Creates and initialises a LandespiParams object with default parameters.
# S4 method for 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_exp = 0, latent_period_var
= 0, infectious_period_exp = 0, infectious_period_var = 0, sigmoid_kappa = 0,
sigmoid_sigma = 0, sigmoid_plateau = 1),
PI0 = 0,
DispHost = vector(),
DispPatho = vector(),
OutputDir = normalizePath(character(getwd())),
OutputGPKG = "landsepi_landscape.gpkg",
Outputs = list(epid_outputs = "", evol_outputs = "", thres_breakdown = NA, GLAnoDis =
NA, audpc100S = NA),
TimeParam = list(),
Seed = NULL,
...
)a LandsepiParam object.
a landscape as sf object.
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.
a dataframe of parameters associated with each host genotype (i.e. cultivars, lines) when cultivated in pure crops.
a list containing, for each host genotype, the indices of carried resistance genes.
a data.frame of parameters associated with each resistance gene and with the evolution of each corresponding pathogenicity gene.
a list of pathogen aggressiveness parameters on a susceptible host for a pathogen genotype not adapted to resistance.
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.
a vectorized matrix giving the probability of host dispersal from any field of the landscape to any other field
a vectorized matrix giving the probability of pathogen dispersal from any field of the landscape to any other field.
the directory for simulation outputs
the name of the output GPKG file containing parameters of the deployment strategy
a list of outputs parameters.
a list of time parameters.
an integer used as seed value (for random number generator).
more options