aquaphy {deSolve} | R Documentation

## 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:

- low molecular weight carbohydrates (LMW), the product of photosynthesis,

- storage molecules (RESERVE) and

- the 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.

Two versions of the model are included.

- In the default model, 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).

- In another version, the light is imposed as a forcing function data set.

This model is written in `FORTRAN`.

### Usage

    aquaphy(times, y, parms, PAR = NULL, ...)

### Arguments

`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.
`PAR` | a data set of the photosynthetically active radiation (light intensity), if `NULL`, on-off PAR is used,
`...` | 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 ‘doc/examples/dynload’ subdirectory of the package.

### Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

### 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.

### See Also

`ccl4model`, the CCl4 inhalation model.

### Examples

    ## ======================================================
    ##
    ## Example 1. PAR an on-off function
    ##
    ## ======================================================

    ## -----------------------------
    ## 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, PAR= on-off", cex = 1.5)

    ## -----------------------------
    ## Summary model output
    ## -----------------------------
    t(summary(out))

    ## ======================================================
    ##
    ## Example 2. PAR a forcing function data set
    ##
    ## ======================================================

    times <- seq(0, 24*20, 1)

    ## -----------------------------
    ## create the forcing functions
    ## -----------------------------

    ftime  <- seq(0,500,by=0.5)
    parval <- pmax(0,250 + 350*sin(ftime*2*pi/24)+
       (runif(length(ftime))-0.5)*250)
    Par    <- matrix(nc=2,c(ftime,parval))

    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

    out <- aquaphy(times, state, parameters, Par)

    plot(out, which = c("PAR", "Chlorophyll", "DIN", "NCratio"),
         xlab = "time, hours",
         ylab = c("uEinst/m2/s", "ug/l", "mmolN/m3", "molN/molC"))

    mtext(outer = TRUE, side = 3, "AQUAPHY, PAR=forcing", cex = 1.5)

    # Now all variables plotted in one figure...
    plot(out, which = 1:9, type = "l")

    par(mfrow = c(1, 1))

[Package deSolve version 1.24 Index]