observer: Get or Set an Observer Functions to an 'simObj' Object

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

Description

Get or set a user-defined observer to enable user-specified storage of simulation results, visualisation or logging.

Usage

observer(obj, ...)
observer(obj) <- value

Arguments

obj	A valid simObj instance.
value	A function specifying an observer, see Details.
...	Reserved for method consistency.

Details

The observer can be used with solver iteration or a user-defined solver function. It does not work with differential equations solvers.

The observer is a function with the following arguments:

function(state)

or:

function(state, time, i, out, y)

Where state is the actual state of the system, time and i are the simulation time and the indexof the time step respectively, out is the output of the actual simulation collected so far. The original object used in the simulation is passed via y and can be used to get access on parameter values or model equations.

If available, the observer function is called for every time step in the iteration. It can be used for calculations “on the fly” to reduce memory of saved data, for user-specified animation or for logging purposes.

If the value returned by observer is a vector, than resulting out will be a data.frame, otherwise it will be a list of all states.

Value

The observer function either modifies obj or it returns the assigned observer function or NULL (the default).

See Also

iteration for the iteration solver,

parms for accessor and replacement functions of other slots,

simecol-package for an overview of the package.

Examples

## load model "diffusion"
data(diffusion)

solver(diffusion) # solver is iteration, supports observer
times(diffusion) <- c(from=0, to=20, by=1) # to can be increased, to e.g. 100

### == Example 1 ===============================================================

## assign an observer for visualisation
observer(diffusion) <- function(state) {
  ## numerical output to the screen
  cat("mean x=", mean(state$x),
      ", mean y=", mean(state$y),
      ", sd   x=", sd(state$x),
      ", sd   y=", sd(state$y), "\n")
  ## animation
  par(mfrow = c(2, 2))
  plot(state$x, state$y, xlab = "x", ylab = "y", pch = 16, 
    col = "red", xlim = c(0, 100))
  hist(state$y)
  hist(state$x)
  
  ## default case: 
  ## return the state --> iteration stores full state in "out"
  state
}

sim(diffusion)

### == Example 2 ===============================================================

## an extended observer with full argument list
observer(diffusion) <- function(state, time, i, out, y) {
  ## numerical output to the screen
  cat("index =", i,
      ", time =", time,
      ", sd   x=", sd(state$x),
      ", sd   y=", sd(state$y), "\n")
  ## animation
  par(mfrow = c(2, 2))
  plot(state$x, state$y, xlab = "x", ylab = "y", pch = 16, 
    col = "red", xlim = c(0, 100))
  hist(state$y)
  hist(state$x)
  if (is.matrix(out)) # important because out may be NULL for the first call
    matplot(out[,1], out[,-1]) # dynamic graph of sd in both directions
  
  ## return a vector with summary information
  c(times = time, sdx=sd(state$x), sdy=sd(state$y))
}

diffusion <- sim(diffusion)

### == Restore default =========================================================

observer(diffusion) <- NULL # delete observer
diffusion <- sim(diffusion)

simecol documentation built on Oct. 7, 2021, 9:20 a.m.