setDispersalPathogen {landsepi}

Set pathogen dispersal

Description

Updates a LandsepiParams object with a pathogen dispersal matrix. Note that landscape parameters must be set before updating setting dispersal.

Usage

setDispersalPathogen(params, mat_clonal, mat_sex = NULL)

Arguments

params

a LandsepiParams Object.

mat_clonal

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).

mat_sex

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).

Details

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).

Value

a LandsepiParam object.

See Also

loadDispersalPathogen

Examples

## Not run: 
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

## End(Not run)