CIFsm: Cumulative incidence function estimate and weighted summary...
In CIFsmry: Weighted summary of cumulative incidence functions

Description Usage Arguments Details Value Author(s) References Examples

View source: R/simu.R

Estimate the cumulative incidence function for cause of interest in two-sample study. Provide the weighted summary statistics based on given method and weight.

1	CIFsm(ds,method="dif",pp = 0,qq = 0,conf.bd=T,n.sim=500)

`ds`	`ds` is a dataset contains the time, cause of event and group. For cause, 0 means censoring, 1 is the cause of event, 2 is all other causes. Two groups need to be coded as 1 and 2.
`method`	`method` can be chosen from "dif"=risk difference, "rr"=risk ratio and "or"=odds ratio
`pp`	first parameter of weight function
`qq`	second parameter of weight function
`conf.bd`	logical; if TRUE, create confidence band cut point. Set to FALSE if the confidence band is not needed, which reduces the computational time
`n.sim`	number of simulations used in creating confidence band; will be ineffective if `conf.bd` is FALSE

The estimates and summary statistics are described in Zhang and Fine (2008).

`sample`	Total sample size from both groups
`used`	Sample used in analysis. Subject with missing value in any of the three variables (time, cause or group) will be excluded from analysis
`size`	Sample size for each group
`njp`	Total number of unique event time points in two groups
`tjp`	Unique event time points from both groups
`ny1`	Number of subject at risk in group 1
`f1`	Estimate of cumulative incidence function for group 1
`f1.se`	Standard error of cumulative incidence function for group 1
`ny2`	Number of subject at risk in group 2
`f2`	Estimate of cumulative incidence function for group 2
`f2.se`	Standard error of cumulative incidence function for group 2
`dif`	Estimate of difference in cumulative incidence (risk difference) between the 2 groups
`dif.se`	Standard error of the risk difference
`dif.pv`	P-value of the risk difference
`rr`	Risk ratio of the cumulative incidence between the 2 groups
`rr.se`	Standard error of the risk ratio
`rr.pv`	P-value of the risk ratio
`or`	Odds ratio of the cumulative incidence between the 2 groups
`or.se`	Standard error of the odds ratio
`or.pv`	P-value of the odds ratio
`cbcut`	95% confidence band cut point of risk difference, risk ratio and odds ratio based on simulation method.
`method`	Method used for the weighted summary statistics
`weight`	Weight used for the weighted summary statistics
`region`	Time range of the data
`nbd`	Index of beginning and end of the data. For internal use only
`ave`	Time integrated weighted summary statistics
`avese`	Standard error of the time integrated weighted summary statistics
`ci95`	95% confidence interval of the time integrated weighted summary statistics
`avepval`	P-value of the time integrated weighted summary statistics
`wt`	Weight assigned at each unique event time point

Jianing Li

M.J. Zhang and J.P. Fine. Summarizing difference in cumulative incidence functions. Statistics in Medicine, 27:4939-4949, 2008.

J. Li, M.J. Zhang and J. Le-Rademacher. Weighted Summary of two Cumulative Incidence Functions with R-CIFsmry Package. Computer Methods and Programs in Biomedicine[Submitted].

library(CIFsmry)
data(sim.dat)
out <- CIFsm(sim.dat,pp=0,qq=0)
out$avepval
plot(out$tjp,out$f1,type="s",ylim=c(0,1),yaxt="n",xaxt="n",xlab="Time",ylab="CIF",
     lty=1,lwd=1)
points(out$tjp,out$f2,type="s",lty=1,lwd=3)
axis(1,at=seq(0,6,by=1),cex=0.6)
axis(2,at=seq(0,1,by=0.2),cex=0.6)
legend("bottomright",c("1","2"),title="group",lty=1,lwd=c(1,3))

out10 <- CIFsm(sim.dat,pp=1,qq=0)
out10$avepval