dualContinuous: Dual-host pathogen in structured (continuous) hosts...
In nosoi: A Forward Agent-Based Transmission Chain Simulator

dualContinuous

R Documentation

Dual-host pathogen in structured (continuous) hosts populations

Description

This function runs a dual-host transmission chain simulation, with structured hosts populations (such as spatial features) in a shared continuous space. The simulation stops either at the end of given time (specified by length.sim) or when the number of hosts infected threshold (max.infected) is passed. The movement of hosts on the continuous space map is a random walk (Brownian motion) that can be modified towards a biased random walk where hosts tend to be attracted to higher values of the environmental variable defined by the raster.

Usage

dualContinuous(
  length.sim,
  max.infected.A,
  max.infected.B,
  init.individuals.A,
  init.individuals.B,
  init.structure.A,
  init.structure.B,
  structure.raster.A,
  structure.raster.B,
  pExit.A,
  param.pExit.A,
  timeDep.pExit.A = FALSE,
  diff.pExit.A = FALSE,
  hostCount.pExit.A = FALSE,
  pMove.A,
  param.pMove.A,
  timeDep.pMove.A = FALSE,
  diff.pMove.A = FALSE,
  hostCount.pMove.A = FALSE,
  sdMove.A,
  param.sdMove.A,
  diff.sdMove.A = FALSE,
  timeDep.sdMove.A = FALSE,
  hostCount.sdMove.A = FALSE,
  attracted.by.raster.A = FALSE,
  nContact.A,
  param.nContact.A,
  timeDep.nContact.A = FALSE,
  diff.nContact.A = FALSE,
  hostCount.nContact.A = FALSE,
  pTrans.A,
  param.pTrans.A,
  timeDep.pTrans.A = FALSE,
  diff.pTrans.A = FALSE,
  hostCount.pTrans.A = FALSE,
  prefix.host.A = "H",
  pExit.B,
  param.pExit.B,
  timeDep.pExit.B = FALSE,
  diff.pExit.B = FALSE,
  hostCount.pExit.B = FALSE,
  pMove.B,
  param.pMove.B,
  timeDep.pMove.B = FALSE,
  diff.pMove.B = FALSE,
  hostCount.pMove.B = FALSE,
  sdMove.B,
  param.sdMove.B,
  diff.sdMove.B = FALSE,
  timeDep.sdMove.B = FALSE,
  hostCount.sdMove.B = FALSE,
  attracted.by.raster.B = FALSE,
  nContact.B,
  param.nContact.B,
  timeDep.nContact.B = FALSE,
  diff.nContact.B = FALSE,
  hostCount.nContact.B = FALSE,
  pTrans.B,
  param.pTrans.B,
  timeDep.pTrans.B = FALSE,
  diff.pTrans.B = FALSE,
  hostCount.pTrans.B = FALSE,
  prefix.host.B = "V",
  print.progress = TRUE,
  print.step = 10
)

Arguments

`length.sim`	specifies the length (in unit of time) over which the simulation should be run.
`max.infected.A`	specifies the maximum number of individual hosts A that can be infected in the simulation.
`max.infected.B`	specifies the maximum number of individual hosts B that can be infected in the simulation.
`init.individuals.A`	number of initially infected individuals (hosts A).
`init.individuals.B`	number of initially infected individuals (hosts B).
`init.structure.A`	in which location the initially infected host-A individuals are located. A vector of coordinates in the same coordinate space as the raster (NA if init.individual.A is 0).
`init.structure.B`	in which location the initially infected host-B individuals are located. A vector of coordinates in the same coordinate space as the raster (NA if init.individual.B is 0).
`structure.raster.A`	raster object defining the environmental variable for host-type A.
`structure.raster.B`	raster object defining the environmental variable for host B.
`pExit.A`	function that gives the probability to exit the simulation for an infected host A (either moving out, dying, etc.).
`param.pExit.A`	parameter names (list of functions) for the pExit for host-type A.
`timeDep.pExit.A`	is pExit of host-type A dependent on the absolute time of the simulation (TRUE/FALSE)?
`diff.pExit.A`	does pExit of host-type A depend on the environmental variable (set by the raster) (TRUE/FALSE).
`hostCount.pExit.A`	does pExit of host-type A vary with the host count (of either host-type A or B) in each raster cell? (TRUE/FALSE); if TRUE, diff.pExit.A should be TRUE.
`pMove.A`	function that gives the probability of a host moving as a function of time for host-type A.
`param.pMove.A`	parameter names (list of functions) for the pMove for host-type A.
`timeDep.pMove.A`	is pMove of host-type A dependent on the absolute time of the simulation (TRUE/FALSE)?
`diff.pMove.A`	does pMove of host-type A depend on the environmental variable (set by the raster) (TRUE/FALSE).A.
`hostCount.pMove.A`	does pMove of host-type A vary with the host count (of either host-type A or B) in each raster cell? (TRUE/FALSE); if TRUE, diff.pMove.A should be TRUE.
`sdMove.A`	function that gives the distance traveled for host-type A (based on coordinates); output is the standard deviation value for the Brownian motion.
`param.sdMove.A`	parameter names (list of functions) for sdMove for host-type A.
`diff.sdMove.A`	does sdMove of host-type A depend on the environmental variable (set by the raster) (TRUE/FALSE).
`timeDep.sdMove.A`	is sdMove of host-type A dependent on the absolute time of the simulation (TRUE/FALSE) ?
`hostCount.sdMove.A`	does sdMove varies with the host count (of either host-type A or B) in each raster cell? (TRUE/FALSE); diff.sdMove.A should be TRUE.
`attracted.by.raster.A`	should the host-type A be attracted by higher values in the environmental raster? (TRUE/FALSE).
`nContact.A`	function that gives the number of potential transmission events per unit of time for host-type A.
`param.nContact.A`	parameter names (list of functions) for param.nContact for host-type A.
`timeDep.nContact.A`	is nContact of host-type A dependent on the absolute time of the simulation (TRUE/FALSE)?
`diff.nContact.A`	does nContact of host-type A depend on the environmental variable (set by the raster) (TRUE/FALSE).
`hostCount.nContact.A`	does nContact vary with the host count (of either host-type A or B) in each raster cell?? (TRUE/FALSE); diff.nContact.A should be TRUE.
`pTrans.A`	function that gives the probability of transmit a pathogen as a function of time since infection for host A.
`param.pTrans.A`	parameter names (list of functions) for the pExit for host A.
`timeDep.pTrans.A`	is pTrans of host-type A dependent on the absolute time of the simulation (TRUE/FALSE)?
`diff.pTrans.A`	does pTrans of host-type A depend on the environmental variable (set by the raster) (TRUE/FALSE).
`hostCount.pTrans.A`	does pTrans vary with the host count (of either host-type A or B) in each raster cell? (TRUE/FALSE); diff.pTrans.A should be TRUE.
`prefix.host.A`	character(s) to be used as a prefix for the host A identification number.
`pExit.B`	function that gives the probability to exit the simulation for an infected host B (either moving out, dying, etc.).
`param.pExit.B`	parameter names (list of functions) for the pExit for host-type B.
`timeDep.pExit.B`	is pExit of host-type B dependent on the absolute time of the simulation (TRUE/FALSE)?
`diff.pExit.B`	does pExit of host-type B depend on the environmental variable (set by the raster) (TRUE/FALSE).
`hostCount.pExit.B`	does pExit of host-type B vary with the host count (of either host-type A or B) in each raster cell? (TRUE/FALSE); if TRUE, diff.pExit.B should be TRUE.
`pMove.B`	function that gives the probability of a host moving as a function of time for host-type B.
`param.pMove.B`	parameter names (list of functions) for the pMove for host-type B.
`timeDep.pMove.B`	is sdMove of host-type B dependent on the absolute time of the simulation (TRUE/FALSE) for host-type B.
`diff.pMove.B`	does pMove of host-type B depend on the environmental variable (set by the raster) (TRUE/FALSE).
`hostCount.pMove.B`	does pMove of host-type B vary with the host count (of either host-type A or B) in each raster cell? (TRUE/FALSE); if TRUE, diff.pMove.B should be TRUE.
`sdMove.B`	function that gives the distance traveled for host-type B (based on coordinates); output is the standard deviation value for the Brownian motion.
`param.sdMove.B`	parameter names (list of functions) for sdMove for host-type B.
`diff.sdMove.B`	does sdMove of host-type B depend on the environmental variable (set by the raster) (TRUE/FALSE).
`timeDep.sdMove.B`	is sdMove of host-type B dependent on the absolute time of the simulation (TRUE/FALSE) ?
`hostCount.sdMove.B`	does sdMove of host-type B vary with the host count (of either host-type A or B) in each raster cell? (TRUE/FALSE); if TRUE, diff.sdMove.B should be TRUE.
`attracted.by.raster.B`	should the host-type B be attracted by higher values in the environmental raster? (TRUE/FALSE)
`nContact.B`	function that gives the number of potential transmission events per unit of time for host B.
`param.nContact.B`	parameter names (list of functions) for param.nContact for host-type B.
`timeDep.nContact.B`	is nContact of host-type B dependent on the absolute time of the simulation (TRUE/FALSE)?
`diff.nContact.B`	does nContact of host-type B depend on the environmental variable (set by the raster) (TRUE/FALSE).
`hostCount.nContact.B`	does nContact of host-type B vary with the host count (of either host-type A or B) in each raster cell? (TRUE/FALSE); if TRUE, diff.nContact.B should be TRUE.
`pTrans.B`	function that gives the probability of transmit a pathogen as a function of time since infection for host B.
`param.pTrans.B`	parameter names (list of functions) for the pExit for host-type B.
`timeDep.pTrans.B`	is pTrans of host-type B dependent on the absolute time of the simulation (TRUE/FALSE)?
`diff.pTrans.B`	does pTrans of host-type B depend on the environmental variable (set by the raster) (TRUE/FALSE).
`hostCount.pTrans.B`	does pTrans of host-type B vary with the host count (of either host-type A or B) in each raster cell? (TRUE/FALSE); if TRUE, diff.pTrans.B should be TRUE.
`prefix.host.B`	character(s) to be used as a prefix for the host B identification number.
`print.progress`	if TRUE, displays a progress bar (current time/length.sim).
`print.step`	print.progress is TRUE, step with which the progress message will be printed.

Details

The pExit and pTrans functions should return a single probability (a number between 0 and 1), and nContact a positive natural number (positive integer) or 0.

The param arguments should be a list of functions or NA. Each item name in the parameter list should have the same name as the argument in the corresponding function.

The use of timeDep (switch to TRUE) makes the corresponding function use the argument prestime (for "present time").

Value

An object of class nosoiSim, containing all results of the simulation.

Raster

The structure raster(s) provided provided should of class raster. High values of the environmental variable can attract hosts if attracted.by.raster is TRUE. Raster have to share the same space (i.e. also the same cell size and ID).

Order of Arguments

The user specified function's arguments should follow this order: t (mandatory), prestime (optional, only if timeDep is TRUE), current.env.value (optional, only if diff is TRUE), host.count.A or host.count.B (optional, only if hostCount is TRUE) and parameters specified in the list.

Structure Parameters

The pMove function should return a single probability (a number between 0 and 1), and sdMove a real number (keep in mind this number is related to your coordinate space).

The use of diff (switch to TRUE) makes the corresponding function use the argument current.env.value (for "current environmental value").

The use of hostCount (switch to TRUE) makes the corresponding function use the argument host.count.

Suffixes

The suffix .A or .B specifies if the considered function or parameter concerns host type A or B.

Examples


library(raster)

#Generating a raster for the movement
set.seed(860)

test.raster <- raster(nrows=100, ncols=100, xmn=-50, xmx=50, ymn=-50,ymx=50)
test.raster[] <- runif(10000, -80, 180)
test.raster <- focal(focal(test.raster, w=matrix(1, 5, 5), mean), w=matrix(1, 5, 5), mean)

t_incub_fct <- function(x){rnorm(x,mean = 5,sd=1)}
p_max_fct <- function(x){rbeta(x,shape1 = 5,shape2=2)}
p_Move_fct  <- function(t){return(0.1)}

sdMove_fct = function(t,current.env.value){return(100/(current.env.value+1))}

p_Exit_fct  <- function(t){return(0.08)}

proba <- function(t,p_max,t_incub){
 if(t <= t_incub){p=0}
 if(t >= t_incub){p=p_max}
 return(p)
}

time_contact = function(t){round(rnorm(1, 3, 1), 0)}

start.pos <- c(0,0)

set.seed(805)
test.nosoi <- nosoiSim(type="dual", popStructure="continuous",
                      length.sim=200,
                      max.infected.A=500,
                      max.infected.B=500,
                      init.individuals.A=1,
                      init.individuals.B=0,
                      init.structure.A=start.pos,
                      init.structure.B=NA,
                      structure.raster.A=test.raster,
                      structure.raster.B=test.raster,
                      pExit.A=p_Exit_fct,
                      param.pExit.A=NA,
                      timeDep.pExit.A=FALSE,
                      diff.pExit.A=FALSE,
                      pMove.A=p_Move_fct,
                      param.pMove.A=NA,
                      timeDep.pMove.A=FALSE,
                      diff.pMove.A=FALSE,
                      diff.sdMove.A=TRUE,
                      sdMove.A=sdMove_fct,
                      param.sdMove.A=NA,
                      attracted.by.raster.A=TRUE,
                      nContact.A=time_contact,
                      param.nContact.A=NA,
                      timeDep.nContact.A=FALSE,
                      diff.nContact.A=FALSE,
                      pTrans.A=proba,
                      param.pTrans.A=list(p_max=p_max_fct,
                                          t_incub=t_incub_fct),
                      timeDep.pTrans.A=FALSE,
                      diff.pTrans.A=FALSE,
                      prefix.host.A="H",
                      pExit.B=p_Exit_fct,
                      param.pExit.B=NA,
                      timeDep.pExit.B=FALSE,
                      diff.pExit.B=FALSE,
                      pMove.B=p_Move_fct,
                      param.pMove.B=NA,
                      timeDep.pMove.B=FALSE,
                      diff.pMove.B=FALSE,
                      diff.sdMove.B=TRUE,
                      sdMove.B=sdMove_fct,
                      param.sdMove.B=NA,
                      attracted.by.raster.B=TRUE,
                      nContact.B=time_contact,
                      param.nContact.B=NA,
                      timeDep.nContact.B=FALSE,
                      diff.nContact.B=FALSE,
                      pTrans.B=proba,
                      param.pTrans.B=list(p_max=p_max_fct,
                                          t_incub=t_incub_fct),
                      timeDep.pTrans.B=FALSE,
                      diff.pTrans.B=FALSE,
                      prefix.host.B="V")
test.nosoi

nosoi documentation built on May 29, 2024, 9 a.m.