daphnia_deb: Bioenergetic (Dynamic Energy Budget = DEB) Model of Daphnia

In simecolModels: Model collection for the simecol package

Description

The DEB model is the core model of a framework for the simulation of growth and reproduction of Daphnia at varying conditions of food concentration and temperature. It is an individual level model that simulates allocation of assimilated carbon into somatic growth, maintenance costs, and reproduction on the basis of a closed carbon budget.

Usage

daphnia_deb()

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 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.

See Also

sim, parms, init, times.

Examples

################ Basic use ########################
dap2 <- daphnia <- daphnia_deb()

parms(dap2)["kappa"] <- 0.4
inputs(dap2) <- data.frame(t.kelvin=293.15, food=5)

test  <- sim(daphnia)
test2 <- sim(dap2)

plot(test)
plot(test2)

######### Figure 2 of Rinke and Vijverberg #########

## a set of different scenarios
foodconc <- c(0.1,0.25,1)     # food concentrations evaluated
temp     <- c(5,10,15,20,25)  # temperatures evaluated

dat.temp <- NULL       # data frame for storage of multiple scenarios
for(f in foodconc){    # food loop
    for(t in temp){    # temperature loop
      daphnia@inputs <- data.frame(food=f, t.kelvin=t+273.15)
      ## numerical integration
      out <- as.data.frame(out(sim(daphnia, atol=1e-4, rtol=1e-4)))
      ## preparation of outputs
      out <- cbind(out, food = f, temp = t,
                   length = equations(daphnia)$weight2length(out$weight, parms(daphnia)["l2w"])
                  )
      dat.temp <- rbind(dat.temp,out)
    }
}

## renewal of the row-names
## necessary because cbind() mangles row-names
row.names(dat.temp)<-1:nrow(dat.temp)

## write the data in an ASCII-file
# write.table(dat.temp,"dat_temp.dat", quote=F, row.names=F)


## set some plotting-related parameters
par(mfrow=c(1,3), las=1, cex.lab=1.7,
    cex.axis=1.6, cex.main=1.3, mgp=c(3.5,1,0),
    mar=c(5,5.3,4,0.2), lwd=1.5)

day <- seq(0,50,2) # scaling of the time axis
for(f in foodconc){ # food-loop
    plot(0,0,type="n", ylim=c(0,3), xlim=c(0,50),
         ylab="Length (mm)", xlab= "Time (d)", main="")
    if(f==0.1)
      title(main=expression(paste("0.1 mgC ", l^{-1})), cex.main=1.8)
    if(f==0.25)
      title(main=expression(paste("0.25 mgC ", l^{-1})), cex.main=1.8)
    if(f==1)
      title(main=expression(paste("1.0 mgC ", l^{-1})), cex.main=1.8)

    for(t in temp){ # temperature-loop
        lines(dat.temp$time[dat.temp$food==f & dat.temp$temp==t],
        dat.temp$length[dat.temp$food==f & dat.temp$temp==t],
              lty = match(t, temp))
    }
}

## draw a legend, NOTE: \260 is encoding for degree
legend(50,0,c("  5\260C","10\260C","15\260C","20\260C","25\260C"),
       xjust=1, yjust=0, lwd=1.5, lty=1:5, cex=1.5, bty="n")

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