Package index • 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