casewise.test | R Documentation |
Estimates the casewise concordance based on Concordance and marginal estimate using timereg and performs test for independence
casewise.test(conc, marg, test = "no-test", p = 0.01)
conc |
Concordance |
marg |
Marginal estimate |
test |
Type of test for independence assumption. "conc" makes test on concordance scale and "case" means a test on the casewise concordance |
p |
check that marginal probability is greater at some point than p |
Uses cluster based conservative standard errors for marginal and sometimes only the uncertainty of the concordance estimates. This works prettey well, alternatively one can use also the funcions Casewise for a specific time point
Thomas Scheike
## Reduce Ex.Timings library("timereg") data("prt",package="mets"); prt <- force.same.cens(prt,cause="status") prt <- prt[which(prt$id %in% sample(unique(prt$id),7500)),] ### marginal cumulative incidence of prostate cancer times <- seq(60,100,by=2) outm <- timereg::comp.risk(Event(time,status)~+1,data=prt,cause=2,times=times) cifmz <- predict(outm,X=1,uniform=0,resample.iid=1) cifdz <- predict(outm,X=1,uniform=0,resample.iid=1) ### concordance for MZ and DZ twins cc <- bicomprisk(Event(time,status)~strata(zyg)+id(id), data=prt,cause=c(2,2)) cdz <- cc$model$"DZ" cmz <- cc$model$"MZ" ### To compute casewise cluster argument must be passed on, ### here with a max of 100 to limit comp-time outm <- timereg::comp.risk(Event(time,status)~+1,data=prt, cause=2,times=times,max.clust=100) cifmz <- predict(outm,X=1,uniform=0,resample.iid=1) cc <- bicomprisk(Event(time,status)~strata(zyg)+id(id),data=prt, cause=c(2,2),se.clusters=outm$clusters) cdz <- cc$model$"DZ" cmz <- cc$model$"MZ" cdz <- casewise.test(cdz,cifmz,test="case") ## test based on casewise cmz <- casewise.test(cmz,cifmz,test="conc") ## based on concordance plot(cmz,ylim=c(0,0.7),xlim=c(60,100)) par(new=TRUE) plot(cdz,ylim=c(0,0.7),xlim=c(60,100)) slope.process(cdz$casewise[,1],cdz$casewise[,2],iid=cdz$casewise.iid) slope.process(cmz$casewise[,1],cmz$casewise[,2],iid=cmz$casewise.iid)
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