LandsepiParams: Class LandsepiParams

In landsepi: Landscape Epidemiology and Evolution

Class LandsepiParams

Description

Landsepi simulation parameters

Details

An object of class LandsepiParams that can be created by calling createSimulParams

Slots

Landscape

a landscape as sf object. See loadLandscape

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. See loadCroptypes, setCroptypes and allocateCroptypeCultivars

Cultivars

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

CultivarsGenes

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

Genes

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

Pathogen

a list of i. pathogen aggressiveness parameters on a susceptible host for a pathogen genotype not adapted to resistance and ii. sexual reproduction parameters. See loadPathogen and setPathogen

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 step.

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. See setInoculum

DispHost

a vectorized matrix giving the probability of host dispersal from any field of the landscape to any other field. See loadDispersalHost and setDispersalHost

DispPathoClonal

a vectorized matrix giving the probability of pathogen dispersal (clonal propagules) from any field of the landscape to any other field. See loadDispersalPathogen and setDispersalPathogen

DispPathoSex

a vectorized matrix giving the probability of pathogen dispersal (sexual propagules) from any field of the landscape to any other field. See loadDispersalPathogen and setDispersalPathogen

Treatment

a list of parameters to simulate the effect of chemical treatments on the pathogen, see loadTreatment and setTreatment

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. See loadOutputs and setOutputs

TimeParam

a list of time parameters. See setTime

Seed

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

landsepi documentation built on Aug. 8, 2025, 6:24 p.m.