#The exported methods for the results from

#predict from parameters simulations

#' @include study.R sfn.R eventPrediction_package.R

NULL

##' Class that contains results from the predict function of the \code{Study} object

##' 

##' Three of the slots of this class (grid, critical.data, predict.data) are data frames with

##' the number of events, recruitment details and cumulative time at risk at given time. See the 

##' vignette for details of these data frames and the \code{AnalysisResults} class in general.

##' 

##' @param critical.HR The critical hazard ratio at the time the critical number of events

##' is expected to occur or NA if single arm trial

##' @param critical.data A data frame with 1 row contain the time, event and recruitment details

##' for the time at which the critical number of events is expected to occur. 

##' The data frame has 0 rows if the expected time is > study duration or the trial had a single arm

##' @param critical.events.req the number of events (not rounded) required for the study's 

##' requested power and alpha or NA if single arm study

##' @param av.hr The average hazard ratio = the study hazard ratio if no lag, see the

##' vignette for how this is calculated if there is a lag. For single arm studies this is NA.

##' @param grid A data frame with rows contain the time, event and recruitment details

##' at times used to plot the event curves

##' @param predict.data A data frame with rows contain the time, event and recruitment details

##' at times / number of events requested to predicted by the user when calling the predict function.

##' @param study The \code{Study} object used to calculate the results

##' @param list The \code{Sfn} objects containing the survival functions for the results. 

##' @export

setClass( "AnalysisResults",

          slots= c( critical.HR = "numeric", critical.data="data.frame",

                    critical.events.req = "numeric", av.hr = "numeric", 

                    grid="data.frame",predict.data="data.frame",study="Study",

                    sfns="list") ) 

# Constructor for AnalysisResults class

# should not be called by users

# @param ... parameters to be passed to the new("AnalysisResults",...) function

# @return An object of type AnalysisResults

AnalysisResults <- function(...){

  new("AnalysisResults",...)

}

##' @name show

##' @rdname show-methods

##' @aliases show,AnalysisResults-method

##' @export

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

  function(object) {

    show(object@study)

    if(!is.na(object@av.hr)){

      cat(paste("Average HR",round(object@av.hr,digits=2),"\n"))

    }

    if(nrow(object@predict.data)>0){

      cat("Predicted Values:\n")

      print(object@predict.data)

    }

    if(nrow(object@critical.data)>0){

      cat("Critical Number of Events:\n")

      print(object@critical.data)

    }

    if(!is.na(object@critical.HR)){

      cat(paste("Critical HR",round(object@critical.HR,digits=2),"\n"))

    }

  }

)

##' @name summary 

##' @param options A \code{DisplayOptions} object

##' @rdname summary-methods

##' @aliases summary,AnalysisResults-method

##' @export

setMethod('summary',signature(object="AnalysisResults") ,

  function(object, options = DisplayOptions()) {

     cat(getFromParameterText(object,options))              

  }          

)

##' @name LatexSurvivalFn

##' @rdname LatexSurvivalFn-methods

##' @aliases LatexSurvivalFn,AnalysisResults-method

##' @param decimalplaces The number of decimal places to output for the 

##' rate and shape parameters

##' @export

setMethod("LatexSurvivalFn",

    signature("AnalysisResults"),

    function(results,decimalplaces=3){

      shape <- c("a","\\alpha") 

      if(!isSingleArm(results@study)){

        ans <- "Control Arm:\n"

        lambda <- c("\\lambda_{c1}","\\lambda_{c2}")

      }

      else{

        ans <- ''

        lambda <- c("\\lambda_1","\\lambda_2")

      }

      lambda <- c(lambda,"\\lambda_d") 

      ans <- paste(ans,LatexSurvivalFn(results@sfns[[1]],decimalplaces=decimalplaces,lambda=lambda,shape=shape))

      if(!isSingleArm(results@study)){

        lambda <- c("\\lambda_{e1}","\\lambda_{e2}","\\lambda_d")

        ans <- paste(ans,"Experimental Arm:\n")

        ans <- paste(ans,LatexSurvivalFn(results@sfns[[2]],decimalplaces=decimalplaces,lambda=lambda,shape=shape))

      }

      if(results@sfns[[1]]@dropout.lambda!=0){

        ans <- paste(ans,"Dropout rate given by \\( \\lambda_d \\)")

        if(results@sfns[[1]]@dropout.shape!=1){

          ans <- paste(ans,"and shape given by \\( \\alpha \\)")

        }

        ans <- paste(ans,".",sep="")

      }      

      ans

    }

)