AgriLand                Landscape allocation
Cultivars_list          Cultivars Type list
LandsepiParams          Class LandsepiParams
allocateCroptypeCultivars
                        Allocate cultivars to one croptype
allocateCultivarGenes   Allocate genes to a cultivar
allocateLandscapeCroptypes
                        Allocate croptypes to the landscape
antideriv_verhulst      Antiderivative of the Verhulst logistic
                        function
checkCroptypes          Check croptypes
checkCultivars          Check cultivars
checkCultivarsGenes     Check cultivars genes
checkDispersalHost      Check host dispersal
checkDispersalPathogen
                        Check pathogen dispersal
checkGenes              Check genes
checkInoculum           Check inoculum
checkLandscape          Check the landscape
checkOutputs            Check outputs
checkPI0_mat            Check the array PI0_mat when entered manually
                        in 'loadInoculum()'.
checkPathogen           Check pathogen
checkSimulParams        Check simulation parameters
checkTime               Check time
checkTreatment          Check treatment
compute_audpc100S       Compute AUDPC in a single 100% susceptible
                        field
createSimulParams       Create a LandsepiParams object.
demo_landsepi           Package demonstration
dispP                   Dispersal matrices for rust fungi of cereal
                        crops.
epid_output             Generation of epidemiological and economic
                        model outputs
evol_output             Generation of evolutionary model outputs
getMatrixCroptypePatho
                        Get the "croptype/pathogen genotype"
                        compatibility matrix.
getMatrixCultivarPatho
                        Get the "cultivar/pathogen genotype"
                        compatibility matrix.
getMatrixGenePatho      Get the "resistance gene/pathogen genotype"
                        compatibility matrix.
getMatrixPolyPatho      Get the "polygon/pathogen genotype"
                        compatibility matrix.
initialize,LandsepiParams-method
                        LandsepiParams
inoculumToMatrix        Inoculum To Matrix
invlogit                Inverse logit function
is.in.01                is.in.01
is.positive             is.positive
is.strict.positive      is.strict.positive
is.wholenumber          is.wholenumber
landscapeTEST           Landscapes
landsepi-package        Landscape Epidemiology and Evolution
loadCroptypes           Load Croptypes
loadCultivar            Load a cultivar
loadDispersalHost       Load a host dispersal matrix
loadDispersalPathogen   Load pathogen dispersal matrices
loadGene                Load a gene
loadInoculum            Load Inoculum
loadLandscape           Load a landscape
loadOutputs             Load outputs
loadPathogen            Load pathogen parameters
loadSimulParams         Load simulation parameters
loadTreatment           Load treatment parameters
logit                   Logit function
model_landsepi          Model for Landscape Epidemiology & Evolution
multiN                  Allocation of cultivars
periodic_cov            Periodic covariance function
plot_allocation         Plotting allocation of croptypes in a landscape
plot_freqPatho          Plotting pathotype frequencies
plotland                Plotting the landscape
price_reduction         Price reduction function
print                   print
resetCultivarsGenes     Reset cultivars genes
runShinyApp             runShinyApp
runSimul                Run a simulation
saveDeploymentStrategy
                        Save landscape and deployment strategy
setCroptypes            Set croptypes
setCultivars            Set cultivars
setDispersalHost        Set host dispersal
setDispersalPathogen    Set pathogen dispersal
setGenes                Set genes
setInoculum             Set inoculum
setLansdcape            Set the landscape
setOutputs              Set outputs
setPathogen             Set the pathogen
setSeed                 Set the seed
setSeedValue            setSeedValue
setTime                 Set time parameters
setTreatment            Set chemical treatments
show                    show
simul_landsepi          Simulation with input parameters as
                        data.frames.
summary                 summary
survivalProbToMatrix    Survival probability To Matrix
switch_patho_to_aggr    Switch from index of genotype to indices of
                        agressiveness on different components
updateReproSexProb      Update the probability of sexual reproduction
updateSurvivalProb      Update pathogen survival probability during the
                        off-season
video                   Generation of a video
