Package CIFsmry. July 10, Index 6
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1 Type Package Package CIFsmry July 10, 2016 Title Weighted summary of cumulative incidence functions Version Date Author Jianing Li Maintainer Jianing Li Depends R(>= 3.0.1) Estimate of cumulative incidence function in two samples. Provide weighted summary statistics based on various methods and weights. License GPL (>= 2) NeedsCompilation yes Repository CRAN Date/Publication :39:40 R topics documented: CIFsm print.cifsm sim.dat summary.cifsm Index 6 CIFsm Cumulative incidence function estimate and weighted summary statistics 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
2 2 CIFsm Usage CIFsm(ds,method="dif",pp = 0,qq = 0,conf.bd=T,n.sim=500) Arguments ds method pp qq conf.bd n.sim 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 can be chosen from "dif"=risk difference, "rr"=risk ratio and "or"=odds ratio first parameter of weight function second parameter of weight function logical; if TRUE, create confidence band cut point. Set to FALSE if the confidence band is not needed, which reduces the computational time number of simulations used in creating confidence band; will be ineffective if conf.bd is FALSE Details Value The estimates and summary statistics are described in Zhang and Fine (2008). sample used size njp tjp Total sample size from both groups Sample used in analysis. Subject with missing value in any of the three variables (time, cause or group) will be excluded from analysis Sample size for each group Total number of unique event time points in two groups 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 dif.pv rr rr.se rr.pv Standard error of the risk difference P-value of the risk difference Risk ratio of the cumulative incidence between the 2 groups Standard error of the risk ratio P-value of the risk ratio
3 CIFsm 3 or or.se or.pv cbcut method weight region nbd ave avese ci95 avepval wt Odds ratio of the cumulative incidence between the 2 groups Standard error of the odds ratio P-value of the odds ratio 95% confidence band cut point of risk difference, risk ratio and odds ratio based on simulation method. Method used for the weighted summary statistics Weight used for the weighted summary statistics Time range of the data Index of beginning and end of the data. For internal use only Time integrated weighted summary statistics Standard error of the time integrated weighted summary statistics 95% confidence interval of the time integrated weighted summary statistics P-value of the time integrated weighted summary statistics 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: , 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]. Examples 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
4 4 sim.dat print.cifsm Print CIFsm object Usage Print the estimated of cumulative incidence functions and point-wise summary statistics. ## S3 method for class 'CIFsm' print(x,...) Arguments x Details CIFsm object from function CIFsm... additional arguments to print() Risk set, cumulative incidence function estimate, standard error and p-value of each group. Pointwise summary statistics estimate, standard error and p-value. See Also CIFsm sim.dat Simulated competing risk data Format Source Simulated data with 100 subjects and 3 variates: time, cause and group. The data has 100 rows and 3 columns. time a numeric vector. Survival time. cause a numeric vector code. Survival status. 1: failure from the cause of interest; 2: failure from other causes; 0: censored. group a numeric vector code. 1: group 1; 2: group 2. Simulated data
5 summary.cifsm 5 Examples data(sim.dat) names(sim.dat) table(sim.dat$cause) table(sim.dat$group) tapply(sim.dat$time,sim.dat$group,summary) summary.cifsm Summary of weighted time-integrated summary statistics Usage Summary statistic estimate, standard error, 95% confidence interval, p-value depending the method and weight. ## S3 method for class 'CIFsm' summary(object,...) Arguments object See Also object of function CIFsm... additional arguments to summary() CIFsm
6 Index Topic cumulative incidence function CIFsm, 1 print.cifsm, 4 summary.cifsm, 5 Topic datasets sim.dat, 4 Topic summary statistics CIFsm, 1 Topic weight function CIFsm, 1 CIFsm, 1, 4, 5 print.cifsm, 4 sim.dat, 4 summary.cifsm, 5 6
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