#Contains the functions for SingleSimDetails class

#part of the predict from data part of the package

#see class definition below

##' Class containing the subject level event data

##' for each simulation

##' 

##' A class which contains the recruitment times

##' event times and event types of all subjects and all

##' simulations for a predict from data simulation. 

##' This class is created when performing simulation and does not 

##' need to be constructed manually 

##'  

##' @slot event.type A matrix (1 row per subject, 1 column per simulation) of

##' the reason subjects leave trial. 0 is have event, 1 is drop out and 2 is drop out due to follow up

##' @slot event.times A matrix (1 row per subject, 1 column per simulation) of

##' dates (as numeric) subjects leave the trial

##' @slot rec.times A matrix (1 row per subject, 1 column per simulation) of

##' recruitment dates (as numeric). 

##' Therefore event.times[i,j] - rec.times[i,j] + 1 is the time on study for

##' subject i in simulation j

##' @export

setClass("SingleSimDetails", 

         slots=list(

           event.type="matrix",

           event.times="matrix",

           rec.times="matrix"

         )

) 

# Constructor of SingleSimDetails object

# @param event.type A matrix (1 row per subject, 1 column per simulation) of

# the reason subjects leave trial. 0 is have event, 1 is drop out and 2 is censored due to 

# completing follow up period

# @param event.times A matrix (1 row per subject, 1 column per simulation) of

# dates (as numeric) subjects leave the trial

# @param rec.times A matrix (1 row per subject, 1 column per simulation) of

# recruitment dates (as numeric). 

# Therefore event.times[i,j] - rec.times[i,j] + 1 is the time on study for

# subject i in simulation j

SingleSimDetails <- function(event.type,event.times,rec.times){

  new("SingleSimDetails",event.type=event.type,

      event.times=event.times,rec.times=rec.times)

}

##' @name CalculateDaysAtRisk

##' @rdname CalculateDaysAtRisk-methods  

##' @aliases CalculateDaysAtRisk,SingleSimDetails-method

##' @export

setMethod("CalculateDaysAtRisk","SingleSimDetails",

 function(object,times){

  unlist(lapply(times,function(x){

    cutoff <- as.numeric(x,origin="1970-01-01")

    time.at.risk <-  matrix(pmax(0, pmin(cutoff,object@event.times) - object@rec.times + 1),

                            ncol=ncol(object@event.times))

    median(apply(time.at.risk,2,sum))

  }))

})