General presentation of the package | Initialisation of simulation parameters | Setting the seed and time parameters | Setting pathogen parameters | Setting the landscape and pathogen dispersal | Setting croptypes, cultivars and resistance genes | Cultivars | Resistance genes | Allocating genes to cultivars | Allocating cultivars to croptypes | Allocating croptypes to fields of the landscape | Setting the inoculum | Scenario 1 (default). Only the avirulent pathogen on the susceptible cultivar in all fields (global inoculum) | Scenario 2. Only the avirulent pathogen on the susceptible cultivar in only some fields (local inoculum) | Scenario 3. A diversity of pathogen genotypes in the inoculum, in all fields (global inoculum) | Scenario 4. A diversity of pathogen genotypes in the inoculum, in some fields only (local inoculum) | Scenario 5. Custom 3D array to define the inoculum | Visualization | Updating the survival probability during the off-season | Setting chemical treatments | Choosing output variables | Equations | Parameterisation | Running the simulation

Initialisation of simulation parameters, seed, time and landscape parameters | Setting the probability of sexual reproduction | Setting the time of release of propagules produced at the end of a cropping season | Sexual propagules | Clonal propagules | Setting pathogen dispersal (both for sexual and clonal propagules) | Setting recombination between resistance genes | Setting croptypes, cultivars and resistance genes | Running the simulation

Write the experimental design | Run the simulations | Compute your own output variables

Using your own landscape | Using your own croptype allocation | Computing the dispersal matrix | An example | Plotting landscape and dispersal