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>.
| Version: | 1.1.2 |
| Depends: | methods, utils, grDevices (≥ 3.0.0), graphics (≥ 3.0.0), R (≥ 3.3.0), sp (≥ 1.0-17) |
| Imports: | Rcpp (≥ 0.9.0), stats (≥ 3.0.2), Matrix, mvtnorm, fields, splancs, sf, DBI, RSQLite, foreach, parallel, doParallel |
| LinkingTo: | Rcpp, testthat |
| Suggests: | testthat, shiny, shinyjs, DT, knitr, rmarkdown |
| Published: | 2022-03-02 |
| Author: | Loup Rimbaud [aut],
Julien Papaix [aut],
Jean-François Rey 
[aut, cre],
Jean-Loup Gaussen [ctb] |
| Maintainer: | Jean-François Rey <jean-francois.rey at inrae.fr> |
| BugReports: | https://gitlab.paca.inrae.fr/CSIRO-INRA/landsepi/-/issues |
| License: | GPL-2 | GPL-3 | file LICENSE [expanded from: GPL (≥ 2) | file LICENSE] |
| URL: | https://csiro-inra.pages.biosp.inrae.fr/landsepi/, https://gitlab.paca.inrae.fr/CSIRO-INRA/landsepi |
| NeedsCompilation: | yes |
| SystemRequirements: | C++11, gsl |
| Citation: | landsepi citation info |
| CRAN checks: | landsepi results |
Documentation:
| Reference manual: | landsepi.pdf |
| Vignettes: |
1 - Running a simple simulation 2 - Running a numerical experimental design 3 - Parameterising landscape and dispersal 5 - Poster 4 - list of parameters |
Downloads:
| Package source: | landsepi_1.1.2.tar.gz |
| Windows binaries: | r-devel: landsepi_1.1.2.zip, r-release: landsepi_1.1.2.zip, r-oldrel: landsepi_1.1.2.zip |
| macOS binaries: | r-release (arm64): landsepi_1.1.2.tgz, r-oldrel (arm64): landsepi_1.1.2.tgz, r-release (x86_64): landsepi_1.1.2.tgz, r-oldrel (x86_64): landsepi_1.1.2.tgz |
| Old sources: | landsepi archive |
Linking:
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