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landsepi (version 1.2.5)

Landscape Epidemiology and Evolution

Description

A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies. It is based on a spatial geometry for describing the landscape and allocation of different cultivars, a dispersal kernel for the dissemination of the pathogen, and a SEIR ('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step. It provides a useful tool to assess the performance of a wide range of deployment options with respect to their epidemiological, evolutionary and economic outcomes. Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett, Peter H Thrall (2018) .

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Version

Install

install.packages('landsepi')

Monthly Downloads

286

Version

1.2.5

License

GPL (>= 2) | file LICENSE

Maintainer

Jean-Francois Rey

Last Published

February 27th, 2023

Functions in landsepi (1.2.5)

AgriLand

Landscape allocation
CultivarBDD2Params

CultivarBDD2Params
Cultivars_list

Cultivars Type list
CroptypeBDD2Params

CroptypeBDD2Params
CultivarGeneBDD2Params

CultivarGeneBDD2Params
GPKGAddTables

GPKGAddTables
checkGenes

Check genes
GPKGAddInputData

GPKGAddInputData
antideriv_verhulst

Antiderivative of the Verhulst logistic function
checkInoculum

Check inoculum
GeneBDD2Params

GeneBDD2Params
allocateCultivarGenes

Allocate genes to a cultivar
allocateLandscapeCroptypes

Allocate croptypes to the landscape
LandsepiParams

Class LandsepiParams
checkTime

Check time
checkCultivars

Check cultivars
checkCroptypes

Check croptypes
compute_audpc100S

Compute AUDPC in a 100% susceptible field
allocateCroptypeCultivars

Allocate cultivars to one croptype
createLandscapeGPKG

createLandscapeGPKG
checkTreatment

Check treatment
checkCultivarsGenes

Check cultivars genes
createSimulParams

Create a LandsepiParams object.
checkDispersalHost

Check host dispersal
demo_landsepi

Package demonstration
checkDispersalPathogen

Check pathogen dispersal
checkLandscape

Check the landscape
checkOutputs

Check outputs
getGPKGGeneIDForCultivar

getGPKGGeneIDForCultivar
getGPKGGenes

getGPKGGenes
evol_output

Generation of evolutionary model outputs
checkPathogen

Check pathogen
getGPKGCultivars

getGPKGCultivars
is.positive

is.positive
is.strict.positive

is.strict.positive
loadDispersalPathogen

Load pathogen dispersal matrices
loadGene

Load a gene
getGPKGArea

getGPKGArea
checkSimulParams

Check simulation parameters
loadTreatment

Load treatment parameters
getGPKGCroptypes

getGPKGCroptypes
getGPKGCultivarsGenes

getGPKGCultivarsGenes
params2CroptypeBDD

params2CroptypeBDD
logit

Logit function
dispP

Dispersal matrices for rust fungi of cereal crops.
params2CultivarBDD

params2CultivarBDD
model_landsepi

Model for Landscape Epidemiology & Evolution
multiN

Allocation of cultivars
getGPKGCroptypesRaw

getGPKGCroptypesRaw
epid_output

Generation of epidemiological and economic model outputs
is.wholenumber

is.wholenumber
invlogit

Inverse logit function
landscapeTEST

Landscapes
is.in.01

is.in.01
runSimul

Run a simulation
loadLandscape

Load a landscape
loadOutputs

Load outputs
saveDeploymentStrategy

Save landscape and deployment strategy
landsepi-package

Landscape Epidemiology and Evolution
show

show
loadCroptypes

Load Croptypes
loadPathogen

Load pathogen parameters
params2GeneBDD

params2GeneBDD
getGPKGRotation

getGPKGRotation
initialize,LandsepiParams-method

LandsepiParams
periodic_cov

Periodic covariance function
loadCultivar

Load a cultivar
plot_allocation

Plotting allocation of croptypes in a landscape
setCroptypes

Set croptypes
simul_landsepi

Simulation with input parameters as data.frames.
setCultivars

Set cultivars
params2GeneListBDD

params2GeneListBDD
price_reduction

Price reduction function
setSeed

Set the seed
print

print
loadDispersalHost

Load a host dispersal matrix
loadSimulParams

Load simulation parameters
setLansdcape

Set the landscape
setSeedValue

setSeedValue
setOutputs

Set outputs
summary

summary
resetCultivarsGenes

Reset cultivars genes
switch_patho_to_aggr

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

runShinyApp
setDispersalHost

Set host dispersal
setGenes

Set genes
setInoculum

Set inoculum
setDispersalPathogen

Set pathogen dispersal
video

Generation of a video
setPathogen

Set the pathogen
plot_freqPatho

Plotting pathotype frequencies
plotland

Plotting the landscape
setReproSexProb

Set the vector of probabilities of sexual reproduction
setTime

Set time parameters
setTreatment

Set chemical treatments