Package: landsepi 1.5.1
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:
landsepi_1.5.1.tar.gz
landsepi_1.5.1.tar.gz(r-4.5-noble)landsepi_1.5.1.tar.gz(r-4.4-noble)
landsepi_1.5.1.tgz(r-4.4-emscripten)landsepi_1.5.1.tgz(r-4.3-emscripten)
landsepi.pdf |landsepi.html✨
landsepi/json (API)
NEWS
# Install 'landsepi' in R: |
install.packages('landsepi', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Pkgdown:https://csiro-inra.pages.biosp.inrae.fr
- dispP_1 - Dispersal matrices for rust fungi of cereal crops.
- dispP_2 - Dispersal matrices for rust fungi of cereal crops.
- dispP_3 - Dispersal matrices for rust fungi of cereal crops.
- dispP_4 - Dispersal matrices for rust fungi of cereal crops.
- dispP_5 - Dispersal matrices for rust fungi of cereal crops.
- landscapeTEST1 - Landscapes
- landscapeTEST2 - Landscapes
- landscapeTEST3 - Landscapes
- landscapeTEST4 - Landscapes
- landscapeTEST5 - Landscapes
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:56f91311b9. Checks:OK: 1 NOTE: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 23 2024 |
R-4.5-linux-x86_64 | NOTE | Nov 23 2024 |
Exports:AgriLandallocateCroptypeCultivarsallocateCultivarGenesallocateLandscapeCroptypesantideriv_verhulstcheckSimulParamscompute_audpc100ScreateSimulParamsdemo_landsepiepid_outputevol_outputgetMatrixCroptypePathogetMatrixCultivarPathogetMatrixGenePathogetMatrixPolyPathoinoculumToMatrixinvlogitis.in.01is.positiveis.strict.positiveis.wholenumberloadCroptypesloadCultivarloadDispersalHostloadDispersalPathogenloadGeneloadInoculumloadLandscapeloadOutputsloadPathogenloadSimulParamsloadTreatmentlogitmodel_landsepimultiNperiodic_covplot_allocationplot_freqPathoplotlandprice_reductionprintrunShinyApprunSimulsaveDeploymentStrategysetCroptypessetCultivarssetDispersalHostsetDispersalPathogensetGenessetInoculumsetLandscapesetOutputssetPathogensetSeedsetSeedValuesetTimesetTreatmentshowsimul_landsepisummarysurvivalProbToMatrixswitch_patho_to_aggrupdateReproSexProbupdateSurvivalProbvideo
Dependencies:bitbit64blobbriocachemcallrclassclassIntclicodetoolscpp11crayonDBIdescdeSolvediffobjdigestdoParalleldotCall64e1071evaluatefastmapfieldsforeachfsglueiteratorsjsonliteKernSmoothlatticelifecyclemagrittrmapsMASSMatrixmemoisemvtnormpkgbuildpkgconfigpkgloadplogrpraiseprocessxproxypsR6RcpprlangrprojrootRSQLites2sfspspamsplancstestthatunitsvctrsviridisLitewaldowithrwk
1 - Running a simple simulation
Rendered fromO1-run_simple_simul.Rmd
usingknitr::rmarkdown
on Nov 23 2024.Last update: 2024-09-24
Started: 2021-07-26
2 - Running a numerical experimental design
Rendered fromO2-run_exp_design.Rmd
usingknitr::rmarkdown
on Nov 23 2024.Last update: 2024-09-04
Started: 2021-07-26
3 - Parameterising landscape and dispersal
Rendered fromO3-landscape_dispersal.Rmd
usingknitr::rmarkdown
on Nov 23 2024.Last update: 2023-07-19
Started: 2021-07-26
4 - Running a simple simulation with a pathogen with mixed reproduction system
Rendered fromO4-run_sex_repro.Rmd
usingknitr::rmarkdown
on Nov 23 2024.Last update: 2024-09-24
Started: 2022-10-05
5 - list of parameters
Rendered fromlist_of_parameters.Rnw
usingutils::Sweave
on Nov 23 2024.Last update: 2023-02-27
Started: 2020-07-01
6 - Poster
Rendered fromlandsepi_poster.Rnw
usingutils::Sweave
on Nov 23 2024.Last update: 2023-02-27
Started: 2021-07-26
Landsepi - Bibliography
Rendered fromO5-bibliography.Rmd
usingknitr::rmarkdown
on Nov 23 2024.Last update: 2024-09-04
Started: 2024-09-04