initialize-methods: LandsepiParams
In landsepi: Landscape Epidemiology and Evolution

initialize,LandsepiParams-method

R Documentation

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),
  ReproSexProb = vector(),
  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.
`ReproSexProb`	a vector of size TimeParam$nTSpY +1 (end of season) of the probabilities for an infectious host to reproduce via sex rather than via cloning at each time step (days).
`PI0`	initial probability for the first host (whose index is 0) to be infectious (i.e. state I) at the beginning of the simulation. Must be between 0 and 1.
`DispHost`	a vectorized matrix giving the probability of host dispersal from any field of the landscape to any other field
`DispPathoClonal`	a vectorized matrix giving the probability of pathogen dispersal from any field of the landscape to any other field.
`DispPathoSex`	a vectorized matrix giving the probability of pathogen dispersal from any field of the landscape to any other field (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).
`...`	more options