Cumulative incidence function estimate and weighted summary statistics
Description
Estimate the cumulative incidence function for cause of interest in twosample study. Provide the weighted summary statistics based on given method and weight.
Usage
1  CIFsm(ds,method="dif",pp = 0,qq = 0,conf.bd=T,n.sim=500)

Arguments
ds 

method 

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 
Details
The estimates and summary statistics are described in Zhang and Fine (2008).
Value
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 
Pvalue 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 
Pvalue 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 
Pvalue 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 
Pvalue of the time integrated weighted summary statistics 
wt 
Weight assigned at each unique event time point 
Author(s)
Jianing Li
References
M.J. Zhang and J.P. Fine. Summarizing difference in cumulative incidence functions. Statistics in Medicine, 27:49394949, 2008.
J. Li, M.J. Zhang and J. LeRademacher. Weighted Summary of two Cumulative Incidence Functions with RCIFsmry Package. Computer Methods and Programs in Biomedicine[Submitted].
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13  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

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