updateSurvivalProb {landsepi}

Update pathogen survival probability during the off-season

Description

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.

Usage

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).

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].

Value

a LandsepiParams object updated.

See Also

survivalProbToMatrix

Examples

## Not run: 
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)

## End(Not run)