R/RcppR6.R

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

## Generated by RcppR6: do not edit by hand
## Version: 0.2.4
## Hash: b68d4f7343991d9679244b27c138c288

##' @importFrom Rcpp evalCpp
##' @importFrom R6 R6Class
##' @useDynLib MASH
NULL

##' A class for queueing human events. Header file defined [here](https://github.com/slwu89/RcppQueues/blob/master/inst/include/RcppQueues/HumanEventQ.hpp) and `RcppR6` export handled [here](https://github.com/slwu89/RcppQueues/blob/master/inst/HumanEventQ.yml). Bound to \code{Human$EventQueue} in class \code{\link{Human}}
##' @title Human Event Queue
##' @param initQ reserve memory for \code{initQ} number of events
##' @section Methods:
##'   * firstEvent: return first event in queue as named R list
##'   * firstTime: return 'tEvent' slot in first event in queue
##'   * rmFirstEventFromQ: remove first event in queue and update \code{queueN}
##'   * rmTagFromQ(const std::string &tag): remove all events with certain tag from queue and update \code{queueN}
##'   * get_queueN: return \code{queueN}
##'   * get_EventQ: return entire \code{EventQ} as R list
##'   * addEvent2Q(Rcpp::List event): add a list to the \code{EventQ} in correct time order and update \code{queueN}
##' @section Fields:
##'   * EventQ: \code{std::vector<Rcpp::List>}
##'   * queueN: integer value of size of queue.
##' @md
##' @export
`HumanEventQ` <- function(initQ=100) {
  HumanEventQ__ctor(initQ)
}
.R6_HumanEventQ <-
  R6::R6Class(
    "HumanEventQ",
    inherit=,
    portable=TRUE,
    public=list(
      .ptr=NULL,
      initialize = function(ptr) {
        self$.ptr <- ptr
      },
      firstEvent = function() {
        HumanEventQ__firstEvent(self)
      },
      firstTime = function() {
        HumanEventQ__firstTime(self)
      },
      rmFirstEventFromQ = function() {
        HumanEventQ__rmFirstEventFromQ(self)
      },
      rmTagFromQ = function(tag) {
        HumanEventQ__rmTagFromQ(self, tag)
      },
      get_queueN = function() {
        HumanEventQ__get_queueN(self)
      },
      addEvent2Q = function(event) {
        HumanEventQ__addEvent2Q(self, event)
      },
      get_EventQ = function() {
        HumanEventQ__get_EventQ(self)
      }),
    active=list())

##' A class for recording generic histories comprised of event times (double precision floats) and events (strings).
##' @title Generic History
##' @param N reserve memory for \code{N} number of events
##' @section Methods:
##'   * track_history: record an event from arguments 'tEvent' (double) and 'event' (string)
##'   * get_history: return history as a named list
##' @section Fields:
##'   * eventT: \code{std::vector<double>}
##'   * events: \code{std::vector<std::string>}
##' @md
##' @export
`HistoryGeneric` <- function(N=100) {
  HistoryGeneric__ctor(N)
}
.R6_HistoryGeneric <-
  R6::R6Class(
    "HistoryGeneric",
    inherit=,
    portable=TRUE,
    public=list(
      .ptr=NULL,
      initialize = function(ptr) {
        self$.ptr <- ptr
      },
      track_history = function(tEvent, event) {
        HistoryGeneric__track_history(self, tEvent, event)
      },
      get_history = function() {
        HistoryGeneric__get_history(self)
      }),
    active=list())

##' A class for recording travel histories comprised of event times (double precision floats) and locations (integers).
##' @title Travel History
##' @param N reserve memory for \code{N} number of events
##' @section Methods:
##'   * track_travel: record an event from arguments 'tEvent' (double) and 'event' (string)
##'   * get_travelHistory: return history as a named list
##' @section Fields:
##'   * tTravel: \code{std::vector<double>}
##'   * locationH: \code{std::vector<int>}
##' @md
##' @export
`HistoryTravel` <- function(N=100) {
  HistoryTravel__ctor(N)
}
.R6_HistoryTravel <-
  R6::R6Class(
    "HistoryTravel",
    inherit=,
    portable=TRUE,
    public=list(
      .ptr=NULL,
      initialize = function(ptr) {
        self$.ptr <- ptr
      },
      track_travel = function(tTravel, locationH) {
        HistoryTravel__track_travel(self, tTravel, locationH)
      },
      get_travelHistory = function() {
        HistoryTravel__get_travelHistory(self)
      }),
    active=list())

##' A class for storing parameters and state variables of human-stage PfSI infections.
##' @title PfSI Human Stage Pathogen Class
##' @param PfID_init PfID derived from the tile level PfPedigree
##' @param tInf_init time of current infection (successful mosquito to human transmission event)
##' @param b_init infected mosquito to human transmission efficiency
##' @param c_init infected human to mosquito transmission efficiency
##' @param damID_init female gametocyte 'mother'
##' @param sireID_init male gametocyte 'father'
##' @param infected_init infection status
##' @param chemoprophylaxis_init chemoprophylaxis protection status
##' @section Methods:
##'   * get_PfID:
##'   * push_PfID:
##'   * get_tInf:
##'   * push_tInf:
##'   * get_b:
##'   * set_b:
##'   * get_c:
##'   * set_c:
##'   * get_damID:
##'   * push_damID:
##'   * get_sireID:
##'   * push_sireID:
##'   * get_infected:
##'   * set_infected:
##'   * get_chemoprophylaxis:
##'   * set_chemoprophylaxis:
##' @section Fields:
##'   * a field: talk about me
##' @md
##' @export
`humanPfSI` <- function(PfID_init, tInf_init=-1, b_init=0.55, c_init=0.15, damID_init=-1, sireID_init=-1, infected_init=FALSE, chemoprophylaxis_init=FALSE) {
  humanPfSI__ctor(PfID_init, tInf_init, b_init, c_init, damID_init, sireID_init, infected_init, chemoprophylaxis_init)
}
.R6_humanPfSI <-
  R6::R6Class(
    "humanPfSI",
    inherit=,
    portable=TRUE,
    public=list(
      .ptr=NULL,
      initialize = function(ptr) {
        self$.ptr <- ptr
      },
      get_PfID = function() {
        humanPfSI__get_PfID(self)
      },
      push_PfID = function(PfID_new) {
        humanPfSI__push_PfID(self, PfID_new)
      },
      back_PfID = function() {
        humanPfSI__back_PfID(self)
      },
      get_tInf = function() {
        humanPfSI__get_tInf(self)
      },
      push_tInf = function(tInf_new) {
        humanPfSI__push_tInf(self, tInf_new)
      },
      get_b = function() {
        humanPfSI__get_b(self)
      },
      set_b = function(b_new) {
        humanPfSI__set_b(self, b_new)
      },
      get_c = function() {
        humanPfSI__get_c(self)
      },
      set_c = function(c_new) {
        humanPfSI__set_c(self, c_new)
      },
      get_damID = function() {
        humanPfSI__get_damID(self)
      },
      push_damID = function(damID_new) {
        humanPfSI__push_damID(self, damID_new)
      },
      get_sireID = function() {
        humanPfSI__get_sireID(self)
      },
      push_sireID = function(sireID_new) {
        humanPfSI__push_sireID(self, sireID_new)
      },
      get_infected = function() {
        humanPfSI__get_infected(self)
      },
      set_infected = function(infected_new) {
        humanPfSI__set_infected(self, infected_new)
      },
      get_chemoprophylaxis = function() {
        humanPfSI__get_chemoprophylaxis(self)
      },
      set_chemoprophylaxis = function(chemoprophylaxis_new) {
        humanPfSI__set_chemoprophylaxis(self, chemoprophylaxis_new)
      },
      track_history = function(tEvent, event) {
        humanPfSI__track_history(self, tEvent, event)
      },
      get_history = function() {
        humanPfSI__get_history(self)
      }),
    active=list())

##' A class for storing parameters and state variables of mosquito-stage PfSI infections.
##' @title PfSI Mosquito Stage Pathogen Class
##' @param PfID_init PfID derived from the infecting human's gametocytes
##' @param tInf_init time of current infection (successful human to mosquito transmission event)
##' @param damID_init female gametocyte 'mother'
##' @param sireID_init male gametocyte 'father'
##' @param infected_init infection status
##' @section Methods:
##'   * get_PfID:
##'   * set_PfID:
##'   * get_tInf:
##'   * set_tInf:
##'   * get_damID:
##'   * set_damID:
##'   * get_sireID:
##'   * set_sireID:
##'   * get_infected:
##'   * set_infected:
##' @section Fields:
##'   * a field: talk about me
##' @md
##' @export
`mosquitoPfSI` <- function(PfID_init, tInf_init=-1, damID_init=-1, sireID_init=-1, infected_init=FALSE) {
  mosquitoPfSI__ctor(PfID_init, tInf_init, damID_init, sireID_init, infected_init)
}
.R6_mosquitoPfSI <-
  R6::R6Class(
    "mosquitoPfSI",
    inherit=,
    portable=TRUE,
    public=list(
      .ptr=NULL,
      initialize = function(ptr) {
        self$.ptr <- ptr
      },
      get_PfID = function() {
        mosquitoPfSI__get_PfID(self)
      },
      set_PfID = function(PfID_new) {
        mosquitoPfSI__set_PfID(self, PfID_new)
      },
      get_tInf = function() {
        mosquitoPfSI__get_tInf(self)
      },
      set_tInf = function(tInf_new) {
        mosquitoPfSI__set_tInf(self, tInf_new)
      },
      get_damID = function() {
        mosquitoPfSI__get_damID(self)
      },
      set_damID = function(damID_new) {
        mosquitoPfSI__set_damID(self, damID_new)
      },
      get_sireID = function() {
        mosquitoPfSI__get_sireID(self)
      },
      set_sireID = function(sireID_new) {
        mosquitoPfSI__set_sireID(self, sireID_new)
      },
      get_infected = function() {
        mosquitoPfSI__get_infected(self)
      },
      set_infected = function(infected_new) {
        mosquitoPfSI__set_infected(self, infected_new)
      }),
    active=list())

##' A class for storing parameters and state variables of human-stage PfMOI infections.
##' @title PfMOI Human Stage Pathogen Class
##' @param PfID_init PfID derived from the tile level PfPedigree
##' @param tInf_init initial time of current infection (successful mosquito to human transmission event)
##' @param MOI_init initial multiplicity of infection
##' @param damID_init initial female gametocyte 'mother'
##' @param sireID_init initial male gametocyte 'father'
##' @param chemoprophylaxis_init chemoprophylaxis protection status
##' @section Methods:
##'   * get_PfID:
##'   * push_PfID:
##'   * get_tInf:
##'   * push_tInf:
##'   * get_MOI:
##'   * set_MOI:
##'   * get_b:
##'   * set_b:
##'   * get_c:
##'   * set_c:
##'   * get_damID:
##'   * push_damID:
##'   * get_sireID:
##'   * push_sireID:
##'   * get_chemoprophylaxis:
##'   * set_chemoprophylaxis:
##' @section Fields:
##'   * a field: talk about me
##' @md
##' @export
`humanPfMOI` <- function(PfID_init, tInf_init=-1, MOI_init=0, b_init=0.55, c_init=0.15, damID_init=-1, sireID_init=-1, chemoprophylaxis_init=FALSE) {
  humanPfMOI__ctor(PfID_init, tInf_init, MOI_init, b_init, c_init, damID_init, sireID_init, chemoprophylaxis_init)
}
.R6_humanPfMOI <-
  R6::R6Class(
    "humanPfMOI",
    inherit=,
    portable=TRUE,
    public=list(
      .ptr=NULL,
      initialize = function(ptr) {
        self$.ptr <- ptr
      },
      get_PfID = function() {
        humanPfMOI__get_PfID(self)
      },
      push_PfID = function(PfID_new) {
        humanPfMOI__push_PfID(self, PfID_new)
      },
      get_tInf = function() {
        humanPfMOI__get_tInf(self)
      },
      push_tInf = function(tInf_new) {
        humanPfMOI__push_tInf(self, tInf_new)
      },
      get_MOI = function() {
        humanPfMOI__get_MOI(self)
      },
      set_MOI = function(MOI_new) {
        humanPfMOI__set_MOI(self, MOI_new)
      },
      get_b = function() {
        humanPfMOI__get_b(self)
      },
      set_b = function(b_new) {
        humanPfMOI__set_b(self, b_new)
      },
      get_c = function() {
        humanPfMOI__get_c(self)
      },
      set_c = function(c_new) {
        humanPfMOI__set_c(self, c_new)
      },
      get_damID = function() {
        humanPfMOI__get_damID(self)
      },
      push_damID = function(damID_new) {
        humanPfMOI__push_damID(self, damID_new)
      },
      get_sireID = function() {
        humanPfMOI__get_sireID(self)
      },
      push_sireID = function(sireID_new) {
        humanPfMOI__push_sireID(self, sireID_new)
      },
      get_chemoprophylaxis = function() {
        humanPfMOI__get_chemoprophylaxis(self)
      },
      set_chemoprophylaxis = function(chemoprophylaxis_new) {
        humanPfMOI__set_chemoprophylaxis(self, chemoprophylaxis_new)
      },
      add_Infection = function(PfID_new, damID_new, sireID_new) {
        humanPfMOI__add_Infection(self, PfID_new, damID_new, sireID_new)
      },
      clear_Infection = function(PfID_ix) {
        humanPfMOI__clear_Infection(self, PfID_ix)
      },
      get_Infection = function() {
        humanPfMOI__get_Infection(self)
      },
      track_history = function(tEvent, event) {
        humanPfMOI__track_history(self, tEvent, event)
      },
      get_history = function() {
        humanPfMOI__get_history(self)
      }),
    active=list())

##' A class for storing parameters and state variables of mosquito-stage PfMOI infections.
##' @title PfMOI Mosquito Stage Pathogen Class
##' @param PfID_init PfID derived from the infecting human's gametocyte ID
##' @param tInf_init time of current infection (successful human to mosquito transmission event)
##' @param MOI_init initial multiplicity of infection
##' @param damID_init female gametocyte 'mother'
##' @param sireID_init male gametocyte 'father'
##' @section Methods:
##'   * get_PfID:
##'   * push_PfID:
##'   * get_tInf:
##'   * push_tInf:
##'   * get_MOI:
##'   * set_MOI:
##'   * get_damID:
##'   * set_damID:
##'   * get_sireID:
##'   * set_sireID:
##' @section Fields:
##'   * a field: talk about me
##' @md
##' @export
`mosquitoPfMOI` <- function(PfID_init, tInf_init=-1, MOI_init=0, damID_init=-1, sireID_init=-1) {
  mosquitoPfMOI__ctor(PfID_init, tInf_init, MOI_init, damID_init, sireID_init)
}
.R6_mosquitoPfMOI <-
  R6::R6Class(
    "mosquitoPfMOI",
    inherit=,
    portable=TRUE,
    public=list(
      .ptr=NULL,
      initialize = function(ptr) {
        self$.ptr <- ptr
      },
      get_PfID = function() {
        mosquitoPfMOI__get_PfID(self)
      },
      push_PfID = function(PfID_new) {
        mosquitoPfMOI__push_PfID(self, PfID_new)
      },
      get_tInf = function() {
        mosquitoPfMOI__get_tInf(self)
      },
      push_tInf = function(tInf_new) {
        mosquitoPfMOI__push_tInf(self, tInf_new)
      },
      get_MOI = function() {
        mosquitoPfMOI__get_MOI(self)
      },
      set_MOI = function(MOI_new) {
        mosquitoPfMOI__set_MOI(self, MOI_new)
      },
      get_damID = function() {
        mosquitoPfMOI__get_damID(self)
      },
      push_damID = function(damID_new) {
        mosquitoPfMOI__push_damID(self, damID_new)
      },
      get_sireID = function() {
        mosquitoPfMOI__get_sireID(self)
      },
      push_sireID = function(sireID_new) {
        mosquitoPfMOI__push_sireID(self, sireID_new)
      },
      add_Infection = function(PfID_new, tInf_new, damID_new, sireID_new) {
        mosquitoPfMOI__add_Infection(self, PfID_new, tInf_new, damID_new, sireID_new)
      },
      get_Infection = function(PfID_ix) {
        mosquitoPfMOI__get_Infection(self, PfID_ix)
      },
      get_InfectionIx = function(ix) {
        mosquitoPfMOI__get_InfectionIx(self, ix)
      },
      get_InfectionEIP = function(incubation) {
        mosquitoPfMOI__get_InfectionEIP(self, incubation)
      },
      which_EIP = function(incubation) {
        mosquitoPfMOI__which_EIP(self, incubation)
      }),
    active=list())

##' Initialize a risk queue for a feeding site object. This function is a method for \code{\link{FeedingSite}}.
##' @title MICRO Risk Queue
##' @section Methods:
##'   * get_N:
##'   * set_N:
##'   * get_who:
##'   * push_who:
##'   * get_pTm:
##'   * set_pTm:
##'   * get_w:
##'   * push_w:
##'   * set_nOther:
##'   * get_nOther:
##'   * add_OtherHost:
##'   * get_OtherHost:
##' @section Fields:
##'   * a field:
##' @md
##' @export
`RiskQ` <- function() {
  RiskQ__ctor()
}
.R6_RiskQ <-
  R6::R6Class(
    "RiskQ",
    inherit=,
    portable=TRUE,
    public=list(
      .ptr=NULL,
      initialize = function(ptr) {
        self$.ptr <- ptr
      },
      get_N = function() {
        RiskQ__get_N(self)
      },
      set_N = function(N_new) {
        RiskQ__set_N(self, N_new)
      },
      get_who = function() {
        RiskQ__get_who(self)
      },
      push_who = function(who_new) {
        RiskQ__push_who(self, who_new)
      },
      get_pTm = function() {
        RiskQ__get_pTm(self)
      },
      push_pTm = function(pTm_new) {
        RiskQ__push_pTm(self, pTm_new)
      },
      get_w = function() {
        RiskQ__get_w(self)
      },
      push_w = function(w_new) {
        RiskQ__push_w(self, w_new)
      },
      add_HumanHost = function(who_new, pTm_new, w_new) {
        RiskQ__add_HumanHost(self, who_new, pTm_new, w_new)
      },
      get_HumanHost = function() {
        RiskQ__get_HumanHost(self)
      },
      get_HumanHostIx = function(ix) {
        RiskQ__get_HumanHostIx(self, ix)
      },
      clear_HumanHost = function() {
        RiskQ__clear_HumanHost(self)
      },
      get_nOther = function() {
        RiskQ__get_nOther(self)
      },
      set_nOther = function(nOther_new) {
        RiskQ__set_nOther(self, nOther_new)
      },
      add_OtherHost = function(otherW_new, typeID_new) {
        RiskQ__add_OtherHost(self, otherW_new, typeID_new)
      },
      get_OtherHost = function() {
        RiskQ__get_OtherHost(self)
      }),
    active=list())

##' ImagoQ
##' @title MICRO Imago Queue
##' @section Methods:
##'   * clear_ImagoQ:
##'   * clear_ImagoQTime:
##'   * add_ImagoQ:
##'   * track_ImagoQ:
##'   * get_N:
##'   * set_N:
##'   * get_ImagoQ:
##'   * get_ImagoQTime:
##' @section Fields:
##'   * a field:
##' @md
##' @export
`ImagoQ` <- function() {
  ImagoQ__ctor()
}
.R6_ImagoQ <-
  R6::R6Class(
    "ImagoQ",
    inherit=,
    portable=TRUE,
    public=list(
      .ptr=NULL,
      initialize = function(ptr) {
        self$.ptr <- ptr
      },
      clear_ImagoQ = function() {
        ImagoQ__clear_ImagoQ(self)
      },
      clear_ImagoQTime = function(time) {
        ImagoQ__clear_ImagoQTime(self, time)
      },
      add_ImagoQ = function(N_new, tEmerge_new, genotype_new, damID_new, sireID_new) {
        ImagoQ__add_ImagoQ(self, N_new, tEmerge_new, genotype_new, damID_new, sireID_new)
      },
      track_ImagoQ = function(time) {
        ImagoQ__track_ImagoQ(self, time)
      },
      get_N = function() {
        ImagoQ__get_N(self)
      },
      set_N = function(N_new) {
        ImagoQ__set_N(self, N_new)
      },
      get_ImagoQ = function() {
        ImagoQ__get_ImagoQ(self)
      },
      get_ImagoQTime = function(tNow, clear) {
        ImagoQ__get_ImagoQTime(self, tNow, clear)
      }),
    active=list())

##' EggQ
##' @title MICRO Egg Queue
##' @section Methods:
##'   * clear_EggQ:
##'   * clear_EggQTime:
##'   * add_EggQ:
##'   * track_EggQ:
##'   * get_N:
##'   * set_N:
##'   * get_EggQ:
##'   * get_EggQTime:
##' @section Fields:
##'   * a field:
##' @md
##' @export
`EggQ` <- function() {
  EggQ__ctor()
}
.R6_EggQ <-
  R6::R6Class(
    "EggQ",
    inherit=,
    portable=TRUE,
    public=list(
      .ptr=NULL,
      initialize = function(ptr) {
        self$.ptr <- ptr
      },
      clear_EggQ = function() {
        EggQ__clear_EggQ(self)
      },
      clear_EggQTime = function(time) {
        EggQ__clear_EggQTime(self, time)
      },
      add_EggQ = function(N_new, tOviposit_new, genotype_new, damID_new, sireID_new) {
        EggQ__add_EggQ(self, N_new, tOviposit_new, genotype_new, damID_new, sireID_new)
      },
      track_EggQ = function(time) {
        EggQ__track_EggQ(self, time)
      },
      get_N = function() {
        EggQ__get_N(self)
      },
      set_N = function(N_new) {
        EggQ__set_N(self, N_new)
      },
      get_EggQ = function() {
        EggQ__get_EggQ(self)
      },
      get_EggQTime = function(tNow, clear) {
        EggQ__get_EggQTime(self, tNow, clear)
      }),
    active=list())

##' Initialize an EL4P pool inside an aquatic site or for a well-mixed macrosimulation tile.
##' This class is nested inside \code{\link{AquaticSite}} or \code{\link{MacroTile}}.
##' Note that genotype corresponding to index 0 is always the wild type.
##' @title Aquatic Ecology EL4P Class
##' @section Methods:
##'   * get_N:
##'   * set_N:
##'   * get_who:
##'   * push_who:
##'   * get_pTm:
##'   * set_pTm:
##'   * get_w:
##'   * push_w:
##'   * set_nOther:
##'   * get_nOther:
##'   * add_OtherHost:
##'   * get_OtherHost:
##' @section Fields:
##'   * a field:
##' @md
##' @export
`EL4P` <- function(numGenotypes, psi_new, alpha_new, p_new) {
  EL4P__ctor(numGenotypes, psi_new, alpha_new, p_new)
}
.R6_EL4P <-
  R6::R6Class(
    "EL4P",
    inherit=,
    portable=TRUE,
    public=list(
      .ptr=NULL,
      initialize = function(ptr) {
        self$.ptr <- ptr
      },
      oneStep = function() {
        EL4P__oneStep(self)
      },
      oneStep_GEL4P = function(M, eqAqua, G, lifespan) {
        EL4P__oneStep_GEL4P(self, M, eqAqua, G, lifespan)
      },
      burnIn_GEL4P = function(M, eqAqua, G, lifespan, tMax) {
        EL4P__burnIn_GEL4P(self, M, eqAqua, G, lifespan, tMax)
      },
      G2K_GEL4P = function(eqAqua, G, lifespan, tMax) {
        EL4P__G2K_GEL4P(self, eqAqua, G, lifespan, tMax)
      },
      checkDX_GEL4P = function(eqAqua, G, lifespan, tMax) {
        EL4P__checkDX_GEL4P(self, eqAqua, G, lifespan, tMax)
      },
      addEggs = function(eggs_N, genotype) {
        EL4P__addEggs(self, eggs_N, genotype)
      },
      get_allGenotypes = function() {
        EL4P__get_allGenotypes(self)
      },
      get_genotypeIx = function(ix) {
        EL4P__get_genotypeIx(self, ix)
      },
      get_psi = function() {
        EL4P__get_psi(self)
      },
      set_psi = function(psi_new) {
        EL4P__set_psi(self, psi_new)
      },
      get_alpha = function() {
        EL4P__get_alpha(self)
      },
      set_alpha = function(alpha_new) {
        EL4P__set_alpha(self, alpha_new)
      },
      get_p = function() {
        EL4P__get_p(self)
      },
      set_p = function(p_new) {
        EL4P__set_p(self, p_new)
      },
      get_numGenotypes = function() {
        EL4P__get_numGenotypes(self)
      },
      get_totalLambda = function() {
        EL4P__get_totalLambda(self)
      },
      get_specificLambda = function(ix) {
        EL4P__get_specificLambda(self, ix)
      },
      reset = function() {
        EL4P__reset(self)
      },
      set_pop = function(initPop) {
        EL4P__set_pop(self, initPop)
      }),
    active=list())

##' Class to store female mosquito histories; \code{\link{MicroMosquitoFemale}} and \code{\link{MicroMosquito}}
##' @title Mosquito Female History Class
##' @section Methods:
##'   * historyInit: initialize the mosquito history
##'   * historyTrack: track history at the end of a generic bout (MBITES-XX-Bouts.R)
##'   * historyFeed: track history from a host encounter (MBITES-XX-HostEncounter.R)
##'   * calcBionomics: calculate bionomic parameters upon mosquito death; not intended to be directly called by user.
##'   * exportHistory: export the mosquito history object as a named list which consists of the following components:
##'     * stateH: state trajectory
##'     * timeH: transition times
##'     * ixH: sites visited
##'     * pSetH: point sets visited
##'     * feedAllH: number of blood meals
##'     * feedAllT: times of blood meals
##'     * feedHumanH: number of blood meals on human hosts
##'     * feedHumanT: times of blood meals on human hosts
##'     * feedIxH: ids of all blood hosts
##'     * bmSizeH: size of blood meal
##'     * batchH: size of egg batch
##'     * bionomics_mBatch: mean egg batch size
##'     * bionomics_tBatch: total egg production (sum of all egg batches)
##'     * bionomics_bmInt: all bloodmeal intervals
##'     * bionomics_bmIntH: human bloodmeal intervals
##'     * bionomics_lifespan: lifespan
##' @md
##' @export
`MosquitoFemaleHistory` <- function() {
  MosquitoFemaleHistory__ctor()
}
.R6_MosquitoFemaleHistory <-
  R6::R6Class(
    "MosquitoFemaleHistory",
    inherit=,
    portable=TRUE,
    public=list(
      .ptr=NULL,
      initialize = function(ptr) {
        self$.ptr <- ptr
      },
      historyInit = function(privateEnv) {
        MosquitoFemaleHistory__historyInit(self, privateEnv)
      },
      historyTrack = function(privateEnv, alive) {
        MosquitoFemaleHistory__historyTrack(self, privateEnv, alive)
      },
      historyFeed = function(privateEnv) {
        MosquitoFemaleHistory__historyFeed(self, privateEnv)
      },
      calcBionomics = function() {
        MosquitoFemaleHistory__calcBionomics(self)
      },
      exportHistory = function() {
        MosquitoFemaleHistory__exportHistory(self)
      }),
    active=list())