Description Usage Format Author(s) References See Also Examples
Phytoplankton model with uncoupled carbon and nitrogen assimilation.
lgal biomass is described via 3 different state variables:
[LMW
] low molecular weight carbohydrates, the product
of photosynthesis,
[RESERVE
] storage molecules and
[PROTEINS
] the biosynthetic and photosynthetic apparatus.
All these state variables are expressed in mmol C m-3. Only proteins contain nitrogen and chlorophyll, at a fixed amount (i.e. using a fixed stoichiometric ratio).
As the relative amount of proteins changes in the algae, so does the N:C and the Chl:C ratio.
An additional state variable, dissolved inorganic nitrogen (DIN) has units of mmol N m-3.
1 | Aquaphy()
|
An S4 object according to the odeModel
specification.
The object contains the following slots:
main
Aquaphy 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 algal state variables
and DIN.
Karline Soetaert
Chapter 2.8.2 from the book by Soetaert and Herman, 2009. A practical guide to ecological Modelling. Using R as a simulation platform Springer.
Lancelot, C., Veth, C. and Mathot, S. (1991). Modelling ice-edge phytoplankton bloom in the Scotia-Weddel sea sector of the Southern Ocean during spring 1988. Journal of Marine Systems 2, 333-346.
R-package simecol for a description of the simObj class
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 32 33 34 35 36 37 38 39 40 41 42 | # initialize model
aquaphy <- Aquaphy()
# show model code, parameter settings,...
print(aquaphy)
# run simulation
out <- out(sim(aquaphy))
# plot results
par(mfrow=c(2,2), oma=c(0,0,3,0))
col <- grey(0.9)
plot (out$time, out$Chlorophyll, type="l", main="Chlorophyll",
xlab="time, hours", ylab=expression(paste(mu, g/l)))
polygon(out$time, out$PAR-10, col=col, border=NA)
box()
lines (out$time, out$Chlorophyll, lwd=2 )
plot (out$time, out$DIN, type="l",main="DIN",
xlab="time, hours", ylab="mmolN/m3")
polygon(out$time,out$PAR-10,col=col,border=NA);box()
lines (out$time,out$DIN ,lwd=2 )
plot (out$time, out$NCratio, type="n", main="NCratio",
xlab="time, hours", ylab="molN/molC")
polygon(out$time, out$PAR-10, col=col, border=NA)
box()
lines (out$time, out$NCratio, lwd=2 )
plot (out$time, out$PhotoSynthesis, type="l", main="PhotoSynthesis",
xlab="time, hours", ylab="mmolC/m3/hr")
polygon(out$time, out$PAR-10, col=col, border=NA);box()
lines (out$time, out$PhotoSynthesis, lwd=2 )
mtext(outer=TRUE, side=3, "AQUAPHY", cex=1.5)
# SUMMARY model output: #
t(summary(out))
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