cuminc: Cumulative Incidence Analysis

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

View source: R/cmprsk.R

Description

Estimate cumulative incidence functions from competing risks data and test equality across groups

Usage

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cuminc(ftime, fstatus, group, strata, rho=0, cencode=0,
subset, na.action=na.omit)

Arguments

ftime

failure time variable

fstatus

variable with distinct codes for different causes of failure and also a distinct code for censored observations

group

estimates will calculated within groups given by distinct values of this variable. Tests will compare these groups. If missing then treated as all one group (no test statistics)

strata

stratification variable. Has no effect on estimates. Tests will be stratified on this variable. (all data in 1 stratum, if missing)

rho

Power of the weight function used in the tests.

cencode

value of fstatus variable which indicates the failure time is censored.

subset

a logical vector specifying a subset of cases to include in the analysis

na.action

a function specifying the action to take for any cases missing any of ftime, fstatus, group, strata, or subset.

Value

A list with components giving the subdistribution estimates for each cause in each group, and a component Tests giving the test statistics and p-values for comparing the subdistribution for each cause across groups (if the number of groups is >1). The components giving the estimates have names that are a combination of the group name and the cause code. These components are also lists, with components

time

the times where the estimates are calculated

est

the estimated sub-distribution functions. These are step functions (all corners of the steps given), so they can be plotted using ordinary lines() commands. Estimates at particular times can be located using the timepoints() function.

var

the estimated variance of the estimates, which are estimates of the asymptotic variance of Aalen (1978).

Author(s)

Robert Gray

References

Gray RJ (1988) A class of K-sample tests for comparing the cumulative incidence of a competing risk, ANNALS OF STATISTICS, 16:1141-1154.

Kalbfleisch and Prentice (1980) THE ANALYSIS OF FAILURE TIME DATA, p 168-9.

Aalen, O. (1978) Nonparametric estimation of partial transition probabilities in multiple decrement models, ANNALS OF STATISTICS, 6:534-545.

See Also

plot.cuminc timepoints print.cuminc

Examples

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set.seed(2)
ss <- rexp(100)
gg <- factor(sample(1:3,100,replace=TRUE),1:3,c('a','b','c'))
cc <- sample(0:2,100,replace=TRUE)
strt <- sample(1:2,100,replace=TRUE)
print(xx <- cuminc(ss,cc,gg,strt))
plot(xx,lty=1,color=1:6)
# see also test.R, test.out

Example output

Loading required package: survival
Tests:
       stat        pv df
1 0.1110522 0.9459873  2
2 0.1344095 0.9350037  2
Estimates and Variances:
$est
            1         2         3         4
a 1 0.1997374 0.3337599 0.4082169 0.4082169
b 1 0.2582589 0.3116745 0.3116745 0.3116745
c 1 0.2194354 0.2813451 0.2813451 0.2813451
a 2 0.2641725 0.4428692 0.4428692 0.4428692
b 2 0.2669364 0.4479557 0.5280790 0.6082023
c 2 0.2471892 0.4400615 0.4400615 0.4400615

$var
              1           2           3           4
a 1 0.005842447 0.009576915 0.013764577 0.013764577
b 1 0.007508487 0.009432554 0.009432554 0.009432554
c 1 0.006644662 0.009550507 0.009550507 0.009550507
a 2 0.008127032 0.011168223 0.011168223 0.011168223
b 2 0.008030980 0.014868553 0.016688860 0.016481796
c 2 0.006941955 0.016574813 0.016574813 0.016574813

cmprsk documentation built on May 29, 2017, 8 p.m.