 computed median time to event. However, the output of that function was such that the median is not accessible by the user (it can only be read off the output). This function makes the median and any other quantile accessible by the user.

Usage

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quantileKM(time, event, group = NA, quant = 0.5, conf.level = 0.95, 
    conftype = c("log", "log-log", "plain", "none")[2], conflower = 
    c("usual", "peto", "modified")[1])

Arguments

time

Event times, censored or observed.

event

Censoring indicator, 1 for event, 0 for censored.

group

Quantiles can be computed for several survival curves, defined by group.

quant

Quantile to be computed. Real number in [0, 1].

conf.level

Significance level for confidence interval for the time to event quantile.

conftype

Type of confidence interval to be computed. For possible choices see above, and for specifications regarding the different options confer the help file of the function survfit.

conflower

Controls modified lower limits to the curve, the upper limit remains unchanged. See survfit for details.

Value

n

Number of observations used.

events

Number of events.

quantile

Quantile estimate.

lower.ci

Lower limit of confidence interval.

upper.ci

Upper limit of confidence interval.

Author(s)

Kaspar Rufibach
kaspar.rufibach@gmail.com

References

Computation of confidence intervals is done according to

Brookmeyer, R. and Crowley, J. (1982). A Confidence Interval for the Median Survival Time. Biometrics, 38, 29–41.

See Also

Partly based on the function survfit.

Examples

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## use Acute Myelogenous Leukemia survival data contained in package 'survival'
time <- leukemia[, 1]; status <- leukemia[, 2]; x <- as.factor(leukemia[, 3])
plot(survfit(Surv(time, status) ~ x, conf.type = "none"), mark = "/", col = 1:2)

## median time to event
qKM <- quantileKM(time, status, group = x, quant = 0.5, conf.level = 0.95, 
    conftype = "log")
qKM

## extract results
qKM$quantities

## comparison to standard function (median time to event not accessible by user)
quant.surv <- survfit(Surv(time, status) ~ x, conf.int = 0.95)
quant.surv

## compute 0.25 quantile
qKM2 <- quantileKM(time, status, group = x, quant = 0.25, conf.level = 0.95, 
    conftype = "log")
qKM2

biostatUZH documentation built on May 21, 2017, 12:50 a.m.

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