Package: landsepi 1.5.3

landsepi: Landscape Epidemiology and Evolution

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) <doi:10.1371/journal.pcbi.1006067>.

Authors:Loup Rimbaud [aut], Marta Zaffaroni [aut], Jean-François Rey [aut, cre], Julien Papaix [aut], Jean-Loup Gaussen [ctb], Manon Couty [ctb]

landsepi_1.5.3.tar.gz
landsepi_1.5.3.zip(r-4.7-x86_64)landsepi_1.5.3.zip(r-4.7-arm64)landsepi_1.5.3.zip(r-4.6-x86_64)landsepi_1.5.3.zip(r-4.6-arm64)landsepi_1.5.3.zip(r-4.5-x86_64)
landsepi_1.5.3.tgz(r-4.6-x86_64)landsepi_1.5.3.tgz(r-4.6-arm64)landsepi_1.5.3.tgz(r-4.5-x86_64)landsepi_1.5.3.tgz(r-4.5-arm64)
landsepi_1.5.3.tar.gz(r-4.7-arm64)landsepi_1.5.3.tar.gz(r-4.7-x86_64)landsepi_1.5.3.tar.gz(r-4.6-arm64)landsepi_1.5.3.tar.gz(r-4.6-x86_64)
landsepi_1.5.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
landsepi/json (API)

# Install 'landsepi' in R:
install.packages('landsepi', repos = c('https://mechantrouquin.r-universe.dev', 'https://cloud.r-project.org'))

Pkgdown/docs site:https://landsepi.pages-forge.inrae.fr

Uses libs:
  • gsl– GNU Scientific Library (GSL)
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

gslcpp

3.29 score 28 scripts 633 downloads 1 mentions 65 exports 61 dependencies

Last updated from:c263668cf3. Checks:13 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE184
linux-devel-x86_64NOTE181
source / vignettesOK266
linux-release-arm64NOTE184
linux-release-x86_64NOTE210
macos-release-arm64NOTE172
macos-release-x86_64NOTE630
macos-oldrel-arm64NOTE115
macos-oldrel-x86_64NOTE408
windows-devel-arm64NOTE402
windows-devel-x86_64NOTE262
windows-release-arm64NOTE400
windows-release-x86_64NOTE179
windows-oldrel-x86_64NOTE155
wasm-releaseOK148

Exports:AgriLandallocateCroptypeCultivarsallocateCultivarGenesallocateLandscapeCroptypesantideriv_verhulstcheckSimulParamscompute_audpc100ScreateSimulParamsdemo_landsepiepid_outputevol_outputgetMatrixCroptypePathogetMatrixCultivarPathogetMatrixGenePathogetMatrixPolyPathoinoculumToMatrixinvlogitis.in.01is.positiveis.strict.positiveis.wholenumberloadCroptypesloadCultivarloadDispersalHostloadDispersalPathogenloadGeneloadInoculumloadLandscapeloadOutputsloadPathogenloadSimulParamsloadTreatmentlogitmodel_landsepimultiNperiodic_covplot_allocationplot_freqPathoplotlandprice_reductionprintrunShinyApprunSimulsaveDeploymentStrategysetCroptypessetCultivarssetDispersalHostsetDispersalPathogensetGenessetInoculumsetLandscapesetOutputssetPathogensetSeedsetSeedValuesetTimesetTreatmentshowsimul_landsepisummarysurvivalProbToMatrixswitch_patho_to_aggrupdateReproSexProbupdateSurvivalProbvideo

Dependencies:bitbit64blobbriocachemcallrclassclassIntclicodetoolscpp11crayonDBIdescdeSolvediffobjdoParalleldotCall64e1071evaluatefastmapfieldsforeachfsglueiteratorsjsonliteKernSmoothlatticelifecyclemagrittrmapsMatrixmemoisemvtnormotelpkgbuildpkgconfigpkgloadpraiseprocessxproxypsR6RColorBrewerRcpprlangrprojrootRSQLites2sfspspamsplancstestthatunitsvctrsviridisLitewaldowithrwk

1 - Running a simple simulation
General presentation of the package | Initialisation of simulation parameters | Setting the seed and time parameters | Setting pathogen parameters | Setting the landscape and pathogen dispersal | Setting croptypes, cultivars and resistance genes | Cultivars | Resistance genes | Allocating genes to cultivars | Allocating cultivars to croptypes | Allocating croptypes to fields of the landscape | Setting the inoculum | Scenario 1 (default). Only the avirulent pathogen on the susceptible cultivar in all fields (global inoculum) | Scenario 2. Only the avirulent pathogen on the susceptible cultivar in only some fields (local inoculum) | Scenario 3. A diversity of pathogen genotypes in the inoculum, in all fields (global inoculum) | Scenario 4. A diversity of pathogen genotypes in the inoculum, in some fields only (local inoculum) | Scenario 5. Custom 3D array to define the inoculum | Visualization | Updating the survival probability during the off-season | Setting chemical treatments | Choosing output variables | Equations | Parameterisation | Running the simulation
Rendered fromO1-run_simple_simul.Rmdusingknitr::rmarkdown

Last update: 2024-09-24
Started: 2021-07-26

4 - Running a simple simulation with a pathogen with mixed reproduction system
Initialisation of simulation parameters, seed, time and landscape parameters | Setting the probability of sexual reproduction | Setting the time of release of propagules produced at the end of a cropping season | Sexual propagules | Clonal propagules | Setting pathogen dispersal (both for sexual and clonal propagules) | Setting recombination between resistance genes | Setting croptypes, cultivars and resistance genes | Running the simulation
Rendered fromO4-run_sex_repro.Rmdusingknitr::rmarkdown

Last update: 2024-09-24
Started: 2022-10-05

2 - Running a numerical experimental design
Write the experimental design | Run the simulations | Compute your own output variables
Rendered fromO2-run_exp_design.Rmdusingknitr::rmarkdown

Last update: 2024-09-04
Started: 2021-07-26

Landsepi - Bibliography
Rendered fromO5-bibliography.Rmdusingknitr::rmarkdown

Last update: 2024-09-04
Started: 2024-09-04

3 - Parameterising landscape and dispersal
Using your own landscape | Using your own croptype allocation | Computing the dispersal matrix | An example | Plotting landscape and dispersal
Rendered fromO3-landscape_dispersal.Rmdusingknitr::rmarkdown

Last update: 2023-07-19
Started: 2021-07-26

5 - list of parameters
Rendered fromlist_of_parameters.Rnwusingutils::Sweave

Last update: 2023-02-27
Started: 2020-07-01

6 - Poster
Rendered fromlandsepi_poster.Rnwusingutils::Sweave

Last update: 2023-02-27
Started: 2021-07-26

Readme and manuals

Help Manual

Help pageTopics
Landscape Epidemiology and Evolutionlandsepi-package landsepi
Landscape allocationAgriLand
Allocate cultivars to one croptypeallocateCroptypeCultivars
Allocate genes to a cultivarallocateCultivarGenes
Allocate croptypes to the landscapeallocateLandscapeCroptypes
Antiderivative of the Verhulst logistic functionantideriv_verhulst
Check croptypescheckCroptypes
Check cultivarscheckCultivars
Check cultivars genescheckCultivarsGenes
Check host dispersalcheckDispersalHost
Check pathogen dispersalcheckDispersalPathogen
Check genescheckGenes
Check inoculumcheckInoculum
Check the landscapecheckLandscape
Check outputscheckOutputs
Check pathogencheckPathogen
Check the array PI0_mat when entered manually in 'loadInoculum()'.checkPI0_mat
Check simulation parameterscheckSimulParams
Check timecheckTime
Check treatmentcheckTreatment
Compute AUDPC in a single 100% susceptible fieldcompute_audpc100S
Create a LandsepiParams object.createSimulParams
Cultivars Type listCultivars_list
Package demonstrationdemo_landsepi
Dispersal matrices for rust fungi of cereal crops.dispP dispP_1 dispP_2 dispP_3 dispP_4 dispP_5
Generation of epidemiological and economic model outputsepid_output
Generation of evolutionary model outputsevol_output
Get the "croptype/pathogen genotype" compatibility matrix.getMatrixCroptypePatho
Get the "cultivar/pathogen genotype" compatibility matrix.getMatrixCultivarPatho
Get the "resistance gene/pathogen genotype" compatibility matrix.getMatrixGenePatho
Get the "polygon/pathogen genotype" compatibility matrix.getMatrixPolyPatho
LandsepiParamsinitialize,LandsepiParams-method
Inoculum To MatrixinoculumToMatrix
Inverse logit functioninvlogit
is.in.01is.in.01
is.positiveis.positive
is.strict.positiveis.strict.positive
is.wholenumberis.wholenumber
LandscapeslandscapeTEST landscapeTEST1 landscapeTEST2 landscapeTEST3 landscapeTEST4 landscapeTEST5
Class LandsepiParamsLandsepiParams LandsepiParams-class
Load CroptypesloadCroptypes
Load a cultivarloadCultivar
Load a host dispersal matrixloadDispersalHost
Load pathogen dispersal matricesloadDispersalPathogen
Load a geneloadGene
Load InoculumloadInoculum
Load a landscapeloadLandscape
Load outputsloadOutputs
Load pathogen parametersloadPathogen
Load simulation parametersloadSimulParams
Load treatment parametersloadTreatment
Logit functionlogit
Model for Landscape Epidemiology & Evolutionmodel_landsepi
Allocation of cultivarsmultiN
Periodic covariance functionperiodic_cov
Plotting allocation of croptypes in a landscapeplot_allocation
Plotting pathotype frequenciesplot_freqPatho
Plotting the landscapeplotland
Price reduction functionprice_reduction
printprint print,LandsepiParams-method
Reset cultivars genesresetCultivarsGenes
runShinyApprunShinyApp
Run a simulationrunSimul
Save landscape and deployment strategysaveDeploymentStrategy
Set croptypessetCroptypes
Set cultivarssetCultivars
Set host dispersalsetDispersalHost
Set pathogen dispersalsetDispersalPathogen
Set genessetGenes
Set inoculumsetInoculum
Set the landscapesetLandscape setLansdcape
Set outputssetOutputs
Set the pathogensetPathogen
Set the seedsetSeed
setSeedValuesetSeedValue
Set time parameterssetTime
Set chemical treatmentssetTreatment
showshow show,LandsepiParams-method
Simulation with input parameters as data.frames.simul_landsepi
summarysummary summary,LandsepiParams-method
Survival probability To MatrixsurvivalProbToMatrix
Switch from index of genotype to indices of agressiveness on different componentsswitch_patho_to_aggr
Update the probability of sexual reproductionupdateReproSexProb
Update pathogen survival probability during the off-seasonupdateSurvivalProb
Generation of a videovideo