Update pathogen survival probability during the off-season

update survival probability of the pathogen with a probability value for every simulated year (number of years = Nyears) and every croptype (number of croptypes = Ncroptypes). Note that time parameters, pathogen and croptypes must be set before updating survival probabilities.

updateSurvivalProb(params, mat_year = NULL, mat_croptype = NULL, mat = NULL)

Arguments

params

a LandsepiParams object

mat_year

a vector of size Nyear, giving survival probabilities for every year (replicated for every croptype).

mat_croptype

a vector of size Ncroptypes, giving survival probabilities for every croptype (replicated for every year).

mat

a matrix of dimension (Nyears, Ncroptypes) giving survival probabilities for every year (rows) and every croptype (columns).

Value

a LandsepiParams object updated.

Details

Unless the matrix mat is filled, the matrix containing the survival probability during the offseason is computed for every year and croptype with mat[year, croptype] = mat_year[year] * mat_croptype[croptype].

Examples

if (FALSE) {
simul_params <- createSimulParams()
simul_params <- setTime(simul_params, Nyears=10, nTSpY=120)
simul_params <- setPathogen(simul_params, loadPathogen("rust"))

cultivar1 <- loadCultivar(name = "Susceptible", type = "growingHost")
cultivar2 <- loadCultivar(name = "Resistant", type = "growingHost")
cultivars <- data.frame(rbind(cultivar1, cultivar2), stringsAsFactors = FALSE)
simul_params <- setCultivars(simul_params, cultivars)

croptypes <- loadCroptypes(simul_params
, names = c("Susceptible crop", "Resistant crop", "Mixture"))
croptypes <- allocateCroptypeCultivars(croptypes, "Susceptible crop", "Susceptible")
croptypes <- allocateCroptypeCultivars(croptypes, "Resistant crop", "Resistant")
croptypes <- allocateCroptypeCultivars(croptypes, "Mixture", c("Susceptible", "Resistant"))
simul_params <- setCroptypes(simul_params, croptypes)
Ncroptypes <- nrow(simul_params@Croptypes)
Nyears <- simul_params@TimeParam$Nyears

## Same probability in every croptype:
simul_params <- updateSurvivalProb(simul_params, mat_year=1:Nyears/100)
simul_params@Pathogen
## Same probability every year:
simul_params <- updateSurvivalProb(simul_params, mat_croptype=1:Ncroptypes/10)
simul_params@Pathogen
## specific probability for different croptypes and years:
simul_params <- updateSurvivalProb(simul_params
, mat_year=1:Nyears/100, mat_croptype=1:Ncroptypes/10)
simul_params@Pathogen
## One probability per year and per croptype:
simul_params <- updateSurvivalProb(simul_params
, mat=matrix(runif(Nyears*Ncroptypes), ncol=Ncroptypes))
simul_params@Pathogen
survivalProbToMatrix(simul_params)
}