1library(cmprsk) 2 3options(warn=-1) 4RNGversion("1.6.2") 5options(warn=0) 6 7set.seed(2) 8ss <- rexp(100) 9gg <- factor(sample(1:3,100,replace=TRUE),1:3,c('a','b','c')) 10cc <- sample(0:2,100,replace=TRUE) 11strt <- sample(1:2,100,replace=TRUE) 12dd <- data.frame(ss=abs(rnorm(100))) 13d2 <- data.frame(ssd=ss,ggd=gg,ccd=cc,strtd=strt,X=c(rep(1,80),rep(0,20))) 14gg2 <- gg 15gg2[c(5,10,50)] <- NA 16print(xx <- cuminc(dd$ss,cc,gg,strt)) 17print(xx <- cuminc(d2$ssd,d2$ccd)) 18print(xx <- cuminc(ss,cc)) 19print(xx <- cuminc(ss,cc,gg,strt)) 20plot(xx) 21plot(xx,lty=1,color=1:6) 22print(xx <- cuminc(dd$ss,cc,gg2,strt)) 23print(xx <- cuminc(ss,cc,gg2,strt,subset=d2$X == 1)) 24attach(d2) 25print(xx <- cuminc(ssd,ccd,gg2,strtd,subset=X == 1)) 26print(xx <- cuminc(ssd,ccd,gg2,strtd,subset=gg != 'b')) 27print(xx <- cuminc(ssd,ccd,gg2,strtd,subset=ggd != 'b')) 28print(xx <- cuminc(ssd,ccd,gg2,strtd,subset=gg2 != 'b')) 29detach(d2) 30 31cv <- matrix(sample(0:1,3*100,replace=TRUE),ncol=3) 32cv[c(1,10,20)] <- NA 33print(xx <- crr(ss,cc,cv)) 34cov2 <- cbind(cv[,1],cv[,1]) 35tf <- function(uft) cbind(uft,uft^2) 36print(ww <- crr(ss,cc,cv,cov2,tf=tf,cengroup=cv[,3])) 37plot(ww$uft,ww$res[,1]) 38lines(lowess(ww$uft,ww$res[,1],iter=0,f=.75)) 39print(wp <- predict(ww,rbind(c(1,1,1),c(0,0,0)),rbind(c(1,1),c(0,0)))) 40plot(wp) 41plot(wp,lty=1,col=c(2,4)) 42d2 <- cbind(d2,cv3=cv[,3],cv1=cv[,1]) 43attach(d2) 44print(ww <- crr(ssd,ccd,cbind(cv[,1:2],cv3),cov2,tf=tf,cengroup=cv3)) 45print(ww <- crr(ssd,ccd,cbind(cv[,1:2],cv3),cov2,tf=tf)) 46print(ww <- crr(ssd,ccd,cbind(cv[,1:2],cv3),cbind(cv1,cv1),tf=tf,cengroup=cv3)) 47print(ww <- crr(ssd,ccd,cbind(cv[,1:2],cv3),cbind(cv1,cv1),tf=tf,cengroup=cv3,subset=X == 1)) 48print(summary(ww)) 49detach(d2) 50print(ww <- crr(ss,cc,cv,cov2,tf=tf,cengroup=cv[,3],subset=d2$X==1)) 51print(ww <- crr(ss,cc,cv,cov2,tf=tf,cengroup=cv[,3],failcode=2)) 52print(ww <- crr(ss,cc,cv,cov2,tf=tf,cengroup=cv[,3],cencode=2)) 53print(ww <- crr(ss,cc,cv[,1])) 54print(ww <- crr(ss,cc,cov2=cv[,1],tf=function(x) x)) 55print(summary(ww)) 56