initialize-methods: Methods for Function 'initialize' in Package 'simecol'

In simecol: Simulation of Ecological (and Other) Dynamic Systems

Methods for Function ‘initialize’ in Package ‘simecol’

Description

This function is used to initialize objects derived from the simObj superclass, it is by default automatically called during object creation and by sim.

Usage

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

Arguments

.Object	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. As a side effect end to ensure consistency, initialize clears outputs stored in slot out from former simulations.

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 = "lsoda",
  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))                     # initialize called automatically
plot(sim(lv_efr))                     # automatic initialization, different figure

lv_efr<- initialize(lv_efr)           # re-initialize manually
plot(sim(lv_efr, initialize = FALSE)) # simulation with that configuration
    

simecol documentation built on June 8, 2025, 10:45 a.m.