- 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.