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: 1.2.2
Depends: R (≥ 3.5.0), 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: 2022-10-06
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]
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
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
5 - Poster
4 - list of parameters

Downloads:

Package source: landsepi_1.2.2.tar.gz
Windows binaries: r-devel: landsepi_1.2.2.zip, r-release: landsepi_1.2.2.zip, r-oldrel: landsepi_1.1.2.zip
macOS binaries: r-release (arm64): landsepi_1.2.2.tgz, r-oldrel (arm64): landsepi_1.2.2.tgz, r-release (x86_64): landsepi_1.2.2.tgz, r-oldrel (x86_64): landsepi_1.2.2.tgz
Old sources: landsepi archive

Linking:

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