setPathogen.Rd
Updates a LandsepiParams object with pathogen parameters
setPathogen(params, patho_params)
a LandsepiParams Object.
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
.
a LandsepiParams object
a set of parameters representative of rust fungi, downy mildew or black sigatoka
can be loaded via loadPathogen
.
if (FALSE) {
simul_params <- createSimulParams()
simul_params <- setPathogen(simul_params, loadPathogen())
simul_params@Pathogen
}