getMatrixPolyPatho: Get the "polygon/pathogen genotype" compatibility matrix.

Description

Build the matrix indicating if infection is possible at the beginning of the season for every combination of polygon (rows) and pathogen genotype (columns).

Usage

getMatrixPolyPatho(params)

Value

an interaction matrix composed of 0 and 1 values.

Arguments

params: a LandsepiParams object.

Details

For each polygon, there is either possibility of infection by the pathogen genotype (value of 1), either complete protection (value of 0)

Examples

Run this code

if (FALSE) {
simul_params <- createSimulParams()
simul_params <- setTime(simul_params, Nyears = 1, nTSpY = 80)
simul_params <- setLandscape(simul_params, loadLandscape(id = 1))
gene1 <- loadGene(name = "MG 1", type = "majorGene")
gene2 <- loadGene(name = "MG 2", type = "majorGene")
genes <- data.frame(rbind(gene1, gene2), stringsAsFactors = FALSE)
simul_params <- setGenes(simul_params, genes)
cultivar1 <- loadCultivar(name = "Susceptible", type = "wheat")
cultivar2 <- loadCultivar(name = "Resistant1", type = "wheat")
cultivar3 <- loadCultivar(name = "Resistant2", type = "wheat")
cultivar4 <- loadCultivar(name = "Pyramid", type = "wheat")
cultivars <- data.frame(rbind(cultivar1, cultivar2, cultivar3, cultivar4)
, stringsAsFactors = FALSE)
simul_params <- setCultivars(simul_params, cultivars)
simul_params <- allocateCultivarGenes(simul_params, "Resistant1", c("MG 1"))
simul_params <- allocateCultivarGenes(simul_params, "Resistant2", c("MG 2"))
simul_params <- allocateCultivarGenes(simul_params, "Pyramid", c("MG 1", "MG 2"))
croptypes <- loadCroptypes(simul_params,
                           names = c("Susceptible crop",
                                     "Resistant crop 1",
                                     "Mixture S+R",
                                     "Mixture R1+R2",
                                     "Pyramid crop"))
croptypes <- allocateCroptypeCultivars(croptypes, "Susceptible crop", "Susceptible")
croptypes <- allocateCroptypeCultivars(croptypes, "Resistant crop 1", "Resistant1")
croptypes <- allocateCroptypeCultivars(croptypes, "Mixture S+R", c("Susceptible", "Resistant1"))
croptypes <- allocateCroptypeCultivars(croptypes, "Mixture R1+R2", c("Resistant1", "Resistant2"))
croptypes <- allocateCroptypeCultivars(croptypes, "Pyramid crop", c("Pyramid"))
simul_params <- setCroptypes(simul_params, croptypes)
simul_params <- allocateLandscapeCroptypes(simul_params, rotation_period = 0,
prop=rep(1/5,5), aggreg=3 , rotation_sequence = croptypes$croptypeID)
getMatrixPolyPatho(simul_params)
}