initialize,LandsepiParams-method {landsepi}

LandsepiParams

Description

Creates and initialises a LandsepiParams object with default parameters.

Usage

## S4 method for signature 'LandsepiParams'
initialize(
  .Object,
  Landscape = st_sf(st_sfc()),
  Croptypes = data.frame(),
  Cultivars = data.frame(matrix(ncol = length(.cultivarsColNames), nrow = 0, dimnames =
    list(NULL, .cultivarsColNames))),
  CultivarsGenes = data.frame(),
  Genes = data.frame(matrix(ncol = length(.geneColNames), nrow = 0, dimnames = list(NULL,
    .geneColNames))),
  Pathogen = list(name = "no pathogen", survival_prob = 0, repro_sex_prob = 0,
    infection_rate = 0, propagule_prod_rate = 0, latent_period_mean = 0,
    latent_period_var = 0, infectious_period_mean = 0, infectious_period_var = 0,
    sigmoid_kappa = 0, sigmoid_sigma = 0, sigmoid_plateau = 1,
    sex_propagule_viability_limit = 0, sex_propagule_release_mean = 0,
    clonal_propagule_gradual_release = 0),
  PI0 = 0,
  DispHost = vector(),
  DispPathoClonal = vector(),
  DispPathoSex = vector(),
  Treatment = list(treatment_degradation_rate = 0.1, treatment_efficiency = 0,
    treatment_timesteps = vector(), treatment_cultivars = vector(), treatment_cost = 0,
    treatment_application_threshold = vector()),
  OutputDir = normalizePath(character(getwd())),
  OutputGPKG = "landsepi_landscape.gpkg",
  Outputs = list(epid_outputs = "", evol_outputs = "", thres_breakdown = NA, audpc100S =
    NA),
  TimeParam = list(Nyears = 0, nTSpY = 0),
  Seed = NULL,
  ...
)

Arguments

.Object

a LandsepiParam object.

Landscape

a landscape as sf object.

Croptypes

a dataframe with three columns named 'croptypeID' for croptype index, 'cultivarID' for cultivar index and 'proportion' for the proportion of the cultivar within the croptype.

Cultivars

a dataframe of parameters associated with each host genotype (i.e. cultivars, lines) when cultivated in pure crops.

CultivarsGenes

a list containing, for each host genotype, the indices of carried resistance genes.

Genes

a data.frame of parameters associated with each resistance gene and with the evolution of each corresponding pathogenicity gene.

Pathogen

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

PI0

vector of length Npoly.Nhost.Npatho filled with the initial probabilities for hosts to be infectious (i.e. state I), for each pathogen genotype, at the beginning of the simulation.

DispHost

a vectorized matrix giving the probability of host dispersal from any polygon of the landscape to any other polygon

DispPathoClonal

a vectorized matrix giving the probability of pathogen dispersal from any polygon of the landscape to any other polygon.

DispPathoSex

a vectorized matrix giving the probability of pathogen dispersal from any polygon of the landscape to any other polygon (sexual propagule).

Treatment

a list of chemical treatment parameters (indices of treated cultivars, times of application, efficiency and degradation rate)

OutputDir

the directory for simulation outputs

OutputGPKG

the name of the output GPKG file containing parameters of the deployment strategy

Outputs

a list of outputs parameters.

TimeParam

a list of time parameters.

Seed

an integer used as seed value (for random number generator).

...

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