algaepH: An Algal Model With pH Dynamics

In simecolModels: Model collection for the simecol package

Description

Phytoplankton model which includes pH dynamics.

The algae are either growing on nitrate or on ammonium.

Usage

algaepH()

Format

An S4 object according to the odeModel specification.

The object contains the following slots:

• main algaepH model specifications.

• parms vector with the named parameters of the model - see code

• times simulation time and integration interval.

• init vector with start values for state variables.

Author(s)

Karline Soetaert

References

Chapter 8.5.2. from the book by Soetaert and Herman, 2009. A practical guide to ecological Modelling. Using R as a simulation platform. Springer.

See Also

R-package simecol for a description of the simObj class

Examples

# initialize model
myAlgaepH <- algaepH()

# show model code, parameter settings,...
print(myAlgaepH)

# run simulation
out    <- out(sim(myAlgaepH))                  # algae growing on nitrate
out2   <- out(sim(myAlgaepH,Nitrate=FALSE))    # algae growing on ammonium

# plot results

#------------------------#
# PLOTTING model output: #
#------------------------#

par(mfrow=c(2,2), oma=c(0,0,3,0))
plot (out$time,out$ALGAE,type="l",main="Algae",xlab="time,
      hours",ylab="mmol/m3")
polygon(out$time,out$PAR-10,col="lightgrey",border=NA)
box()
lines (out$time,out$ALGAE  ,lwd=2 )

plot (out$time,out$DIN ,type="l",main="DIN"  ,xlab="time, hours",
      ylab="mmolN/m3", lwd=2)
plot (out$time,out$DIC ,type="l",main="DIC"  ,xlab="time, hours",
      ylab="mmolC/m3", lwd=2)
plot (out$time,out$pH,type="l",main="pH"  ,xlab="time, hours",
      ylab="-", lwd=2)
lines(out2$time,out2$pH,col="red")
legend("bottomright",col=c("black","red"), lwd=c(2,1),
       c("nitrate","ammonium"))
mtext(outer=TRUE,side=3,"Algal growth and pH",cex=1.5)

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