Function reference • landsepi

All functions
`AgriLand()`	Landscape allocation
`Cultivars_list`	Cultivars Type list
`LandsepiParams` `LandsepiParams-class`	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_1` `dispP_2` `dispP_3` `dispP_4` `dispP_5`	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>)`	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
`landscapeTEST1` `landscapeTEST2` `landscapeTEST3` `landscapeTEST4` `landscapeTEST5`	Landscapes
`landsepi-package` `landsepi`	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(<LandsepiParams>)`	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
`setLandscape()`	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(<LandsepiParams>)`	show
`simul_landsepi()`	Simulation with input parameters as data.frames.
`summary(<LandsepiParams>)`	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

Reference

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