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:	1.5.1
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:	2024-09-23
DOI:	10.32614/CRAN.package.landsepi
Author:	Loup Rimbaud [aut], Marta Zaffaroni [aut], Jean-François Rey [aut, cre], Julien Papaix [aut], 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 (source, R code) 2 - Running a numerical experimental design (source, R code) 3 - Parameterising landscape and dispersal (source, R code) 4 - Running a simple simulation with a pathogen with mixed reproduction system (source, R code) Landsepi - Bibliography (source) 6 - Poster (source) 5 - list of parameters (source)

Downloads:

Package source:	landsepi_1.5.1.tar.gz
Windows binaries:	r-devel: landsepi_1.5.1.zip, r-release: landsepi_1.5.1.zip, r-oldrel: landsepi_1.5.1.zip
macOS binaries:	r-release (arm64): landsepi_1.5.1.tgz, r-oldrel (arm64): landsepi_1.5.1.tgz, r-release (x86_64): landsepi_1.5.1.tgz, r-oldrel (x86_64): landsepi_1.5.1.tgz
Old sources:	landsepi archive

Linking:

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