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landsepi (version 1.5.2)

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

295

Version

1.5.2

License

GPL (>= 2) | file LICENSE

Homepage

https://landsepi.pages-forge.inrae.fr/landsepi

Maintainer

Jean-Francois Rey

Last Published

July 31st, 2025

Functions in landsepi (1.5.2)

checkSimulParams

Check simulation parameters

checkDispersalHost

Check host dispersal

checkDispersalPathogen

Check pathogen dispersal

Generation of evolutionary model outputs

Package demonstration

Check the landscape

createSimulParams

Create a LandsepiParams object.

Dispersal matrices for rust fungi of cereal crops.

Check treatment

compute_audpc100S

Compute AUDPC in a single 100% susceptible field

Generation of epidemiological and economic model outputs

getMatrixCroptypePatho

Get the "croptype/pathogen genotype" compatibility matrix.

Check the array PI0_mat when entered manually in loadInoculum().

getMatrixCultivarPatho

Get the "cultivar/pathogen genotype" compatibility matrix.

is.strict.positive

is.strict.positive

getMatrixGenePatho

Get the "resistance gene/pathogen genotype" compatibility matrix.

getMatrixPolyPatho

Get the "polygon/pathogen genotype" compatibility matrix.

Inverse logit function

inoculumToMatrix

Inoculum To Matrix

initialize,LandsepiParams-method

loadDispersalPathogen

Load pathogen dispersal matrices

loadDispersalHost

Load a host dispersal matrix

Load pathogen parameters

plot_allocation

Plotting allocation of croptypes in a landscape

Load a landscape

landsepi-package

Landscape Epidemiology and Evolution

Periodic covariance function

Load a cultivar

Load treatment parameters

Model for Landscape Epidemiology & Evolution

Allocation of cultivars

resetCultivarsGenes

Reset cultivars genes

price_reduction

Price reduction function

saveDeploymentStrategy

Save landscape and deployment strategy

Run a simulation

Plotting pathotype frequencies

setDispersalHost

Set host dispersal

loadSimulParams

Load simulation parameters

Plotting the landscape

Set chemical treatments

setDispersalPathogen

Set pathogen dispersal

survivalProbToMatrix

Survival probability To Matrix

Simulation with input parameters as data.frames.

switch_patho_to_aggr

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

Set the landscape

Generation of a video

Set the pathogen

updateSurvivalProb

Update pathogen survival probability during the off-season

Set time parameters

updateReproSexProb

Update the probability of sexual reproduction

Class LandsepiParams

Check croptypes

antideriv_verhulst

Antiderivative of the Verhulst logistic function

allocateCroptypeCultivars

Allocate cultivars to one croptype

Check cultivars

Cultivars Type list

allocateCultivarGenes

Allocate genes to a cultivar

checkCultivarsGenes

Check cultivars genes

allocateLandscapeCroptypes

Allocate croptypes to the landscape

Landscape allocation