Learn R Programming
⚠️There's a newer version (1.5.1) of this package.Take me there.

landsepi (version 1.3.0)

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) .

Copy Link

Version

Install

install.packages('landsepi')

Monthly Downloads

286

Version

1.3.0

License

GPL (>= 2) | file LICENSE

Maintainer

Jean-Francois Rey

Last Published

July 19th, 2023

Functions in landsepi (1.3.0)

checkInoculum

Check inoculum
checkGenes

Check genes
checkLandscape

Check the landscape
checkOutputs

Check outputs
checkTime

Check time
checkTreatment

Check treatment
checkSimulParams

Check simulation parameters
checkPathogen

Check pathogen
demo_landsepi

Package demonstration
compute_audpc100S

Compute AUDPC in a single 100% susceptible field
initialize,LandsepiParams-method

LandsepiParams
checkDispersalHost

Check host dispersal
checkDispersalPathogen

Check pathogen dispersal
epid_output

Generation of epidemiological and economic model outputs
evol_output

Generation of evolutionary model outputs
dispP

Dispersal matrices for rust fungi of cereal crops.
is.positive

is.positive
is.in.01

is.in.01
createSimulParams

Create a LandsepiParams object.
invlogit

Inverse logit function
loadCroptypes

Load Croptypes
loadCultivar

Load a cultivar
loadDispersalHost

Load a host dispersal matrix
is.strict.positive

is.strict.positive
is.wholenumber

is.wholenumber
loadDispersalPathogen

Load pathogen dispersal matrices
loadGene

Load a gene
loadLandscape

Load a landscape
landscapeTEST

Landscapes
landsepi-package

Landscape Epidemiology and Evolution
periodic_cov

Periodic covariance function
model_landsepi

Model for Landscape Epidemiology & Evolution
logit

Logit function
loadOutputs

Load outputs
multiN

Allocation of cultivars
loadTreatment

Load treatment parameters
plot_freqPatho

Plotting pathotype frequencies
plot_allocation

Plotting allocation of croptypes in a landscape
loadSimulParams

Load simulation parameters
loadPathogen

Load pathogen parameters
saveDeploymentStrategy

Save landscape and deployment strategy
runShinyApp

runShinyApp
print

print
plotland

Plotting the landscape
price_reduction

Price reduction function
setCroptypes

Set croptypes
setOutputs

Set outputs
setCultivars

Set cultivars
setDispersalHost

Set host dispersal
setLansdcape

Set the landscape
setTime

Set time parameters
setInoculum

Set inoculum
setSeedValue

setSeedValue
resetCultivarsGenes

Reset cultivars genes
setSeed

Set the seed
runSimul

Run a simulation
setDispersalPathogen

Set pathogen dispersal
setGenes

Set genes
setReproSexProb

Set the vector of probabilities of sexual reproduction
setPathogen

Set the pathogen
show

show
setTreatment

Set chemical treatments
switch_patho_to_aggr

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

summary
simul_landsepi

Simulation with input parameters as data.frames.
video

Generation of a video
AgriLand

Landscape allocation
allocateCroptypeCultivars

Allocate cultivars to one croptype
antideriv_verhulst

Antiderivative of the Verhulst logistic function
allocateLandscapeCroptypes

Allocate croptypes to the landscape
allocateCultivarGenes

Allocate genes to a cultivar
checkCultivarsGenes

Check cultivars genes
LandsepiParams

Class LandsepiParams
Cultivars_list

Cultivars Type list
checkCultivars

Check cultivars
checkCroptypes

Check croptypes