--- a
+++ b/R/longlagSettings.R
@@ -0,0 +1,119 @@
+# This file contains the class and its constructor which
+# determine how the simulation (from data) procedure deals with subjects
+# who are censored a long time before the analysis date.
+
+##' Class which determines how the simulation (from data) 
+##' procedure deals with subjects
+##' who are censored a long time before the analysis date.
+##' @slot analysis.date The date the event prediction is performed on. If \code{as.Date(NA)}
+##' then the latest censor/event date from the data set will be used as the analysis.date
+##' @slot ndays All subjects who were censored more than \code{ndays} before
+##' \code{analysis.date} will be changed
+##' @slot toWithdraw Logical. If TRUE then the selected subjects will be withdrawn
+##' rather than be censored. If FALSE, their censor date is replaced by \code{analysis.date}
+##' @slot visitschedule number of days between visits for pfs data. If non-zero and 
+##' \code{toWithdraw} is TRUE then the selectedsubjects are censored on the date their
+##' latest visit would have been. See vignette for further details
+##' @slot text The text to be disaplyed when printing the LongLagSettings 
+##' @seealso \code{\link{show,LongLagSettings-method}}
+##' @export
+setClass("LongLagSettings", 
+         slots= list(analysis.date="Date",
+                     ndays="numeric",
+                     toWithdraw="logical",
+                     visitschedule="numeric",
+                     text="character")
+)
+
+
+
+##' @name show
+##' @rdname show-methods
+##' @aliases show,LongLagSettings-method
+##' @export
+setMethod("show", signature(object="LongLagSettings"),
+  function(object) {
+    cat(object@text)
+  }
+)          
+
+
+##' Constructor for \code{LongLagSettings} object
+##' @param analysis.date The date the event prediction is performed on. If \code{as.Date(NA)}
+##' then the latest censor/event date from the data set will be used as the analysis.date
+##' @param ndays All subjects who were censored more than \code{ndays} before
+##' \code{analysis.date} will be changed
+##' @param toWithdraw Logical. If TRUE then the selected subjects will be withdrawn
+##' rather than be censored. If FALSE, their censor date is replaced by \code{analysis.date}
+##' @param visitschedule number of days between visits for pfs data. If non-zero and 
+##' \code{toWithdraw} is TRUE then the selectedsubjects are censored on the date their
+##' latest visit would have been. See vignette for further details
+##' @return A \code{LongLagSettings} object
+##' @export
+LongLagSettings <- function(analysis.date=as.Date(NA),ndays,toWithdraw,visitschedule=0){
+   
+  if(visitschedule < 0 || length(visitschedule) > 1) stop("invalid visit schedule")
+  if(ndays < 0 || length(ndays) > 1) stop("invalid ndays")
+  
+  analysis.date <- FixDates(analysis.date)
+  
+  
+  text <- if(ndays!=0) paste("Subjects with censor date more than",ndays,"days before",analysis.date)
+          else text <- paste("Subjects with censor date before",analysis.date)
+  
+  
+  if(toWithdraw){
+    text <- paste(text, "are withdrawn.")
+  }
+  else{
+    if(visitschedule==0){
+      text <- paste(text," are now censored on ",analysis.date,".",sep="")
+    }
+    else{
+      text <- paste(text," are now censored at the last expected visit date before ",analysis.date,
+                    ", with a visit schedule of ",visitschedule," days." ,sep="")
+    }
+  }
+  
+  new("LongLagSettings",analysis.date=analysis.date,
+      ndays=ndays,toWithdraw=toWithdraw,visitschedule=visitschedule,
+      text=text)
+  
+}
+
+
+# Function to handle subjects who are
+# censored a long time before the analysis date.
+# 
+# @param indat A data frame e.g. EventData@@subject.data
+# @param longlagsettings A \code{longlagsettings} object which controls 
+# how subjects who are censored a long time before the analysis date
+# are handled. 
+# @return The data frame with the \code{longlagsettings} applied 
+DealWithReportingLag <- function(indat,longlagsettings){
+  
+  if(is.null(longlagsettings)){
+    return(indat)
+  }
+  
+  
+  last.date <- LastDate(indat)
+  analysis.date  <- if(is.na(longlagsettings@analysis.date)) as.Date(max(last.date),origin="1970-01-01",na.rm=TRUE) 
+                    else longlagsettings@analysis.date 
+    
+  idx.to.cons <- indat$censored.at.follow.up==0  & indat$withdrawn==0  &  indat$has.event == 0 & 
+                (last.date < (analysis.date - longlagsettings@ndays))
+    
+  if(longlagsettings@toWithdraw){
+    indat$withdrawn[idx.to.cons] <- 1 #time of withdrawal is unchanged
+    return(indat)
+  }
+  
+  indat$time[idx.to.cons] <- as.numeric(analysis.date - indat$rand.date[idx.to.cons]+1)
+  if(longlagsettings@visitschedule != 0){
+    indat$time[idx.to.cons] <- 
+      1+floor((indat$time[idx.to.cons]-1)/longlagsettings@visitschedule) * longlagsettings@visitschedule    
+  }
+  indat
+  
+}
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