R/classDefinitions.R

In rocheben/ibmR: Individual-Based Model in R for phylodynamics studies

setClass("pathogen",
         representation = representation(
           mutationRate="numeric",
           crossProtection="numeric",
           probaInfection="numeric",
           latencyPeriod="numeric",
           infectiousPeriod="numeric",
           recoveryPeriod="numeric",
           name="character",
           id="numeric"
           )
)

setClass("evt",
         representation = representation(
           seasonality="data.frame",
           name="character",
           pathogens="list",
           pathogenLoad="list",
           id="numeric")
)

setClass("population",
         representation = representation(
           evtCtctRate="numeric",
           intraSpecCtctRate="numeric",
           name="character",
           id="numeric")
)

setClass("individual",
         representation = representation(
           popId="population",
           pathogens="list",
           lifespan="numeric")
)

setClass("scheduler",
         representation = representation(
           populations="list",
           individuals="list",
           pathogens="list",
           nbInfected="list",
           matrixContact="matrix",
           interSpecificProtection="list",
           environment="list")
)