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# Class to store information regarding time points
#
# Class is not exported and is for internal convenience only
#
# @slot timePoints A numeric vector; the timepoints used in the analysis
#
# @slot timeDiff A numeric vector; the time differences between the timepoints
#
# @slot tau A numeric object; maximum time
#
# Getters
# .TimePoints(object, ...) {new; defined}
# .NTimes(object, ...) {new; defined}
# .Tau(object, ...) {new; defined}
# .TimeDiff(object, ...) {new; defined}
#
# Methods
# .TimeInfoAsList(object, ...) {new; defined}
#
# Functions
# .timeInfo(timePoints, nTimes, response)
#
setClass(Class = "TimeInfo",
slots = c(timePoints = "numeric",
timeDiff = "numeric",
tau = "numeric"))
### Getters
#-------------------------------------------------------------------------------
# Method to retrieve timepoints
#-------------------------------------------------------------------------------
# Method returns the vector of timepoints used for the analysis
#-------------------------------------------------------------------------------
setGeneric(name = ".TimePoints",
def = function(object, ...) { standardGeneric(".TimePoints") })
setMethod(f = ".TimePoints",
signature = c(object = "ANY"),
definition = function(object, ...) { stop("not allowed") })
setMethod(f = ".TimePoints",
signature = c(object = "TimeInfo"),
definition = function(object, ...) { return( object@timePoints ) })
#-------------------------------------------------------------------------------
# Method to retrieve the number of timepoints
#-------------------------------------------------------------------------------
# Method returns a numeric
#-------------------------------------------------------------------------------
setGeneric(name = ".NTimes",
def = function(object, ...) { standardGeneric(".NTimes") })
setMethod(f = ".NTimes",
signature = c(object = "ANY"),
definition = function(object, ...) { stop("not allowed") })
setMethod(f = ".NTimes",
signature = c(object = "TimeInfo"),
definition = function(object, ...) {
return( length(x = object@timePoints) )
})
#-------------------------------------------------------------------------------
# Method to retrieve the maximum timepoint
#-------------------------------------------------------------------------------
# Method returns a numeric
#-------------------------------------------------------------------------------
setGeneric(name = ".Tau",
def = function(object, ...) { standardGeneric(".Tau") })
setMethod(f = ".Tau",
signature = c(object = "ANY"),
definition = function(object, ...) { stop("not allowed") })
setMethod(f = ".Tau",
signature = c(object = "TimeInfo"),
definition = function(object, ...) { return( object@tau ) })
#-------------------------------------------------------------------------------
# Method to retrieve the difference in timepoints
#-------------------------------------------------------------------------------
# Method returns the vector of the differences in timepoints used for the analysis
#-------------------------------------------------------------------------------
setGeneric(name = ".TimeDiff",
def = function(object, ...) { standardGeneric(".TimeDiff") })
setMethod(f = ".TimeDiff",
signature = c(object = "ANY"),
definition = function(object, ...) { stop("not allowed") })
setMethod(f = ".TimeDiff",
signature = c(object = "TimeInfo"),
definition = function(object, ...) { return( object@timeDiff ) })
#-------------------------------------------------------------------------------
# Method to retrieve timepoints for printing
#-------------------------------------------------------------------------------
# Method returns a list containing 1 element "timePoints" containing the
# vector of timepoints used for the analysis
#-------------------------------------------------------------------------------
setGeneric(name = ".TimeInfoAsList",
def = function(object, ...) {
standardGeneric(".TimeInfoAsList")
})
setMethod(f = ".TimeInfoAsList",
signature = c(object = "ANY"),
definition = function(object, ...) { stop("not allowed") })
setMethod(f = ".TimeInfoAsList",
signature = c(object = "TimeInfo"),
definition = function(object, ...) {
return( list("timePoints" = object@timePoints) )
})
#-------------------------------------------------------------------------------
# Function to verify inputs and create a TimeInfo object
#-------------------------------------------------------------------------------
# Function returns a TimeInfo object
#-------------------------------------------------------------------------------
#' @include VerifyTimePoints.R
.timeInfo <- function(timePoints, nTimes, tau, response) {
# ensure that timePoints and nTimes are appropriate. Methods return a vector
# of unique time points that are sorted in ascending order.
timePoints <- .VerifyTimePoints(timePoints = timePoints,
tau = tau,
nTimes = nTimes,
response = response)
tau <- timePoints$tau
timePoints <- timePoints$timePoints
# the total number of times points
nTimes <- length(x = timePoints)
# deltaT; T_{i} - T_{i-1} i = 1:nTimes with T_0 = 0
# timeDiff <- c(timePoints[-1L] - timePoints[-nTimes], 0)
# this is used for the truncated mean calculation in which it is
# assumed that all t > tau equals tau to t(nTimes+1)-t(nTimes) = 0
timeDiff <- timePoints[-1L] - timePoints[-nTimes]
timeDiff[nTimes] <- 0.0
return( new(Class = "TimeInfo",
"tau" = tau,
"timePoints" = timePoints,
"timeDiff" = timeDiff) )
}
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