setPathogen {landsepi}

Set the pathogen

Description

Updates a LandsepiParams object with pathogen parameters

Usage

setPathogen(params, patho_params)

Arguments

params

a LandsepiParams Object.

patho_params

a list of pathogen aggressiveness parameters on a susceptible host for a pathogen genotype not adapted to resistance:

• infection_rate = maximal expected infection rate of a propagule on a healthy host,

• propagule_prod_rate = maximal expected effective propagule production rate of an infectious host per time step,

• latent_period_mean = minimal expected duration of the latent period,

• latent_period_var = variance of the latent period duration,

• infectious_period_mean = maximal expected duration of the infectious period,

• infectious_period_var = variance of the infectious period duration,

• survival_prob = probability for a propagule to survive the off-season,

• repro_sex_prob = probability for an infectious host to reproduce via sex rather than via cloning,

• sigmoid_kappa = kappa parameter of the sigmoid contamination function,

• sigmoid_sigma = sigma parameter of the sigmoid contamination function,

• sigmoid_plateau = plateau parameter of the sigmoid contamination function,

• sex_propagule_viability_limit = maximum number of cropping seasons up to which a sexual propagule is viable

• sex_propagule_release_mean = average number of seasons after which a sexual propagule is released.

• clonal_propagule_gradual_release = whether or not clonal propagules surviving the bottleneck are gradually released along the following cropping season.

It can be generated manually, or, alternatively, via loadPathogen.

Details

a set of parameters representative of rust fungi, downy mildew or black sigatoka can be loaded via loadPathogen.

Value

a LandsepiParams object

See Also

loadPathogen

Examples

## Not run: 
simul_params <- createSimulParams()
simul_params <- setPathogen(simul_params, loadPathogen())
simul_params@Pathogen

## End(Not run)