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())
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submodel |
the subobject defining a single time-step of the
individual-based simulation (i.e. |
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 |
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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/.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ## 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")
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