setTreatment {landsepi}

Set chemical treatments

Description

Updates a LandsepiParams object with treatment parameters

Usage

setTreatment(params, treatment_params)

Arguments

params

a LandsepiParams Object.

treatment_params

list of parameters related to pesticide treatments:

• treatment_degradation_rate = degradation rate (per time step) of chemical concentration,

• treatment_efficiency = maximal efficiency of chemical treatments (i.e. fractional reduction of pathogen infection rate at the time of application),

• treatment_timesteps = vector of time steps corresponding to treatment application dates,

• treatment_cultivars = vector of indices of the cultivars that receive treatments,

• treatment_cost = cost of a single treatment application (monetary units/ha)

• treatment_application_threshold = vector of thresholds (i.e. disease severity, one for each treated cultivar) above which the treatment is applied in a polygon.

Details

Chemical treatment is applied in a polygon only if disease severity (i.e. I/N) in this polygon exceeds the threshold given by treatment_application_threshold. Treatment efficiency is maximum (i.e. equal to the parameter treatment_efficiency) at the time of treatment application (noted t*); then it decreases with time (i.e. natural pesticide degradation) and host growth (i.e. new biomass is not protected by treatments): protected by treatments):Efficiency of the treatment at time t after the application date is given by: efficiency(t) = treatment\_efficiency / (1 + exp(a-b*C(t))) with C(t)= C_1 * C_2:

• C_1 = exp(- treatment\_degradation\_rate * \Delta t) is the reduction of fungicide concentration due to time (e.g. natural degradation, volatilization, weathering), with \Delta t = t - t* the timelag passed since the time of treatment application.

• C_2 = min(1, N(t*) / N(t)) is the reduction of fungicide concentration due to plant growth, since new plant tissue is not covered by fungicide. N(t*) and N(t) being the number of host individuals a the time of treatment t* and at time t, respectively.

• a \in [3.5 ; 4.5] and b \in [8 ; 9] are shape parameters.

An empty list of treatments (i.e. absence of application) can be loaded using loadPathogen.

Value

a LandsepiParams object

See Also

loadTreatment

Examples

## Not run: 
t <- loadTreatment()
simul_params <- setTreatment(simul_params, t)
simul_params@Treatment

## End(Not run)