initialize-methods {simecol}R Documentation

Methods for Function 'initialize' in Package 'simecol'

Description

This function is used to initialize objects derived from the simObj superclass.

Usage

  ## S4 method for signature 'simObj':
  initialize(.Object, ...)

Arguments

.Object The simObj instance which is to be re-initialized.
... Provided for compatibility with the default method of initialize, or slots of the object which is to be created (in case of new)

Methods

.Object = "ANY"
Generic function: see new.
.Object = "simObj"
The initialize function is normally called implicitly by new to create new objects. It may also be called explicitly to return a cloned and re-initialized object. The simecol version of initialize provides an additonal mechanism to call a user specified function provided in the initfun slot of a simObj instance that can perform computations during the object creation process. The initfunc must have obj as its only argument and must return the modified version of this obj, see examples below.

See Also

simObj, new

Examples

    # Note: new calls initialize and initialize calls initfunc(obj)
    lv_efr <- new("odeModel",
      main = function (time, init, parms, ...) {
        x <- init
        p <- parms
        S <- approxTime1(inputs, time, rule=2)["s.in"]
        dx1 <-   S * p["k1"] * x[1] - p["k2"] * x[1] * x[2]
        dx2 <-     - p["k3"] * x[2] + p["k2"] * x[1] * x[2]
        list(c(dx1, dx2))
      },
      parms  = c(k1=0.2, k2=0.2, k3=0.2),
      times  = c(from=0, to=100, by=0.5),
      init   = c(prey=0.5, predator=1),
      solver = "rk4",
      initfunc = function(obj) {
        tt <- fromtoby(times(obj))
        inputs(obj) <- as.matrix(data.frame(
                time = tt,
                s.in = pmax(rnorm(tt, mean=1, sd=0.5), 0)
              ))
        obj
      }
    )

    plot(sim(lv_efr))           # first call
    plot(sim(lv_efr))           # same figure with identical object

    lv_efr<- initialize(lv_efr) # re-initializes, new random inputs
    plot(sim(lv_efr))           # different figure

[Package simecol version 0.4-2 Index]