groupkm

0th

Percentile

Kaplan-Meier Estimates vs. a Continuous Variable

Function to divide x (e.g. age, or predicted survival at time u created by survest) into g quantile groups, get Kaplan-Meier estimates at time u (a scaler), and to return a matrix with columns x=mean x in quantile, n=number of subjects, events=no. events, and KM=K-M survival at time u, std.err = s.e. of -log K-M. Confidence intervals are based on -log S(t). Instead of supplying g, the user can supply the minimum number of subjects to have in the quantile group (m, default=50). If cuts is given (e.g. cuts=c(0,.1,.2,...,.9,.1)), it overrides m and g. Calls Therneau's survfitKM in the survival package to get Kaplan-Meiers estimates and standard errors.

Keywords
nonparametric, survival
Usage
groupkm(x, Srv, m=50, g, cuts, u, 
        pl=FALSE, loglog=FALSE, conf.int=.95, xlab, ylab,
        lty=1, add=FALSE, cex.subtitle=.7, ...)
Arguments
x
variable to stratify
Srv
a "Surv" object - n x 2 matrix containing survival time and event/censoring 1/0 indicator. Units of measurement come from the "units" attribute of the survival time variable. "Day" is the default.
m
desired minimum number of observations in a group
g
number of quantile groups
cuts
actual cuts in x, e.g. c(0,1,2) to use [0,1), [1,2].
u
time for which to estimate survival
pl
TRUE to plot results
loglog
set to TRUE to plot log(-log(survival)) instead of survival
conf.int
defaults to .95 for 0.95 confidence bars. Set to FALSE to suppress bars.
xlab
if pl=TRUE, is x-axis label. Default is label(x) or name of calling argument
ylab
if pl=TRUE, is y-axis label. Default is constructed from u and time units attribute.
lty
line time for primary line connecting estimates
add
set to TRUE if adding to an existing plot
cex.subtitle
character size for subtitle. Default is .7. Use FALSE to suppress subtitle.
...
plotting parameters to pass to the plot and errbar functions
Value

  • matrix with columns named x (mean predictor value in interval), n (sample size in interval), events (number of events in interval), KM (Kaplan-Meier estimate), std.err (standard error of -log KM)

concept

  • grouping
  • stratification
  • aggregation

See Also

survfit, errbar, cut2, Surv, units

Aliases
  • groupkm
Examples
n <- 1000
set.seed(731)
age <- 50 + 12*rnorm(n)
cens <- 15*runif(n)
h <- .02*exp(.04*(age-50))
d.time <- -log(runif(n))/h
label(d.time) <- 'Follow-up Time'
e <- ifelse(d.time <= cens,1,0)
d.time <- pmin(d.time, cens)
units(d.time) <- "Year"
groupkm(age, Surv(d.time, e), g=10, u=5, pl=TRUE)
#Plot 5-year K-M survival estimates and 0.95 confidence bars by 
#decile of age.  If omit g=10, will have >= 50 obs./group.
Documentation reproduced from package rms, version 2.0-2, License: GPL (>= 2)

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