R/DEPRECATED/PATHOGEN-PfSI-Class.R

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

# #################################################################
# #
# #   MASH-R6
# #   PATHOGEN component
# #   PfSI module R6 class definitions
# #   David Smith, Hector Sanchez, Sean Wu
# #   May 19, 2016
# #
# #################################################################
#
# #' PfSI Mosquito-stage Pathogen Class Definition
# #'
# #' This is a generic PfSI Pathogen object blah blah ...
# #'  categorical summary measure \code{A[j]}. This class inherits from \code{\link{GenericModel}} class.
# #'  Defines the fitting algorithm for a regression model \code{A[j] ~ W + ...}.
# #'
# #' @docType class
# #' @format An \code{\link{R6Class}} generator object
# #' @keywords R6 class
# #' @details
# #' \itemize{
# #' \item{\code{reg}} - .
# #' \item{\code{outvar}} - .
# #' \item{\code{levels}} - .
# #' \item{\code{nbins}} - .
# #' }
# #' @section Methods:
# #' \describe{
# #'   \item{\code{new(reg, DataStorageClass.g0, ...)}}{...}
# #'   \item{\code{fit(data)}}{...}
# #'   \item{\code{predict(newdata)}}{...}
# #'   \item{\code{predictAeqa(newdata)}}{...}
# #' }
# #' @section Active Bindings:
# #' \describe{
# #'   \item{\code{cats}}{...}
# #' }
# #' @export
# mosquitoPfSI <- R6::R6Class(classname="mosquitoPfSI",
#                      portable = TRUE,
#                      cloneable = FALSE,
#                      lock_class = FALSE,
#                      lock_objects = FALSE,
#
#                      #public members
#                      public = list(
#
#                        #initialize
#                        initialize = function(PfID = NULL, tInf = NULL, spz = 0L, damID = NULL, sireID = NULL){
#                          private$PfID = PfID
#                          private$tInf = tInf
#                          private$spz = spz
#                          private$damID = damID
#                          private$sireID = sireID
#                        },
#
#                        #finalize
#                        finalize = function(){
#                         #  print(paste0("mosquitoPfSI object PfID: ",PfID," was garbage collected!"))
#                        },
#
#                        ########################################
#                        #  Accessors, Pointers, and Setters
#                        ########################################
#
#                        # PfID
#                        get_PfID = function(){
#                          return(private$PfID)
#                        },
#                        set_PfID = function(PfID){
#                          private$PfID = PfID
#                        },
#                        push_PfID = function(PfID){
#                          private$PfID = c(private$PfID,PfID)
#                        },
#
#                        # tInf
#                        get_tInf = function(){
#                          return(private$tInf)
#                        },
#                        set_tInf = function(tInf){
#                          private$tInf = tInf
#                        },
#                        push_tInf = function(){
#                          private$tInf = c(private$tInf,tInf)
#                        },
#
#                        # spz
#                        get_spz = function(){
#                          return(private$spz)
#                        },
#                        set_spz = function(spz){
#                          private$spz = spz
#                        },
#                        push_spz = function(){
#                          private$spz = c(private$spz,spz)
#                        },
#
#                        # damID
#                        get_damID = function(){
#                          return(private$damID)
#                        },
#
#                        # sireID
#                        get_sireID = function(){
#                          return(private$sireID)
#                        },
#
#                        # private
#                        get_public = function(){
#                          return(as.list(private))
#                        }
#
#                      ),
#
#                      #private members
#                      private = list(
#
#                        PfID = NULL, # pathogen ID
#                        tInf = NULL, # time of bite (human to mosquito transmission)
#                        spz = NULL, # sporozoites (may be a vector of multiple clonal variants)
#                        damID = NULL, # female gametocyte 'mother'
#                        sireID = NULL # male gametocyte 'father'
#
#                      )
#
# ) #end class definition
#
#
# #' PfSI Human-stage Pathogen Class Definition
# #'
# #' This is a generic PfSI Pathogen object blah blah ...
# #'  categorical summary measure \code{A[j]}. This class inherits from \code{\link{GenericModel}} class.
# #'  Defines the fitting algorithm for a regression model \code{A[j] ~ W + ...}.
# #'
# #' @docType class
# #' @format An \code{\link{R6Class}} generator object
# #' @keywords R6 class
# #' @details
# #' \itemize{
# #' \item{\code{reg}} - .
# #' \item{\code{outvar}} - .
# #' \item{\code{levels}} - .
# #' \item{\code{nbins}} - .
# #' }
# #' @section Methods:
# #' \describe{
# #'   \item{\code{new(reg, DataStorageClass.g0, ...)}}{...}
# #'   \item{\code{fit(data)}}{...}
# #'   \item{\code{predict(newdata)}}{...}
# #'   \item{\code{predictAeqa(newdata)}}{...}
# #' }
# #' @section Active Bindings:
# #' \describe{
# #'   \item{\code{cats}}{...}
# #' }
# #' @export
# humanPfSI <- R6::R6Class(classname="humanPfSI",
#                      portable = TRUE,
#                      cloneable = FALSE,
#                      lock_class = FALSE,
#                      lock_objects = FALSE,
#
#                      #public members
#                      public = list(
#
#                        #initialize
#                        initialize = function(PfID, tInf = NULL, b = 0.55, c = 0.15, damID = NULL, sireID = NULL, infected = FALSE, chemoprophylaxis = FALSE){
#                          private$PfID = PfID
#                          private$tInf = tInf
#                          private$b = b
#                          private$c = c
#                          private$damID = damID
#                          private$sireID = sireID
#                          private$infected = infected
#                          private$chemoprophylaxis = chemoprophylaxis
#                        },
#
#                        #finalize
#                        finalize = function(){
#                         #  print(paste0("humanPfSI object PfID: ",PfID," was garbage collected!"))
#                        },
#
#                        ########################################
#                        #  Accessors, Pointers, and Setters
#                        ########################################
#
#                        get_PfID = function(){
#                          return(private$PfID)
#                        },
#                        set_PfID = function(PfID){
#                          private$PfID = PfID
#                        },
#                        push_PfID = function(PfID){
#                          private$PfID = c(private$PfID,PfID)
#                        },
#
#                        get_tInf = function(){
#                          return(private$tInf)
#                        },
#                        set_tInf = function(tInf){
#                          private$tInf = tInf
#                        },
#                        push_tInf = function(tInf){
#                          private$tInf = c(private$tInf,tInf)
#                        },
#
#                        get_b = function(){
#                          return(private$b)
#                        },
#                        set_b = function(b){
#                          private$b = b
#                        },
#
#                        get_c = function(){
#                          return(private$c)
#                        },
#                        set_c = function(c){
#                          private$c = c
#                        },
#
#                        get_damID = function(){
#                          return(private$damID)
#                        },
#                        set_damID = function(damID){
#                          private$damID = damID
#                        },
#                        push_damID = function(damID){
#                          private$damID = c(private$damID,damID)
#                        },
#
#                        get_sireID = function(){
#                          return(private$sireID)
#                        },
#                        set_sireID = function(sireID){
#                          private$sireID = sireID
#                        },
#                        push_sireID = function(sireID){
#                          private$sireID = c(sireID,private$sireID)
#                        },
#
#                        get_infected = function(){
#                          return(private$infected)
#                        },
#                        set_infected = function(infected){
#                          private$infected = infected
#                        },
#
#                        get_chemoprophylaxis = function(){
#                          return(private$chemoprophylaxis)
#                        },
#                        set_chemoprophylaxis = function(chemoprophylaxis){
#                          private$chemoprophylaxis = chemoprophylaxis
#                        },
#
#                        get_private = function(){
#                          return(as.list(private))
#                        }
#
#                      ),
#
#                      #private members
#                      private = list(
#
#                        PfID = NULL, # pathogen ID
#                        tInf = NULL, # time of infection (mosquito to human transmission)
#                        b = NULL, # transmission efficiency: infected mosquito to human
#                        c = NULL, # transmission efficiency: infected human to mosquito
#                        damID = NULL, # female gametocyte 'mother'
#                        sireID = NULL, # male gametocyte 'father'
#                        infected = NULL,
#                        chemoprophylaxis = NULL
#
#                      )
#
# ) #end class definition