aquaphy {deSolve} | R Documentation |
A phytoplankton model with uncoupled carbon and nitrogen
assimilation as a function of light and Dissolved Inorganic Nitrogen
(DIN) concentration.
Algal biomass is described via 3 different
state variables:
All algal state variables are expressed in mmol C / m^3. Only proteins contain nitrogen and chlorophyll, with 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.
The algae grow in a dilution culture (chemostat): there is constant inflow of DIN and outflow of culture water, including DIN and algae, at the same rate.
There is a day-night illumination regime, i.e. the light is switched on and off at fixed times (where the sum of illuminated + dark period = 24 hours).
aquaphy(times, y, parms, ...)
times |
time sequence for which output is wanted; the first value of times must be the initial time, |
y |
the initial (state) values ("DIN", "PROTEIN", "RESERVE", "LMW"), in that order. |
parms |
vector or list with the aquaphy model parameters; see the example for the order in which these have to be defined. |
... |
any other parameters passed to the integrator ode
(which solves the model). |
The model is implemented primarily to demonstrate the linking of FORTRAN with R-code.
The source can be found in the ‘dynload’ subdirectory of the package.
Karline Soetaert <k.soetaert@nioo.knaw.nl>
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.
Soetaert, K. and Herman, P. (2008). A practical guide to ecological modelling. Using R as a simulation platform. Springer.
ccl4model
, the CCl4 inhalation model.
## ====================== ## the model parameters: ## ====================== parameters <- c(maxPhotoSynt = 0.125, # mol C/mol C/hr rMortPHY = 0.001, # /hr alpha = -0.125/150, # uEinst/m2/s/hr pExudation = 0.0, # - maxProteinSynt = 0.136, # mol C/mol C/hr ksDIN = 1.0, # mmol N/m3 minpLMW = 0.05, # mol C/mol C maxpLMW = 0.15, # mol C/mol C minQuotum = 0.075, # mol C/mol C maxStorage = 0.23, # /h respirationRate= 0.0001, # /h pResp = 0.4, # - catabolismRate = 0.06, # /h dilutionRate = 0.01, # /h rNCProtein = 0.2, # mol N/mol C inputDIN = 10.0, # mmol N/m3 rChlN = 1, # g Chl/mol N parMean = 250., # umol Phot/m2/s dayLength = 15. # hours ) ## ======================= ## The initial conditions ## ======================= state <- c(DIN = 6., # mmol N/m3 PROTEIN = 20.0, # mmol C/m3 RESERVE = 5.0, # mmol C/m3 LMW = 1.0) # mmol C/m3 ## ================== ## Running the model ## ================== times <- seq(0, 24*20, 1) out <- as.data.frame(aquaphy(times, state, parameters)) ## ====================== ## Plotting model output ## ====================== par(mfrow = c(2, 2), oma = c(0, 0, 3, 0)) col <- grey(0.9) ii <- 1:length(out$PAR) plot (times[ii], out$Chlorophyll[ii], type = "l", main = "Chlorophyll", xlab = "time, hours",ylab = "ug/l") polygon(times[ii], out$PAR[ii]-10, col = col, border = NA); box() lines(times[ii], out$Chlorophyll[ii], lwd = 2 ) plot (times[ii], out$DIN[ii], type = "l", main = "DIN", xlab = "time, hours",ylab = "mmolN/m3") polygon(times[ii], out$PAR[ii]-10, col = col, border = NA); box() lines(times[ii], out$DIN[ii], lwd = 2 ) plot (times[ii], out$NCratio[ii], type = "n", main = "NCratio", xlab = "time, hours", ylab = "molN/molC") polygon(times[ii], out$PAR[ii]-10, col = col, border = NA); box() lines(times[ii], out$NCratio[ii], lwd = 2 ) plot (times[ii], out$PhotoSynthesis[ii],type = "l", main = "PhotoSynthesis",xlab = "time, hours", ylab = "mmolC/m3/hr") polygon(times[ii], out$PAR[ii]-10, col = col, border = NA); box() lines(times[ii], out$PhotoSynthesis[ii], lwd = 2 ) mtext(outer = TRUE, side = 3, "AQUAPHY", cex = 1.5) ## ===================== ## Summary model output ## ===================== t(summary(out))