daphnia_ibm: Simple Individual-Based Model of Daphnia

In simecolModels: Model collection for the simecol package

Description

The TeFI model (Temperature-Food-Interaction) is a semi-empirical model that simulates population dynamics of an (with default parametrisation) exponentially growing Daphnia population.

Usage

daphnia_ibm()

Details

To see all details, please have a look into the implementation and the original publications.

Value

S4 object according to the simObj specification. The object contains the following slots:

main	The main equations of the model
parms	a list with the parameters of the model
times	Simulation time and time steps.
inputs	Environmental conditions
solver	Character string with the integration method.
init, initfunc	init is initialized automatically according to the parameter values.

References

Rinke, K. and Petzoldt, T. (2003). Modelling the Effects of Temperature and Food on Individual Growth and Reproduction of Daphnia and their Consequences on the Population Level Limnologica, 33, 293-304.

Petzoldt, T. and K. Rinke (2007). simecol: An Object-Oriented Framework for Ecological Modeling in R. Journal of Statistical Software, 22(9), 1–31. URL http://www.jstatsoft.org/v22/i09/.

See Also

sim, parms, init, times.

Examples

ibm <- daphnia_ibm()

times(ibm)["to"] <- 50
ibm <- sim(ibm)

observer(ibm) <- function(init) {
  print(nrow(init))
  hist(init$age, xlim=c(0,30))
  init
}

ibm <- sim(ibm)

observer(ibm) <- function(res) {
    # eggs, size, age, eggage
    number   <- nrow(res)
    meansize <- mean(res$size)
    meanage  <- mean(res$age)
    meaneggs <- mean(res$eggs)
    c(number=number, meansize=meansize,
      meanage=meanage, meaneggs=meaneggs)
}

## define a user specified plot function
setMethod("plot", c("indbasedModel", "missing"),
  function(x, y, ...) {
    o <- out(x)
    par(mfrow=c(2, 2))
    plot(o$time, o$meanage,  type="l",
      xlab="Time", ylab="Mean age (d)")
    plot(o$time, o$meaneggs, type="l",
      xlab="Time", ylab="Eggs per individual")
    plot(o$time, o$number,   type="l",
      xlab="Time", ylab="Abundance")
    plot(o$time, o$number,   type="l",
      xlab="Time", ylab="Abundance", log="y")
})


ibm <- sim(ibm)
plot(ibm)

simecolModels documentation built on May 2, 2019, 4:59 p.m.