inst/examples/Logistic.R

In f0nzie/rODE: Ordinary Differential Equation (ODE) Solvers Written in R Using S4 Classes

# +++++++++++++++++++++++++++++++++++++++++++++++++++   application:  Logistic.R
# Simulates the logistic equation

setClass("Logistic", slots = c(
        K = "numeric",
        r = "numeric",
        odeSolver = "Verlet",
        counter = "numeric"
        ),
        contains = c("ODE")
)

setMethod("initialize", "Logistic", function(.Object, ...) {
    .Object@K <- 10
    .Object@r <- 1.0
    .Object@state <- vector("numeric", 3)  # x, vx
    .Object@odeSolver <- Verlet(.Object)
    .Object@counter <- 0
    return(.Object)
})

setMethod("doStep", "Logistic", function(object, ...) {
    # cat("state@doStep=", object@state, "\n")
    object@odeSolver <- step(object@odeSolver)
    object@state <- object@odeSolver@ode@state
    object
})

setMethod("getTime", "Logistic", function(object, ...) {
    return(object@state[3])
})


setMethod("init", "Logistic", function(object, initState, r, K, ...) {
    object@r <- r
    object@K <- K
    object@state <- initState
    object@odeSolver <- init(object@odeSolver, getStepSize(object@odeSolver))
    object@counter <- 0
    object
})

setReplaceMethod("init", "Logistic", function(object, ..., value) {
    object@r <- value[["r"]]
    object@K <- value[["K"]]
    object@state <- value[["initState"]]
    object@odeSolver <- init(object@odeSolver, getStepSize(object@odeSolver))
    object@counter <- 0
    object
})


setMethod("getRate", "Logistic", function(object, state, ...) {
    # Computes the rate using the given state.
    object@rate[1] <- state[2]
    object@rate[2] <- object@r * state[1] * (1 - state[1] / object@K)
    object@rate[3] <- 1   # time derivative
    object@counter <- object@counter + 1
    object@rate

})


setMethod("getState", "Logistic", function(object, ...) {
    # Gets the state variables.
    return(object@state)
})

# constructor
Logistic <- function() {
    logistic <- new("Logistic")
    return(logistic)
}