aquaphy: a physiological model of unbalanced algal growth

Description

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: \itemlow molecular weight carbohydrates (LMW), the product of photosynthesis, \itemstorage molecules (RESERVE) and \itemthe biosynthetic and photosynthetic apparatus (PROTEINS). 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).

Usage

aquaphy(times,y,parms,...)

Arguments

times

time sequence for which output is wanted; the first value of times must be the initial time

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)

Details

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.

References

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.

Examples

Run this code

#-----------------------#
  # the model parameters: #
  #-----------------------#
  
  parameters<-c(maxPhotoSynt   =0.125,      #molC/molC/hr
                rMortPHY       =0.001,      #/hr
                alpha          =-0.125/150, #uEinst/m2/s/hr
                pExudation     =0.0,        #-
                maxProteinSynt =0.136,      #molC/molC/hr
                ksDIN          =1.0,        #mmolN/m3
                minpLMW        =0.05,       #molC/molC
                maxpLMW        =0.15,       #molC/molC
                minQuotum      =0.075,      #molC/molC
                maxStorage     =0.23,       #/h
                respirationRate=0.0001,     #/h
                pResp          =0.4,        #-
                catabolismRate =0.06,       #/h
                dilutionRate   =0.01,       #/h
                rNCProtein     =0.2,        #molN/molC
                inputDIN       =10.0,       #mmolN/m3
                rChlN          =1,          #gChl/molN
                parMean        =250.,       #umolPhot/m2/s
                dayLength      =15.         #hours
                )
  
  #-------------------------#
  # the initial conditions: #
  #-------------------------#
  
  state     <-c(DIN     =6.,     #mmolN/m3
                PROTEIN =20.0,   #mmolC/m3
                RESERVE =5.0,    #mmolC/m3
                LMW     =1.0)    #mmolC/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))