setDispersalPathogen.Rd
Updates a LandsepiParams object with a pathogen dispersal matrix. Note that landscape parameters must be set before updating setting dispersal.
setDispersalPathogen(params, mat_clonal, mat_sex = NULL)
a LandsepiParams Object.
a square matrix giving the probability of pathogen dispersal
(clonal propagules) from any polygon of the landscape to any other polygon.
It can be generated manually, or, alternatively, via loadDispersalPathogen
.
The size of the matrix must match the number of polygons in the landscape, and lines of
the matrix may sum to 1 (reflecting boundaries) or be <1 (absorbing boundaries).
a square matrix giving the probability of pathogen dispersal (sexual propagules)
from any polygon of the landscape to any other polygon (default identity matrix) .
It can be generated manually, or, alternatively, via loadDispersalPathogen
.
The size of the matrix must match the number of polygons in the landscape, and lines of
the matrix may sum to 1 (reflecting boundaries) or be <1 (absorbing boundaries).
a LandsepiParam object.
See tutorial (vignettes) on how to use your own landscape and compute your own pathogen dispersal kernel. The dispersal matrix a square matrix whose size is the number of polygons in the landscape and whose elements are, for each line i and each column i' the probability that propagules migrate from polygon i to polygon i'. Lines of the matrix can be normalised to sum to 1 (reflective boundaries); otherwise propagules dispersing outside the landscape are lost (absorbing boundaries).
if (FALSE) {
simul_params <- createSimulParams()
simul_params <- setLandscape(simul_params, loadLandscape(1))
d <- loadDispersalPathogen(1)
simul_params <- setDispersalPathogen(simul_params, d[[1]], d[[2]])
simul_params@DispPathoClonal
}