getMatrixCultivarPatho: Get the "cultivar/pathogen genotype" compatibility matrix.

In landsepi: Landscape Epidemiology and Evolution

Get the "cultivar/pathogen genotype" compatibility matrix.

Description

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

Usage

getMatrixCultivarPatho(params)

Arguments

params

a LandsepiParams object.

Details

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

Value

an interaction matrix composed of 0 and 1 values.

See Also

getMatrixGenePatho, getMatrixCroptypePatho, getMatrixPolyPatho

Examples

## Not run: 
simul_params <- createSimulParams()
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 = "monoResistant1", type = "wheat")
cultivar3 <- loadCultivar(name = "monoResistant2", 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, "monoResistant1", c("MG 1"))
simul_params <- allocateCultivarGenes(simul_params, "monoResistant2", c("MG 2"))
simul_params <- allocateCultivarGenes(simul_params, "Pyramid", c("MG 1", "MG 2"))
getMatrixCultivarPatho(simul_params)

## End(Not run)

landsepi documentation built on Sept. 23, 2024, 5:11 p.m.