landsepi (version 1.5.2)

setInoculum: Set inoculum

Description

Updates a LandsepiParams object with the initial probability for an individual host to be infectious (i.e. state I) at the beginning of the simulation (i.e. t=0).

Usage

setInoculum(params, val = 5e-04)

Value

a LandsepiParams object

Arguments

params

a LandsepiParams object.

val

a numeric value (default = 5e-4) indicating the probability for the first cultivar to be infected by the first pathogen genotype in all polygons of the landscape (must be between 0 and 1). The parameter can also be entered as a 3D array of dimensions (1:Nhost,1:Npatho,1:Npoly) indicating the initial probability to be infectious, for each cultivar, pathogen genotype and polygon (independently from the possible presence of cultivars carrying resistance genes). It can be generated manually or, alternatively, via loadInoculum.

Details

Before setting the inoculum, one can use getMatrixGenePatho(), getMatrixCultivarPatho(), getMatrixCroptypePatho() and getMatrixPolyPatho() to acknowledge which pathogen genotypes are compatible to which genes, cultivars, croptypes and polygons.
Once setInoculum() is used, one can call inoculumToMatrix() to get the inoculum as a 3D array (1:Nhost,1:Npatho,1:Npoly)

See Also

inoculumToMatrix, loadInoculum

Examples

if (FALSE) {
simul_params <- createSimulParams()
simul_params <- setInoculum(simul_params, 1E-3)
simul_params@PI0
}