adamhsparks/epirice: Simulation Modelling of Crop Diseases Using a Susceptible-Exposed-Infectious-Removed (SEIR) Model

Generic simulation modelling of crop diseases using a Susceptible- Exposed-Infectious-Removed ('SEIR') model. This type of model was first described in botanical epidemiology by Zadoks (1971) <doi:10.1094/Phyto-61-600> and implemented in the 'EPIRICE' model by Savary et al. (2012) <doi:10.1016/j.cropro.2011.11.009> detailing the model's development, use and results from modeling global unmanaged epidemics of rice diseases for five major rice diseases, bacterial blight, brown spot, leaf blast, sheath blight and tungro. A second model, 'EPIWHEAT' was published by Savary et al. (2015) <doi:10.1007/s10658-015-0650-7> that added a lesion expansion parameter and modelled potential disease epidemics of leaf (brown) rust and Septoria tritici blotch. Specific functions are provided to simulate all of these diseases with a generic 'SEIR' model function that is suitable for parameterising for use with other pathosystems as demonstrated in Savary et al. 2012 and 2015.

Getting started

Package details

MaintainerAdam Sparks <>
LicenseGPL-3 + file LICENSE
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
adamhsparks/epirice documentation built on April 21, 2021, 12:22 a.m.