daphnia_deb_ibm: Bioenergetic Individual-Based Model of Daphnia
In simecolModels: Model collection for the simecol package

Description Usage Arguments Details Value References See Also Examples

The DEB-IBM model is an individual based simulation of a bioenergetic Daphnia model and a logistic phytoplankton growth model.

1 2	daphnia_deb_phyto() daphnia_deb_ibm(submodel = daphnia_deb_phyto())

submodel

the subobject defining a single time-step of the individual-based simulation (i.e. daphnia_deb_phyto or a compatible variant of it)

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

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.

Rinke, K. (2006). Species-oriented model approaches to Daphnia spp.: linking the individual level to the population level. PhD Thesis. Technische Universität Dresden, Fakultät Forst-, Geo- und Hydrowissenschaften. http://nbn-resolving.de/urn:nbn:de:swb:14-1146736164110-76933

Rinke, K. & Vijverberg, J. (2005). A Model Approach to Evaluate the Effect of Temperature and Food Concentration on Individual Life-history and Population Dynamics of Daphnia. Ecological Modelling, 186, 326-344

Rinke, K.; Vijverberg, J.; Petzoldt, T. & Benndorf, J. (2005). Individual and population level dynamics of Daphnia at varying conditions of food, temperature and fish predation: a model approach. Verh. Internat. Verein. Limnol., 29, 310-314

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/.

sim, parms, init, times.

## load individual-level model (DEB and phyto, differential equations)
submodel <- daphnia_deb_phyto()

## test one outer step alone
m <- sim(submodel)
out(m)

### create individual-based model (IBM, discrete, population dynamics)
### with a newly initialized daphnia_deb_phyto() object as submodel
deb_ibm <- daphnia_deb_ibm()

## set simulation parameters
times(deb_ibm)["to"] <- 2
## the following takes a while !
## Not run: 
times(deb_ibm)["to"] <- 200

## End(Not run)
deb_ibm <- sim(deb_ibm)
o <- out(deb_ibm)


### plot results
par(mfrow=c(3,1))
plot(o$time, o$x1, type="l",
  main="Phytoplankton", col="red", ylim=c(0,0.5),xlab="Day",ylab="mg C / L")
lines(o$time, o$x2, col="blue")
lines(o$time, o$x3, col="green")
plot(o$time, o$abundance, type="l", main="Abundance",xlab="Day", ylab="Ind / L")
bm.mgc <- o$weight * o$abund / 1000
plot(o$time, bm.mgc , type="l", main="Biomass",xlab="Day", ylab="mg C / L")