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) .


Reference manual

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1.0.1 by Jean-Francois Rey, 4 months ago

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Authors: Loup Rimbaud [aut] , Julien Papaix [aut] , Jean-Francois Rey [cre] , Jean-Loup Gaussen [ctb]

Documentation:   PDF Manual  

GPL (>= 2) | file LICENSE license

Imports Rcpp, stats, Matrix, mvtnorm, fields, splancs, sf, DBI, RSQLite, foreach, parallel, doParallel

Depends on methods, utils, grDevices, graphics, sp

Suggests testthat, shiny, shinyjs, DT, knitr, rmarkdown

Linking to Rcpp, testthat

System requirements: C++11, gsl

See at CRAN