All functions

AgriLand()

Landscape allocation

CroptypeBDD2Params()

CroptypeBDD2Params

CultivarBDD2Params()

CultivarBDD2Params

CultivarGeneBDD2Params()

CultivarGeneBDD2Params

Cultivars_list

Cultivars Type list

GPKGAddInputData()

GPKGAddInputData

GPKGAddTables()

GPKGAddTables

GeneBDD2Params()

GeneBDD2Params

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

checkPathogen()

Check pathogen

checkSimulParams()

Check simulation parameters

checkTime()

Check time

createLandscapeGPKG()

createLandscapeGPKG

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

getGPKGArea()

getGPKGArea

getGPKGCroptypes()

getGPKGCroptypes

getGPKGCroptypesRaw()

getGPKGCroptypesRaw

getGPKGCultivars()

getGPKGCultivars

getGPKGCultivarsGenes()

getGPKGCultivarsGenes

getGPKGGeneIDForCultivar()

getGPKGGeneIDForCultivar

getGPKGGenes()

getGPKGGenes

getGPKGRotation()

getGPKGRotation

initialize(<LandsepiParams>)

LandsepiParams

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 _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

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

params2CroptypeBDD()

params2CroptypeBDD

params2CultivarBDD()

params2CultivarBDD

params2GeneBDD()

params2GeneBDD

params2GeneListBDD()

params2GeneListBDD

periodic_cov()

Periodic covariance function

plot_allocation()

Plotting allocation of croptypes in a landscape

plot_freqPatho()

Plotting pathotype frequencies

plotland()

Plotting the landscape

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

setReproSexProb()

set a vector of probabilities for an infectious host to reproduce via sex rather than via cloning.

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

switch_patho_to_aggr()

Switch from index of genotype to indices of agressiveness on different components

video()

Generation of a video