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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: 1.4.0
Depends: R (≥ 4.2.0), sp (≥ 1.0-17)
Imports: methods, utils, stats (≥ 3.0.2), grDevices (≥ 3.0.0), graphics (≥ 3.0.0), parallel, Rcpp (≥ 0.9.0), Matrix (≥ 1.3-0), mvtnorm, fields, splancs, sf, DBI, RSQLite, foreach, doParallel, deSolve
LinkingTo: Rcpp, testthat
Suggests: testthat (≥ 3.0.0), shiny, shinyjs, DT, knitr, rmarkdown
Published: 2024-03-12
Author: Loup Rimbaud ORCID iD [aut], Julien Papaix [aut], Jean-François Rey ORCID iD [aut, cre], Marta Zaffaroni ORCID iD [ctb], Jean-Loup Gaussen [ctb], Manon Couty [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++, gsl
Citation: landsepi citation info
Materials: NEWS
In views: Agriculture
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
4 - Running a simple simulation with a pathogen with mixed reproduction system
6 - Poster
5 - list of parameters

Downloads:

Package source: landsepi_1.4.0.tar.gz
Windows binaries: r-devel: landsepi_1.4.0.zip, r-release: landsepi_1.4.0.zip, r-oldrel: landsepi_1.4.0.zip
macOS binaries: r-release (arm64): landsepi_1.4.0.tgz, r-oldrel (arm64): landsepi_1.4.0.tgz, r-release (x86_64): landsepi_1.4.0.tgz, r-oldrel (x86_64): landsepi_1.4.0.tgz
Old sources: landsepi archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=landsepi to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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