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landsepi (version 1.5.1)

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’) 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

1.5.1

License

GPL (>= 2) | file LICENSE

Homepage

https://csiro-inra.pages.biosp.inrae.fr/landsepi/

Maintainer

Jean-Francois Rey

Last Published

September 23rd, 2024

Functions in landsepi (1.5.1)

allocateLandscapeCroptypes

Allocate croptypes to the landscape

checkSimulParams

Check simulation parameters

Cultivars Type list

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

getMatrixCultivarPatho

Get the "cultivar/pathogen genotype" compatibility matrix.

getMatrixGenePatho

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

Check cultivars

createSimulParams

Create a LandsepiParams object.

checkCultivarsGenes

Check cultivars genes

Class LandsepiParams

Package demonstration

allocateCroptypeCultivars

Allocate cultivars to one croptype

checkDispersalHost

Check host dispersal

loadDispersalHost

Load a host dispersal matrix

loadDispersalPathogen

Load pathogen dispersal matrices

inoculumToMatrix

Inoculum To Matrix

Generation of evolutionary model outputs

Load treatment parameters

Check the landscape

getMatrixCroptypePatho

Get the "croptype/pathogen genotype" compatibility matrix.

is.strict.positive

is.strict.positive

Periodic covariance function

checkDispersalPathogen

Check pathogen dispersal

Check treatment

resetCultivarsGenes

Reset cultivars genes

Dispersal matrices for rust fungi of cereal crops.

compute_audpc100S

Compute AUDPC in a single 100% susceptible field

Inverse logit function

Generation of epidemiological and economic model outputs

Load a landscape

price_reduction

Price reduction function

plot_allocation

Plotting allocation of croptypes in a landscape

getMatrixPolyPatho

Get the "polygon/pathogen genotype" compatibility matrix.

Set the pathogen

initialize,LandsepiParams-method

landsepi-package

Landscape Epidemiology and Evolution

Load pathogen parameters

loadSimulParams

Load simulation parameters

Plotting pathotype frequencies

Load a cultivar

Model for Landscape Epidemiology & Evolution

Set the landscape

survivalProbToMatrix

Survival probability To Matrix

Allocation of cultivars

Plotting the landscape

Set chemical treatments

setDispersalHost

Set host dispersal

setDispersalPathogen

Set pathogen dispersal

switch_patho_to_aggr

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

Generation of a video

Run a simulation

saveDeploymentStrategy

Save landscape and deployment strategy

updateReproSexProb

Update the probability of sexual reproduction

Simulation with input parameters as data.frames.

Set time parameters

updateSurvivalProb

Update pathogen survival probability during the off-season

antideriv_verhulst

Antiderivative of the Verhulst logistic function

allocateCultivarGenes

Allocate genes to a cultivar

Check croptypes

Landscape allocation