dvm_phyto: Phytoplankton Growth Model with Pulsed Grazing

In simecolModels: Model collection for the simecol package

Description

The model simulates a system with two functional groups of phytoplankton and one vertically migrating zooplankton population.

Usage

dvm_phyto()

Value

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

main	The differential equations for two phytoplankton groups, zooplankton and phosporus: Xr biovolume of r-strategist (mg/L), Xk biovolume of k-strategist (mg/L), Z biovolume of zooplankton (mg/L), P phosphorus concentration (mug/L),
parms	Vector with the named parameters of the model, see tables in original publication
times	Simulation time and integration interval.
init	Vector with start values for the state variables.
solver	Character string with the integration method.

References

Petzoldt, T., Rudolf, L., Rinke, K. and Benndorf, J. (2009). Effects of zooplankton diel vertical migration on a phytoplankton community: a scenario analysis of the underlying mechanisms. Ecological Modelling, in press. doi:10.1016/j.ecolmodel.2009.02.0

Examples

# Scenario analysis for the P - X1/X2 - Z - Lake Model with
#  diurnal vertical migration of Daphnia (Z)

sc1 <- sc2 <- sc3 <- sc4 <- sc5 <- dvmphyto <- dvm_phyto()

##   --> uncomment the following line  for Series 2,
##       with completely inedible algae (type "X3")
# parms(dvmphyto)[["ing_max_i"]][2] <- 0

## show parameters
# parms(sc1)

## define scenarios
parms(sc1)["DVM"] <- FALSE

parms(sc2)["DVM"] <- TRUE

parms(sc3)["DVM"] <- TRUE
parms(sc3)[["ing_max_i"]] <- parms(dvmphyto)[["ing_max_i"]]  * 3

parms(sc4)["DVM"] <- TRUE
parms(sc4)[["ing_max_i"]] <- parms(dvmphyto)[["ing_max_i"]]  * 3
parms(sc4)[["resz_max"]]  <- parms(dvmphyto)[["resz_max"]]   * 3
parms(sc4)[["mort_max"]]  <- parms(dvmphyto)[["mort_max"]]   * 3


parms(sc5)["DVM"] <- FALSE
parms(sc5)[["ing_max_i"]] <- parms(dvmphyto)[["ing_max_i"]]  / 3
parms(sc5)[["resz_max"]]  <- parms(dvmphyto)[["resz_max"]]   / 3
parms(sc5)[["mort_max"]]  <- parms(dvmphyto)[["mort_max"]]   / 3


## it is also possible to use "chained cloning" e.g. to clone
## sc5 as copy of sc4 and then to modify the DVM parameter only

## now we simulate the scenarios one after one

o1 <- out(sim(sc1))

## Not run: 
## the simulations take a while, so we skip most of them in package check
o2 <- out(sim(sc2))
o3 <- out(sim(sc3))
o4 <- out(sim(sc4))
o5 <- out(sim(sc5))

## you can now create arbitrary plots and analyses using standard R functions

plot(o1$time/24, o1$Xr, type="l", ylim=c(0,1))
lines(o1$time/24, o1$Xk, col="red")

## End(Not run)

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