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: 1.0.1
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: 2020-07-02
Author: Loup Rimbaud [aut], Julien Papaix [aut], Jean-Francois Rey [cre], Jean-Loup Gaussen [ctb]
Maintainer: Jean-Francois Rey <jean-francois.rey at inrae.fr>
BugReports: https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi/issues
License: GPL-2 | GPL-3 | file LICENSE [expanded from: GPL (≥ 2) | file LICENSE]
URL: https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi
NeedsCompilation: yes
SystemRequirements: C++11, gsl
Citation: landsepi citation info
CRAN checks: landsepi results

Downloads:

Reference manual: landsepi.pdf
Vignettes: 3 - Parameterising landscape and dispersal in landsepi
2 - Running a numerical experimental design
1 - Running a simple simulation
list of parameters
Package source: landsepi_1.0.1.tar.gz
Windows binaries: r-devel: landsepi_0.0.8.zip, r-release: landsepi_0.0.8.zip, r-oldrel: landsepi_0.0.8.zip
macOS binaries: r-release: landsepi_0.0.8.tgz, r-oldrel: landsepi_0.0.8.tgz
Old sources: landsepi archive

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