R/PATHOGEN-PfMOI-SimBite.R

In smitdave/MASH: MASH (Modular Analysis and Simulation for Human Health)

#################################################################
#
#   MASH
#   R6-ified
#   SimBite module for PfMOI
#   David Smith, Hector Sanchez, Sean Wu
#   June 9, 2017
#
#################################################################


#' Initialize SimBite PfMOI Module
#'
#' Generate a list of parameters PfMOI_PAR in \code{\link{HumanPop}} and public methods in \code{\link{Human}}
#'
#' @param PfMOI_PAR optional parameter list generated by \code{\link{PfMOI.Parameters}}, if \code{NULL} this will be set to default values
#' @return Defines a field (list) PfMOI_PAR in \code{\link{HumanPop}} and public methods in \code{\link{Human}}
#' @examples
#' SimBitePfMOI.Setup()
#' @export
SimBitePfMOI.Setup <- function(PfMOI_PAR = NULL, overwrite = TRUE){

  message("Initializing PfMOI SimBite Module")

  ###################################################################
  # Simulated biting on 'Human' Class
  ###################################################################

  # probeHost_PfMOI
  Human$set(which = "public",name = "probeHost_PfMOI",
            value = probeHost_SimBitePfMOI,
            overwrite = overwrite
  )

  # add2Q_SimBitePfMOI
  Human$set(which = "public",name = "add2Q_SimBitePfSI",
            value = add2Q_SimBitePfMOI,
            overwrite = overwrite
  )

  # event_SimBitePfMOI
  Human$set(which = "public",name = "event_SimBitePfMOI",
            value = event_SimBitePfMOI,
            overwrite = overwrite
  )

  Human$set(which = "public",name = "SimBitePfMOI",
            value = SimBitePfMOI,
            overwrite = overwrite
  )

  ###################################################################
  # Tools to initialize simulated biting for 'HumanPop' class
  ###################################################################

  # queueBites
  HumanPop$set(which = "public",name = "queueBites_SimBitePfMOI",
               value = queueBites_SimBitePfMOI,
               overwrite = overwrite
  )

  HumanPop$set(which = "public",name = "queueVaccination_SimBitePfMOI",
               value = queueVaccination_SimBitePfMOI,
               overwrite = overwrite
  )

}


###################################################################
# PfMOI Simulated Host Probing
###################################################################

#' PfMOI \code{Human} Method: Simulated Host Probing
#'
#' This method is a filler for a host probing event in called in \code{\link{SimBitePfMOI}}.
#' If the bite is infectious, the method calls \code{\link{infectiousBite_PfMOI}}, otherwise does nothing.
#' This method is bound to \code{Human$probeHost_PfMOI()} after correct initialization with \code{\link{SimBitePfMOI.Setup}}.
#'
#' @param tBite time of bite
#' @param mosquitoPfMOI \code{\link{mosquitoPfMOI}} object passed from mosquito to human
probeHost_SimBitePfMOI <- function(tBite, mosquitoPfMOI){

  MOI = mosquitoPfMOI$get_MOI()

  if(MOI>0){
    N = self$get_PfMOI_PAR("MosyMaxI")

    infNum = max(MOI,N)
    for(i in 1:infNum){
      infNum = infNum - 1L
      PAR = mosquitoPfMOI$get_InfectionIx(i)
      self$infectiousBite_PfMOI(tBite, PAR)
    }
  }

}


###################################################################
# PfMOI SimBite methods for 'Human'
###################################################################

#' PfMOI SimBite \code{Human} Event: Add PfMOI Simulated Bite Event to Event Queue
#'
#' Simulate a PfMOI infectious bite.
#' This method is bound to \code{Human$add2Q_SimBitePfMOI()}
#' This method adds event \code{\link{event_SimBitePfMOI}} to the event queue.
#' This method is bound to \code{Human$add2Q_SimBitePfMOI()}
#'
#' @param tEvent time of bite
#' @param PAR write me!
add2Q_SimBitePfMOI <- function(tEvent, PAR = NULL){
  PAR = list()
  PAR$mosquitoPfMOI = mosquitoPfMOI(PfID = -1L, tInf = -1L, MOI = 1L, damID = -1L, sireID = -1L)
  private$EventQueue$addEvent2Q(event = self$event_SimBitePfMOI(tEvent = tEvent, PAR = PAR))
}


#' PfMOI SimBite \code{Human} Event: Generate PfMOI Simulated Bite Event
#'
#' Generate PfMOI Simulated Bite event to place in event queue.
#' This method is called from \code{\link{add2Q_SimBitePfMOI}}
#' This method is bound to \code{Human$event_SimBitePfMOI()}
#'  * tag: \code{\link{SimBitePfMOI}}
#' @md
#' @param tEvent time of bite
#' @param PAR named list
#'  * mosquitoPfSI: object of class \code{\link{mosquitoPfMOI}}
#' @md
event_SimBitePfMOI <- function(tEvent, PAR = NULL){
  list(tEvent = tEvent, PAR = PAR, tag = "SimBitePfMOI")
}


#' PfMOI SimBite \code{Human} Event: PfMOI Simulated Bite Event
#'
#' Simulate a PfMOI Simulated Bite. This calls \code{\link{probeHost_PfMOI}} to simulate host probing by an infectious mosquito.
#' This method is bound to \code{Human$SimBitePfMOI()}
#' @param tEvent time of bite
#' @param PAR named list
#'  * mosquitoPfSI: object of class \code{\link{mosquitoPfMOI}}
#' @md
SimBitePfMOI <- function(tEvent, PAR){
  self$probeHost_PfMOI(tEvent, PAR$mosquitoPfMOI)
}


###################################################################
# PfMOI SimBite methods for 'HumanPop'
###################################################################

#' PfMOI SimBite \code{HumanPop} Method: Queue SimBites for Population
#'
#' Add queued bite times to a population; bite times can be generated from \code{\link{SimBite_WaitingTime}}, \code{\link{SimBite_MeanBites}}
#' This method is bound to \code{HumanPop$queueBites_SimBitePfMOI()}
#' @param bites a list of length equal to number of humans where each element is a vector of biting times to add to queue with \code{\link{add2Q_SimBitePfMOI}}.
#' @export
queueBites_SimBitePfMOI <- function(bites){
  for(ixH in 1:self$nHumans){
    print(paste0("queueing simulated bites for human: ",ixH))
    for(tBite in bites[[ixH]]){
      private$pop[[ixH]]$add2Q_SimBitePfSI(tEvent = tBite)
    }
  }
}

#' PfMOI SimBite \code{HumanPop} Method: Queue Vaccination for Population
#'
#' Queue vaccination for a population, calling \code{\link{add2Q_pevaccinatePfMOI}}.
#' If \code{tTreat} is given, queue follow up treatment by calling \code{\link{add2Q_treatPfMOI}}.
#' This method is bound to \code{HumanPop$queueVaccination_SimBitePfMOI()}
#' @param tVaccine time of vaccination
#' @param tTreat time of follow up treatment (if \code{NULL} no treatment)
#' @param fracPop fraction of population that recieves vaccination
#' @export
queueVaccination_SimBitePfMOI <- function(tVaccine, tTreat = NULL, fracPop){
  for(ixH in 1:floor(fracPop*self$nHumans)){
    print(paste0("queueing vaccination for human: ",ixH))
    private$pop[[ixH]]$add2Q_pevaccinatePfMOI(tEvent = tVaccine)
    if(!is.null(tTreat)){
      private$pop[[ixH]]$add2Q_treatPfMOI(tEvent = tTreat)
    }
  }
}