# Landscape Epidemiology and Evolution

## Documentation for package ‘landsepi’ version 1.5.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E G I L M P R S U V

landsepi-package | Landscape Epidemiology and Evolution

## -- A --

AgriLand | Landscape allocation
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

## -- C --

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
checkPI0_mat | Check the array PI0_mat when entered manually in 'loadInoculum()'.
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.
Cultivars_list | Cultivars Type list

## -- D --

demo_landsepi | Package demonstration
dispP | Dispersal matrices for rust fungi of cereal crops.
dispP_1 | Dispersal matrices for rust fungi of cereal crops.
dispP_2 | Dispersal matrices for rust fungi of cereal crops.
dispP_3 | Dispersal matrices for rust fungi of cereal crops.
dispP_4 | Dispersal matrices for rust fungi of cereal crops.
dispP_5 | Dispersal matrices for rust fungi of cereal crops.

## -- E --

epid_output | Generation of epidemiological and economic model outputs
evol_output | Generation of evolutionary model outputs

## -- G --

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.

## -- I --

initialize-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

## -- L --

landscapeTEST | Landscapes
landscapeTEST1 | Landscapes
landscapeTEST2 | Landscapes
landscapeTEST3 | Landscapes
landscapeTEST4 | Landscapes
landscapeTEST5 | Landscapes
landsepi | Landscape Epidemiology and Evolution
LandsepiParams | Class LandsepiParams
LandsepiParams-class | Class LandsepiParams
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

## -- M --

model_landsepi | Model for Landscape Epidemiology & Evolution
multiN | Allocation of cultivars

## -- P --

periodic_cov | Periodic covariance function
plotland | Plotting the landscape
plot_allocation | Plotting allocation of croptypes in a landscape
plot_freqPatho | Plotting pathotype frequencies
price_reduction | Price reduction function
print | print
print-method | print

## -- R --

resetCultivarsGenes | Reset cultivars genes
runShinyApp | runShinyApp
runSimul | Run a simulation

## -- S --

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
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
show-method | show
simul_landsepi | Simulation with input parameters as data.frames.
summary | summary
summary-method | summary
survivalProbToMatrix | Survival probability To Matrix
switch_patho_to_aggr | Switch from index of genotype to indices of agressiveness on different components

## -- U --

updateReproSexProb | Update the probability of sexual reproduction
updateSurvivalProb | Update pathogen survival probability during the off-season

## -- V --

video | Generation of a video