R/DEPRECATED/PATHOGEN-PfMOI-Class.R
In smitdave/MASH: MASH (Modular Analysis and Simulation for Human Health)
#################################################################
#
# MASH-R6
# PATHOGEN component
# PfMOI module R6 class definitions
# David Smith, Hector Sanchez, Sean Wu
# June 9, 2017
#
#################################################################
#################################################################
# Mosquito Stage
#################################################################
#' PfMOI Mosquito-stage Pathogen Class Definition
#'
#' This is the mosquito-stage PfMOI module pathogen object defined in \code{\link{MicroMosquitoFemale}}.
#'
#' @docType class
#' @format An \code{\link{R6Class}} generator object
#' @keywords R6 class
#'
#' @section Methods:
#' * **Constructor**
#' * new: initialize a new \code{Landscape} object
#' * Arguments:
#' * \code{Landscape_PAR}: see \code{\link{Landscape.Parameters}} for parameter generation function.
#' * **Getters & Setters**
#' * get_XX: get \code{private$XX}
#' * Arguments:
#' * \code{ixS}: if \code{NULL} return all sites, otherwise return site indexed by \code{ixS}
#' * set_FeedingSites: set \code{private$FeedingSites}
#' * Arguments:
#' * \code{FeedingSites}: replacement object (see below)
#' * \code{ixS}: if \code{NULL} replace all sites, otherwise replace site indexed by \code{ixS}
#' * **Pointers**
#' * get_TilePointer: get \code{\link{MicroTile}} pointer
#' * set_TilePointer: set \code{\link{MicroTile}} pointer
#'
#'
#'
#'
#'
#' @md
#' @export
mosquitoPfMOI <- R6::R6Class(classname="mosquitoPfMOI",
portable = TRUE,
cloneable = FALSE,
lock_class = FALSE,
lock_objects = FALSE,
#public members
public = list(
#initialize
initialize = function(PfID = NULL, tInf = NULL, MOI = 0L, damID = NULL, sireID = NULL){
private$PfID = PfID
private$tInf = tInf
private$MOI = MOI
private$damID = damID
private$sireID = sireID
},
########################################
# Getters & Setters
########################################
# MOI: Multiplicity of Infection
get_MOI = function(){
return(private$MOI)
},
set_MOI = function(MOI){
private$MOI = MOI
},
increment_MOI = function(){
private$MOI = private$MOI + 1
},
# get_clone: get the mth clonal variant as a list
get_clone = function(m){
list(
PfID = private$PfID[m],
damID = private$damID[m],
sireID = private$sireID[m]
)
},
########################################
# Pointers
########################################
set_MosquitoPointer = function(MosquitoPointer){
private$MosquitoPointer = MosquitoPointer
},
get_MosquitoPointer = function(){
return(private$MosquitoPointer)
}
),
#private members
private = list(
# Fields
MOI = NULL,
PfID = NULL,
sireID = NULL,
damID = NULL,
# Pointers
MosquitoPointer = NULL
)
) #end class definition
#################################################################
# Human Stage
#################################################################
#' PfMOI Human-stage Pathogen Class Definition
#'
#' This is the human-stage PfMOI module pathogen object defined in \code{\link{Human}}.
#'
#' @docType class
#' @format An \code{\link{R6Class}} generator object
#' @keywords R6 class
#'
#' @section Methods:
#' * **Constructor**
#' * new: initialize a new \code{Landscape} object
#' * Arguments:
#' * \code{Landscape_PAR}: see \code{\link{Landscape.Parameters}} for parameter generation function.
#' * **Getters & Setters**
#' * get_XX: get \code{private$XX}
#' * Arguments:
#' * \code{ixS}: if \code{NULL} return all sites, otherwise return site indexed by \code{ixS}
#' * set_FeedingSites: set \code{private$FeedingSites}
#' * Arguments:
#' * \code{FeedingSites}: replacement object (see below)
#' * \code{ixS}: if \code{NULL} replace all sites, otherwise replace site indexed by \code{ixS}
#' * **Pointers**
#' * get_TilePointer: get \code{\link{MicroTile}} pointer
#' * set_TilePointer: set \code{\link{MicroTile}} pointer
#'
#' @section Fields:
#' * **History**
#' * tEvent: time of the event (jump time for embedded CTMC)
#' * events: the new state (state after the jump)
#' * MOI: current multiplicity of infection
#'
#' @md
#' @export
humanPfMOI <- R6::R6Class(classname="humanPfMOI",
portable = TRUE,
cloneable = FALSE,
lock_class = FALSE,
lock_objects = FALSE,
#public members
public = list(
#initialize
initialize = function(PfID = NULL, tInf = NULL, MOI = 0L, b = 0.55, c = 0.15, damID = NULL, sireID = NULL){
if(MOI>0){
private$infected = TRUE
} else {
private$infected = FALSE
}
private$MOI = MOI
private$history$MOI = MOI
private$PfID = PfID
private$tInf = tInf
private$b = b
private$c = c
private$damID = damID
private$sireID = sireID
private$chemoprophylaxis = FALSE
},
########################################
# Infection Dynamics
########################################
# add a new infection
add_Infection = function(PfID, damID, sireID){
private$damID = c(private$damID,damID)
private$sireID = c(private$sireID,sireID)
private$PfID = c(private$PfID,PfID)
private$MOI = private$MOI + 1L
if(!private$infected){
private$infected = TRUE
}
},
# completely clear the infection assoc. with index ix
clear_Infection = function(ix){
private$damID = private$damID[-ix]
private$sireID = private$sireID[-ix]
private$PfID = private$PfID[-ix]
private$MOI = private$MOI - 1L
if(private$MOI==0){
private$infected = FALSE
}
},
########################################
# Getters & Setters
########################################
# infected: am I infected by at least one clonal variant?
get_infected = function(){
return(private$infected)
},
set_infected = function(infected){
private$infected = infected
},
# MOI: Multiplicity of Infection
get_MOI = function(){
return(private$MOI)
},
set_MOI = function(MOI){
private$MOI = MOI
},
increment_MOI = function(){
private$MOI = private$MOI + 1L
},
# PfID: Pf IDs; indicate liver-stage infections
get_PfID = function(){
return(private$PfID)
},
set_PfID = function(PfID){
private$PfID = PfID
},
push_PfID = function(PfID){
private$PfID = c(private$PfID,PfID)
},
# tInf: when was I infected with this clonal variant?
get_tInf = function(){
return(private$tInf)
},
set_tInf = function(tInf){
private$tInf = tInf
},
push_tInf = function(tInf){
private$tInf = c(private$tInf,tInf)
},
# b: infected mosquito to human transmission efficiency
get_b = function(){
return(private$b)
},
set_b = function(b){
private$b = b
},
# c: infected human to mosquito transmission efficiency
get_c = function(){
return(private$c)
},
set_c = function(c){
private$c = c
},
# sireID:
get_sireID = function(){
return(private$sireID)
},
set_sireID = function(sireID){
private$sireID = sireID
},
push_sireID = function(sireID){
private$sireID = c(private$sireID,sireID)
},
# damID:
get_damID = function(){
return(private$damID)
},
set_damID = function(damID){
private$damID = damID
},
push_damID = function(damID){
private$damID = c(private$damID,damID)
},
# chemoprophylaxis: am I currently protected by chemoprophylaxis?
get_chemoprophylaxis = function(){
return(private$chemoprophylaxis)
},
set_chemoprophylaxis = function(chemoprophylaxis){
private$chemoprophylaxis = chemoprophylaxis
},
# return the mth clonal variant (needed for human to mosquito transmission)
get_clone = function(m){
print("get the mth clonal variant as a list")
list(
)
},
########################################
# History
########################################
track_history = function(eventT , event){
private$history$events = c(private$history$events,event)
private$history$eventT = c(private$history$eventT,eventT)
private$history$MOI = c(private$history$MOI,private$MOI)
},
get_history = function(){
return(private$history)
},
########################################
# Pointers
########################################
# HumanPointer: point to the human I exist in!
get_HumanPointer = function(){
return(private$HumanPointer)
},
set_HumanPointer = function(HumanPointer){
private$HumanPointer = HumanPointer
}
),
#private members
private = list(
# Pathogen and immune states
infected = NULL, # boolean flag; TRUE if MOI > 0
MOI = NULL, # my multiplicity of infection
PfID = NULL, # vector of PfID
tInf = NULL, # vector of infection times
b = NULL, # infected mosquito to human transmission efficiency
c = NULL, # infected human to mosquito transmission efficiency
chemoprophylaxis = NULL,
damID = NULL, # vector of female gametocyte parents of this clonal strain
sireID = NULL, # vector of male gametocyte parents of this clonal strain
history = list(events="init",eventT=-1L,MOI=NULL),
# Pointers
HumanPointer = NULL
)
) #end class definition
smitdave/MASH documentation built on May 30, 2019, 5:02 a.m.
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#################################################################
#
# MASH-R6
# PATHOGEN component
# PfMOI module R6 class definitions
# David Smith, Hector Sanchez, Sean Wu
# June 9, 2017
#
#################################################################
#################################################################
# Mosquito Stage
#################################################################
#' PfMOI Mosquito-stage Pathogen Class Definition
#'
#' This is the mosquito-stage PfMOI module pathogen object defined in \code{\link{MicroMosquitoFemale}}.
#'
#' @docType class
#' @format An \code{\link{R6Class}} generator object
#' @keywords R6 class
#'
#' @section Methods:
#' * **Constructor**
#' * new: initialize a new \code{Landscape} object
#' * Arguments:
#' * \code{Landscape_PAR}: see \code{\link{Landscape.Parameters}} for parameter generation function.
#' * **Getters & Setters**
#' * get_XX: get \code{private$XX}
#' * Arguments:
#' * \code{ixS}: if \code{NULL} return all sites, otherwise return site indexed by \code{ixS}
#' * set_FeedingSites: set \code{private$FeedingSites}
#' * Arguments:
#' * \code{FeedingSites}: replacement object (see below)
#' * \code{ixS}: if \code{NULL} replace all sites, otherwise replace site indexed by \code{ixS}
#' * **Pointers**
#' * get_TilePointer: get \code{\link{MicroTile}} pointer
#' * set_TilePointer: set \code{\link{MicroTile}} pointer
#'
#'
#'
#'
#'
#' @md
#' @export
mosquitoPfMOI <- R6::R6Class(classname="mosquitoPfMOI",
portable = TRUE,
cloneable = FALSE,
lock_class = FALSE,
lock_objects = FALSE,
#public members
public = list(
#initialize
initialize = function(PfID = NULL, tInf = NULL, MOI = 0L, damID = NULL, sireID = NULL){
private$PfID = PfID
private$tInf = tInf
private$MOI = MOI
private$damID = damID
private$sireID = sireID
},
########################################
# Getters & Setters
########################################
# MOI: Multiplicity of Infection
get_MOI = function(){
return(private$MOI)
},
set_MOI = function(MOI){
private$MOI = MOI
},
increment_MOI = function(){
private$MOI = private$MOI + 1
},
# get_clone: get the mth clonal variant as a list
get_clone = function(m){
list(
PfID = private$PfID[m],
damID = private$damID[m],
sireID = private$sireID[m]
)
},
########################################
# Pointers
########################################
set_MosquitoPointer = function(MosquitoPointer){
private$MosquitoPointer = MosquitoPointer
},
get_MosquitoPointer = function(){
return(private$MosquitoPointer)
}
),
#private members
private = list(
# Fields
MOI = NULL,
PfID = NULL,
sireID = NULL,
damID = NULL,
# Pointers
MosquitoPointer = NULL
)
) #end class definition
#################################################################
# Human Stage
#################################################################
#' PfMOI Human-stage Pathogen Class Definition
#'
#' This is the human-stage PfMOI module pathogen object defined in \code{\link{Human}}.
#'
#' @docType class
#' @format An \code{\link{R6Class}} generator object
#' @keywords R6 class
#'
#' @section Methods:
#' * **Constructor**
#' * new: initialize a new \code{Landscape} object
#' * Arguments:
#' * \code{Landscape_PAR}: see \code{\link{Landscape.Parameters}} for parameter generation function.
#' * **Getters & Setters**
#' * get_XX: get \code{private$XX}
#' * Arguments:
#' * \code{ixS}: if \code{NULL} return all sites, otherwise return site indexed by \code{ixS}
#' * set_FeedingSites: set \code{private$FeedingSites}
#' * Arguments:
#' * \code{FeedingSites}: replacement object (see below)
#' * \code{ixS}: if \code{NULL} replace all sites, otherwise replace site indexed by \code{ixS}
#' * **Pointers**
#' * get_TilePointer: get \code{\link{MicroTile}} pointer
#' * set_TilePointer: set \code{\link{MicroTile}} pointer
#'
#' @section Fields:
#' * **History**
#' * tEvent: time of the event (jump time for embedded CTMC)
#' * events: the new state (state after the jump)
#' * MOI: current multiplicity of infection
#'
#' @md
#' @export
humanPfMOI <- R6::R6Class(classname="humanPfMOI",
portable = TRUE,
cloneable = FALSE,
lock_class = FALSE,
lock_objects = FALSE,
#public members
public = list(
#initialize
initialize = function(PfID = NULL, tInf = NULL, MOI = 0L, b = 0.55, c = 0.15, damID = NULL, sireID = NULL){
if(MOI>0){
private$infected = TRUE
} else {
private$infected = FALSE
}
private$MOI = MOI
private$history$MOI = MOI
private$PfID = PfID
private$tInf = tInf
private$b = b
private$c = c
private$damID = damID
private$sireID = sireID
private$chemoprophylaxis = FALSE
},
########################################
# Infection Dynamics
########################################
# add a new infection
add_Infection = function(PfID, damID, sireID){
private$damID = c(private$damID,damID)
private$sireID = c(private$sireID,sireID)
private$PfID = c(private$PfID,PfID)
private$MOI = private$MOI + 1L
if(!private$infected){
private$infected = TRUE
}
},
# completely clear the infection assoc. with index ix
clear_Infection = function(ix){
private$damID = private$damID[-ix]
private$sireID = private$sireID[-ix]
private$PfID = private$PfID[-ix]
private$MOI = private$MOI - 1L
if(private$MOI==0){
private$infected = FALSE
}
},
########################################
# Getters & Setters
########################################
# infected: am I infected by at least one clonal variant?
get_infected = function(){
return(private$infected)
},
set_infected = function(infected){
private$infected = infected
},
# MOI: Multiplicity of Infection
get_MOI = function(){
return(private$MOI)
},
set_MOI = function(MOI){
private$MOI = MOI
},
increment_MOI = function(){
private$MOI = private$MOI + 1L
},
# PfID: Pf IDs; indicate liver-stage infections
get_PfID = function(){
return(private$PfID)
},
set_PfID = function(PfID){
private$PfID = PfID
},
push_PfID = function(PfID){
private$PfID = c(private$PfID,PfID)
},
# tInf: when was I infected with this clonal variant?
get_tInf = function(){
return(private$tInf)
},
set_tInf = function(tInf){
private$tInf = tInf
},
push_tInf = function(tInf){
private$tInf = c(private$tInf,tInf)
},
# b: infected mosquito to human transmission efficiency
get_b = function(){
return(private$b)
},
set_b = function(b){
private$b = b
},
# c: infected human to mosquito transmission efficiency
get_c = function(){
return(private$c)
},
set_c = function(c){
private$c = c
},
# sireID:
get_sireID = function(){
return(private$sireID)
},
set_sireID = function(sireID){
private$sireID = sireID
},
push_sireID = function(sireID){
private$sireID = c(private$sireID,sireID)
},
# damID:
get_damID = function(){
return(private$damID)
},
set_damID = function(damID){
private$damID = damID
},
push_damID = function(damID){
private$damID = c(private$damID,damID)
},
# chemoprophylaxis: am I currently protected by chemoprophylaxis?
get_chemoprophylaxis = function(){
return(private$chemoprophylaxis)
},
set_chemoprophylaxis = function(chemoprophylaxis){
private$chemoprophylaxis = chemoprophylaxis
},
# return the mth clonal variant (needed for human to mosquito transmission)
get_clone = function(m){
print("get the mth clonal variant as a list")
list(
)
},
########################################
# History
########################################
track_history = function(eventT , event){
private$history$events = c(private$history$events,event)
private$history$eventT = c(private$history$eventT,eventT)
private$history$MOI = c(private$history$MOI,private$MOI)
},
get_history = function(){
return(private$history)
},
########################################
# Pointers
########################################
# HumanPointer: point to the human I exist in!
get_HumanPointer = function(){
return(private$HumanPointer)
},
set_HumanPointer = function(HumanPointer){
private$HumanPointer = HumanPointer
}
),
#private members
private = list(
# Pathogen and immune states
infected = NULL, # boolean flag; TRUE if MOI > 0
MOI = NULL, # my multiplicity of infection
PfID = NULL, # vector of PfID
tInf = NULL, # vector of infection times
b = NULL, # infected mosquito to human transmission efficiency
c = NULL, # infected human to mosquito transmission efficiency
chemoprophylaxis = NULL,
damID = NULL, # vector of female gametocyte parents of this clonal strain
sireID = NULL, # vector of male gametocyte parents of this clonal strain
history = list(events="init",eventT=-1L,MOI=NULL),
# Pointers
HumanPointer = NULL
)
) #end class definition
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