Landsepi simulation parameters
Landscapea landscape as sf object. See loadLandscape
Croptypesa 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
Cultivarsa dataframe of parameters associated with each host genotype (i.e. cultivars, lines)
when cultivated in pure crops.See loadCultivar and setCultivars
CultivarsGenesa list containing, for each host genotype, the indices of carried resistance genes.
See allocateCultivarGenes
Genesa data.frame of parameters associated with each resistance gene and with the evolution of
each corresponding pathogenicity gene. See loadGene and setGenes
Pathogena 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
ReproSexProba 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.
PI0initial 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
DispHosta vectorized matrix giving the probability of host dispersal
from any field of the landscape to any other field. See loadDispersalHost and setDispersalHost
DispPathoClonala vectorized matrix giving the probability of pathogen dispersal (clonal propagules)
from any field of the landscape to any other field. See loadDispersalPathogen and setDispersalPathogen
DispPathoSexa vectorized matrix giving the probability of pathogen dispersal (sexual propagules)
from any field of the landscape to any other field. See loadDispersalPathogen and setDispersalPathogen
Treatmenta list of parameters to simulate the effect of chemical treatments on the pathogen,
see loadTreatment and setTreatment
OutputDirthe directory for simulation outputs
OutputGPKGthe name of the output GPKG file containing parameters of the deployment strategy
Outputsa list of outputs parameters. See loadOutputs and setOutputs
TimeParama list of time parameters. See setTime
Seedan integer used as seed value (for random number generator). See setTime
An object of class LandsepiParams that can be created by calling createSimulParams