#In predict from parameters it is possible to include a 

#lag in the study definition when calculating event times

#the code associated with this lag is contained here.

#' @include ctrlSpec.R

NULL

##' Parameter settings for when including a lagged effect. 

##' 

##' Note the lambda and HR in the \code{Study} class will be used

##' for time > T

##' @slot Lag.T Lagtime (T)

##' @slot ctrlSpec Control median specification for time period [0,T]

##' @slot L.HazardRatio Hazard for time period [0,T]

##' @seealso \code{\link{show,LagEffect-method}}

##' @export

setClass( "LagEffect", 

          slots=c( 

            Lag.T = "numeric",

            ctrlSpec = "CtrlSpec",

            L.HazardRatio = "numeric"

          ), prototype = prototype( 

            Lag.T = 0,

            ctrlSpec = CtrlSpecfromMedian(as.numeric(NA)),

            L.HazardRatio = as.numeric(NA)

          ),

          validity = function(object){

            ans <- ""

            if(object@Lag.T < 0) ans <- paste(ans,"Invalid Lag.T")

            if(!is.na(object@L.HazardRatio) && (object@L.HazardRatio < 0 || object@L.HazardRatio > 1))

              ans <- paste(ans,"Hazard Ratio must be in [0,1]")

            if(object@Lag.T!=0){

              if(is.na(object@ctrlSpec@median)){

                ans <- paste(ans,"Invalid LagEffect") 

              } 

            }

            else{

              if(!is.na(object@ctrlSpec@median) || !is.na(object@L.HazardRatio)){

                ans <- paste(ans,"Invalid nullLagEffect") 

              } 

            }

            if(ans=="") return(TRUE)

            ans

          }

)

##' @name show

##' @rdname show-methods

##' @aliases show,LagEffect-method

##' @export

setMethod("show", signature(object="LagEffect"), 

  function(object) {

    if(isNullLag(object)){

      cat("No Lag\n")

    }

    else{

      cat(paste(object@Lag.T,"months of lag during which\n"))

      cat(paste("control group survival",object@ctrlSpec@text,"months\n"))

      if(!is.na(object@L.HazardRatio)){

        cat(paste("and the hazard ratio is",object@L.HazardRatio,"\n"))

      }

    }

  }

)

##' LagEffect constructor

##'

##' Note the lambda and HR in the study class will be used

##' for time > T

##' @param Lag.T Lagtime (T)

##' @param L.Ctr.median Control median for time period [0,T]

##' @param L.HazardRatio Hazard for time period [0,T]

##' @return A LagEffect object

##' @export

LagEffect <- function(Lag.T,L.Ctr.median=as.numeric(NA),L.HazardRatio=as.numeric(NA)){

  ctrlSpec <- CtrlSpecfromMedian(L.Ctr.median)

  new("LagEffect",Lag.T=Lag.T,ctrlSpec=ctrlSpec,L.HazardRatio=L.HazardRatio)

}

##' Create a LagEffect object with no lag

##' @return A LagEffect object for which \code{isNullLag()} is TRUE

##' @export

NullLag <- function(){

  NAnumeric <- as.numeric(NA)

  LagEffect(Lag.T=0,L.Ctr.median=NAnumeric,L.HazardRatio=NAnumeric)

}

##' Function to check whether Lag is a null lag

##' 

##' This checks whether the Lag.T slot is 0 

##'    

##' @name isNullLag

##' @docType methods

##' @rdname isNullLag-methods

##' @param Lag A LagEffect object

##' @return TRUE if null lag, FALSE otherwise

##' @export

setGeneric( "isNullLag",

            def=function( Lag )

              standardGeneric( "isNullLag" ) )

##' @rdname isNullLag-methods

##' @aliases isNullLag,LagEffect-method

##' @name isNullLag

##' @export

setMethod( "isNullLag",signature=(Lag="LagEffect"), 

  function( Lag ) {

    Lag@Lag.T==0

})