getCensoringWeights <- function(formula,
data,
times,
cens.model,
influence.curve=FALSE,
censoring.save.memory,
verbose){
data <- copy(data)
if((cens.model != "KaplanMeier")){
if (length(attr(terms(formula),"factors"))==0){
cens.model <- "marginal"
}
}
else{
cens.model <- "marginal"
}
switch(cens.model,
"marginal"={
sFormula <- update(formula,"Surv(riskRegression_time,riskRegression_status)~1")
fit <- prodlim::prodlim(sFormula,data=data,reverse=TRUE,bandwidth="smooth")
IPCW.times <- predict(fit,newdata=data,times=times,level.chaos=1,mode="matrix",type="surv")
IPCW.subject.times <- prodlim::predictSurvIndividual(fit,lag=1)
out <- list(IPCW.times=IPCW.times,
IPCW.subject.times=IPCW.subject.times,
method=cens.model,IC.data=NULL)
if (influence.curve==TRUE){
# Do not yet calculate IF for Nelson-AAlen
# this happens later
out <- c(out,list(IC=NULL))
# out <- c(out,
# list(IC=IC_Nelson_Aalen_cens_time(time=data$riskRegression_time,status=data$riskRegression_status)))
## list(IC=data[,getInfluenceCurve.NelsonAalen(time=riskRegression_time,riskRegression_status=riskRegression_status)]))
}
out
},"cox"={
event = event2 = NULL
sFormula <- update(formula,"Surv(riskRegression_time,riskRegression_status == 0)~.")
tFormula <- update(formula,"Surv(riskRegression_time,riskRegression_status != 0)~.")
wdata <- copy(data)
if (length(unique(wdata[["event"]])) > 2){
wdata[,event2 := as.numeric(event)]
wdata[riskRegression_status == 0,event2 := 0]
wdata[,event2 := NULL]
}
# else {
# fitCSC <- NULL
# }
# wdata[,riskRegression_status:=1-riskRegression_status]
Y <- data[["riskRegression_time"]]
riskRegression_status <- data[["riskRegression_status"]]
## fit Cox model for censoring times
args <- list(x=TRUE,y=TRUE,eps=0.000001,linear.predictors=TRUE)
args$surv <- TRUE
fit <- do.call(rms::cph,c(list(sFormula,data=wdata),args))
if (length(times)==1){
IPCW.times <- matrix(rms::survest(fit,newdata=wdata,times=times,se.fit=FALSE)$surv,ncol=1)
} else{
IPCW.times <- rms::survest(fit,newdata=wdata,times=times,se.fit=FALSE)$surv
}
## only one per subject, so must be a flat vector
## FIXME: really need subject.times only where events occur before times ???
# times.data.minus <- c(0,Y[-length(Y)])
incrementsOfTime <- diff(sort(Y))
minimumIncrement <- min(incrementsOfTime[incrementsOfTime > 0]) #need > 0 in case of ties
IPCW.subject.times <- as.numeric(rms::survest(fit,newdata=wdata,times=Y-minimumIncrement/2,what='parallel',se.fit=FALSE)) #Y-minimumIncrement/2
# subject.times <- Y[(((Y<=max(times))*riskRegression_status)==1)]
out <- list(IPCW.times=IPCW.times,IPCW.subject.times=IPCW.subject.times,method=cens.model)
if (influence.curve==TRUE){
TiMinus = Y-minimumIncrement/2
if (!censoring.save.memory){
## IC is an array with dimension (nlearn, times, newdata)
## IC_G(t,z;x_k)
IC.subject=predictCox(fit, iid = TRUE,
newdata = wdata,
times = TiMinus,
diag=TRUE,
type = "cumhazard")$cumhazard.iid*NROW(data) ## we want the influence function survival.iid*n
IC.times=predictCox(fit, iid = TRUE,
newdata = wdata,
times = times,
type = "cumhazard")$cumhazard.iid*NROW(data)
IC.weights <- list()
for (t.ind in 1:length(times)){
N <- length(Y)
ic.weights <- matrix(0,N,N) ## (i,j)'th entry is f_j(tilde{T}_i-;X_i)/G(tilde{T}_i|X_i) when delta_i != 0 and time_i <= tau; otherwise it is f_j(tau-;X_i)/G(tau | X_i)
# k=0 ## counts subject-times with event before t
for (i in 1:N){
if (Y[i]<=times[t.ind] && riskRegression_status[i] != 0){ ## min(T,C)<=t, note that (residuals==0) => (status==0)
# k=k+1
ic.weights[i,] <- IC.subject[,1,i]
}else if (Y[i] > times[t.ind]){## min(T,C)>t
ic.weights[i,] <- IC.times[,t.ind,i]
}
}
IC.weights[[t.ind]] <- ic.weights
}
IC <- list(censoring.save.memory = censoring.save.memory, IC.weights = IC.weights)
}
else {
IC <- list(censoring.save.memory = censoring.save.memory,
fit=fit,
wdata=wdata,
TiMinus = TiMinus)
}
out <- c(out,list(IC=IC))
}
}, "discrete"={
stop("Use stratification with Cox instead. ")
},
{
if (verbose>0)warning("Using other models (than Cox and Kaplan-Meier) for getting the censoring weights is under construction. ")
vv <- all.vars(formula(delete.response(terms(formula))))
new.formula<-as.formula(paste0("Surv(riskRegression_time,riskRegression_status)",paste0("~",paste0(paste(vv,collapse = "+")))))
wdata <- copy(data)
wdata[,riskRegression_status:=1-riskRegression_status]
input <- list(formula=new.formula,data=wdata)
if (verbose>1)message("Fitting censoring model to data ...", appendLF = FALSE)
fit <- do.call(cens.model,input)
if (verbose>1)message("done!")
if (influence.curve){
if (is.null(data[["event"]])){
new.formula<-as.formula(paste0("Surv(riskRegression_time,riskRegression_status==1)",paste0("~",paste0(paste(vv,collapse = "+")))))
}
else {
new.formula<-as.formula(paste0("Surv(riskRegression_time,riskRegression_event==1)",paste0("~",paste0(paste(vv,collapse = "+")))))
}
input <- list(formula=new.formula,data=wdata)
if (verbose>0)message("Fitting time model to data ...", appendLF = FALSE)
fit.time <- do.call(cens.model,input)
if (verbose>0)message("done!")
}
else {
fit.time <- NULL
}
# IC.data <- list(Stimes = diag(1-predictRisk(fit.time,wdata,wdata$time,1)), Gtimes=diag(1-predictRisk(fit,wdata,wdata$time,1)))
IC.data <- list(fit.time=fit.time,fit.cens=fit,wdata=wdata)
# fit<-Hal9001(new.formula,wdata)
# times.data.minus <- c(0,wdata$time[-length(wdata$time)]) #have to compute the weights for T_i minus not just Ti
IPCW.subject.times <- diag(1-predictRisk(fit,wdata,wdata$time,1)) #computational problem with predictRisk
IPCW.times <- 1-predictRisk(fit,wdata,times,1)
out <- list(
IPCW.times=IPCW.times,
IPCW.subject.times=IPCW.subject.times,
method=cens.model,
IC.data=IC.data)
})
out$dim <- ifelse(cens.model=="KaplanMeier" || cens.model == "marginal",0,1)
out
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.