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landsepi (version 1.1.1)

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<80><99>) 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 Papax, Jean-Franois Rey, Luke G Barrett, Peter H Thrall (2018) .

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Version

Install

install.packages('landsepi')

Monthly Downloads

255

Version

1.1.1

License

GPL (>= 2) | file LICENSE

Maintainer

Jean-Francois Rey

Last Published

October 5th, 2021

Functions in landsepi (1.1.1)

AgriLand

Landscape allocation
allocateCroptypeCultivars

Allocate cultivars to one croptype
CultivarGeneBDD2Params

CultivarGeneBDD2Params
GeneBDD2Params

GeneBDD2Params
GPKGAddTables

GPKGAddTables
allocateCultivarGenes

Allocate genes to a cultivar
CultivarBDD2Params

CultivarBDD2Params
LandsepiParams

Class LandsepiParams
GPKGAddInputData

GPKGAddInputData
checkGenes

Check genes
CroptypeBDD2Params

CroptypeBDD2Params
checkOutputs

Check outputs
checkLandscape

Check the landscape
checkCultivars

Check cultivars
checkTime

Check time
checkCultivarsGenes

Check cultivars genes
getGPKGArea

getGPKGArea
checkInoculum

Check inoculum
getGPKGCultivars

getGPKGCultivars
evol_output

Generation of evolutionary model outputs
createSimulParams

Create a LandsepiParams object.
createLandscapeGPKG

createLandscapeGPKG
demo_landsepi

Package demonstration
checkDispersalHost

Check host dispersal
loadSimulParams

Load simulation parameters
landscapeTEST

Landscapes
loadPathogen

Load pathogen parameters
is.wholenumber

is.wholenumber
is.in.01

is.in.01
is.strict.positive

is.strict.positive
invlogit

Inverse logit function
is.positive

is.positive
checkCroptypes

Check croptypes
allocateLandscapeCroptypes

Allocate croptypes to the landscape
dispP

Dispersal matrices for rust fungi of cereal crops.
saveDeploymentStrategy

Save landscape and deployment strategy
setCroptypes

Set croptypes
runSimul

Run a simulation
params2GeneBDD

params2GeneBDD
initialize,LandsepiParams-method

LandsepiParams
loadCroptypes

Load Croptypes
landsepi-package

Landscape Epidemiology and Evolution
params2CultivarBDD

params2CultivarBDD
getGPKGRotation

getGPKGRotation
setCultivars

Set cultivars
getGPKGCultivarsGenes

getGPKGCultivarsGenes
checkDispersalPathogen

Check pathogen dispersal
checkPathogen

Check pathogen
checkSimulParams

Check simulation parameters
video

Generation of a video
runShinyApp

runShinyApp
setOutputs

Set outputs
setLansdcape

Set the landscape
resetCultivarsGenes

Reset cultivars genes
getGPKGCroptypes

getGPKGCroptypes
loadCultivar

Load a cultivar
loadDispersalHost

Load a host dispersal matrix
getGPKGCroptypesRaw

getGPKGCroptypesRaw
epid_output

Generation of epidemiological and economic model outputs
getGPKGGeneIDForCultivar

getGPKGGeneIDForCultivar
getGPKGGenes

getGPKGGenes
loadGene

Load a gene
loadDispersalPathogen

Load a pathogen dispersal matrix
loadLandscape

Load a landscape
loadOutputs

Load outputs
periodic_cov

Periodic covariance function
setDispersalPathogen

Set pathogen dispersal
setDispersalHost

Set host dispersal
setSeedValue

setSeedValue
params2GeneListBDD

params2GeneListBDD
logit

Logit function
params2CroptypeBDD

params2CroptypeBDD
multiN

Allocation of cultivars
setTime

Set time parameters
plot_allocation

Plotting allocation of croptypes in a landscape
model_landsepi

Model for Landscape Epidemiology & Evolution
plotland

Plotting the landscape
print

print
setPathogen

Set the pathogen
setSeed

Set the seed
switch_patho_to_aggr

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

summary
plot_freqPatho

Plotting pathotype frequencies
setInoculum

Set inoculum
setGenes

Set genes
show

show
simul_landsepi

Simulation with input parameters as data.frames.