setDispersalPathogen: Set pathogen dispersal

In landsepi: Landscape Epidemiology and Evolution

Set pathogen dispersal

Description

Updates a LandsepiParams object with a pathogen dispersal matrix.

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 field of the landscape to any other field. It can be generated manually, or, alternatively, via loadDispersalPathogen. The size of the matrix must match the number of fields 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 field of the landscape to any other field (default identity matrix) . It can be generated manually, or, alternatively, via loadDispersalPathogen. The size of the matrix must match the number of fields 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 disersal matrix a square matrix whose size is the number of fields in the landscape and whose elements are, for each line i and each column i' the probability that propagules migrate from field i to field 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)

landsepi documentation built on July 26, 2023, 5:36 p.m.