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.



This work benefited from ANR project “ArchiV” (2019–2023, grant n°ANR-18-CE32-0004-01), AFB Ecophyto II-Leviers Territoriaux Project ”Médée” (2020–2023), GRDC grant CSP00192 and the CSIRO/INRA linkage program


Configuration and dependencies

Read file “DESCRIPTION” for details on configuration requirements (with linux and R).
The package for compiling needs g++, gsl dev library and ffmpeg (for videos).

Under Linux OS:

sudo apt-get install g++ libgsl2 libgsl-dev ffmpeg

Under Windows use the zip.
> You can install Rtools and get g++, gsl and ffmpeg binaries under Windows (using pacman).

R packages dependencies :
* Rcpp * sp * Matrix (>= 1.3-0) * mvtnorm * fields * splancs * sf
* DBI * RSQLite * foreach * doParallel * deSolve

To install :

install.packages(c("Rcpp","sp","Matrix","mvtnorm","fields","splancs","sf","DBI","RSQLite","foreach","doParallel", "deSolve"))

Shiny interface

You can try the online Landsepi R Shiny App
or run it into R. To run the shiny interface into R you will need the following packages:

Install packages : install.packages(c("shiny","shinyBS", "DT", "shinyjs", "gridExtra", "png", "grid"
, "future", "promises", "tools", "shinyalert"))

The app can be launched with:



Run demonstrations (in 20-year simulations) for different deployment strategies:

demo_landsepi(strat = "MO") ## for a mosaic of cultivars
demo_landsepi(strat = "MI") ## for a mixture of cultivars
demo_landsepi(strat = "RO") ## for a rotation of cultivars
demo_landsepi(strat = "PY") ## for a pyramid of resistance genes

Get started

To get started see the first article