variations on the theme of survSplit

Danardono <daodao99 at student.umu.se> wrote:

While waiting for 2.1, for those who need function[s] for this
survival-splitting business, as I do,   this 'survcut' function below
might be helpful.

It is not an elegant nor efficient function but it works, at least for
some examples below.

Ditto the following, for the case where there are multiple time-varying
(irreversible) binary covariates, here slicing as coarsely as possible.

#
# Create dataset for survival analysis with time-dependent covariate
# Gill-Anderson model
#
x <- data.frame(onset=c(46, 32, 53, 76, 64, 43),
               case=c(1,1,1,0,0,0),
               ooph=c(NA, 30, 38, 50, NA, NA),
               ocp=c(1,1,0,0,1,0),
               parity=c(2,0,1,3,3,2),
               age.preg=c(28,NA,27,20,22,23))

make.dep <- function(onset, case, time.dep, covs=NULL) {
 if (is.null(n.time.dep <- ncol(time.dep))) {
   if (!is.null(time.dep)) {
     n.time.dep <- 1
     time.dep <- as.matrix(time.dep)
   }else{
     n.time.dep <- 0
     warning("No time dependent covariates")
   }
 }
 if (is.null(n.covs <- ncol(covs))) {
   if (!is.null(covs)) {
     n.covs <- 1
     covs <- as.matrix(covs)
   }else{
     n.covs <- 0
   }
 }
 ordered.t <- t(apply(cbind(onset,time.dep),1,sort,na.last=TRUE))
 tot.time.dep <- apply(ordered.t,1,function(x) sum(!is.na(x)))
 ordered.t <- cbind(rep(0, nrow(ordered.t)), ordered.t)
 npars <- 4+n.time.dep+n.covs
 nrecs <- sum(tot.time.dep)
 new.x <- as.data.frame(matrix(nr=nrecs, nc=npars))
 names(new.x) <- c("start", "stop", "event", names(time.dep),names(covs),"episode")
 this.rec<-0
 for(i in 1:length(onset)) {
   for(j in 1:tot.time.dep[i]) {
     this.rec <- this.rec+1
     new.x[this.rec,1] <- ordered.t[i, j]
     new.x[this.rec,2] <- ordered.t[i, j+1]
     new.x[this.rec,3] <- 0
     new.x[this.rec,4:(3+n.time.dep)] <- (ordered.t[i,j]>=time.dep[i,])
     missing <- is.na(new.x[this.rec,])
     new.x[this.rec,missing] <- 0
     if (n.covs>0) {
       new.x[this.rec, (4+n.time.dep):(4+n.time.dep+n.covs)] <- covs[i,]
     }
     new.x[this.rec, npars]<-paste(i,j,sep=".")
   }
   new.x[this.rec,3]<-case[i]
 }
 new.x
}

David Duffy.