Toolbox for Aquatic Ecosystem Modeling

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Description

Classes and methods for implementing aquatic ecosystem models, for running these models, and for visualizing their results.

Models are built by constructing objects of the classes

process-class,
reactor-class,
link-class,
system-class.

A transformation processes (process-class) is defined by a process rate (expression describing the dependence of the rate on substance or organism concentrations and external influence factors) and stoichiometric coefficients that describe how the rate affects different substances or organisms. It is recommended to calculate the stoichiometric coefficients with the function calc.stoich.coef of the package stoichcalc from substance and organism compositions. The output of this function can directly be used for the process definition. A reactor (reactor-class) describes a well-mixed compartment of the environment (or of a laboratory system). For each reactor, inflow, outflow, substance and organism input and transformation processes can be defined. A link (link-class) describes advective and/or diffusive exchange of substances and/or organisms between well-mixed reactors. Finally, a system (system-class) consists of a single reactor or a set of isolated or linked reactors and can be used to describe a community or meta-community model of an ecosystem and the biogeochemical cycles.

Once a model is described by an object of the class system (system-class), simulations can be performed using the member function

calcres,

This function integrates the system of ordinary differential equations numerically using the function ode of the package deSolve and produces time series of the volumes and substance and organisms concentrations as a R matrix. The results can be visualized with arbitrary R functions or a summary of all results can be produced with the function

plotres.

To propagate stochasticity and uncertainty to the results, stochastic parameter time series can be generated with the function

randou

and parameter samples can be sampled with the function

randnorm

to get a sample from the predictive distribution by Monte Carlo simulation.

Details

Package: ecosim
Type: Package
Version: 1.2
Date: 2014-02-11
License: GPL (>= 2)
Depends: deSolve, stoichcalc

Note

The following demos are available:

lakemodel_simple
lakemodel_intermediate
lakemodel_complex
rivermodel_simple
rivermodel_complex

Author(s)

Peter Reichert

Maintainer: Peter Reichert <peter.reichert@eawag.ch>

References

Omlin, M., Reichert, P. and Forster, R., Biogeochemical model of lake Zurich: Model equations and results, Ecological Modelling 141(1-3), 77-103, 2001.

Reichert, P., Borchardt, D., Henze, M., Rauch, W., Shanahan, P., Somlyody, L. and Vanrolleghem, P., River Water Quality Model no. 1 (RWQM1): II. Biochemical process equations, Water Sci. Tech. 43(5), 11-30, 2001.

Reichert, P. and Schuwirth, N., A generic framework for deriving process stoichiometry in environmental models, Environmental Modelling & Software, 25, 1241-1251, 2010.

Soetaert, K., Petzoldt, T., and Woodrow Setzer, R. Solving differential equations in R: Package deSolve. Journal of Statistical Software, 33(9), 2010.

Soetaert, K., Cash, J., and Mazzia, F. Solving Differential Equations in R. Springer, Heidelberg, Germany. 2012.

See Also

deSolve, stoichcalc,

Examples

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# Definition of parameters:
# =========================

param    <- list(k.gro.ALG   = 1,        # 1/d
                 k.gro.ZOO   = 0.8,      # m3/gDM/d
                 k.death.ALG = 0.4,      # 1/d
                 k.death.ZOO = 0.08,     # 1/d
                 K.HPO4      = 0.002,    # gP/m3
                 Y.ZOO       = 0.2,      # gDM/gDM
                 alpha.P.ALG = 0.002,    # gP/gDM
                 A           = 8.5e+006, # m2
                 h.epi       = 4,        # m
                 Q.in        = 4,        # m3/s
                 C.ALG.ini   = 0.05,     # gDM/m3
                 C.ZOO.ini   = 0.1,      # gDM/m3
                 C.HPO4.ini  = 0.02,     # gP/m3
                 C.HPO4.in   = 0.04)     # gP/m3             

# Definition of transformation processes:
# =======================================

# Growth of algae:
# ----------------

gro.ALG   <- new(Class  = "process",
                 name   = "Growth of algae",
                 rate   = expression(k.gro.ALG
                                     *C.HPO4/(K.HPO4+C.HPO4)
                                     *C.ALG),
                 stoich = list(C.ALG  = expression(1),              # gDM/gDM
                               C.HPO4 = expression(-alpha.P.ALG)))  # gP/gDM

# Death of algae:
# ---------------

death.ALG <- new(Class = "process",
                 name   = "Death of algae",
                 rate   = expression(k.death.ALG*C.ALG),
                 stoich = list(C.ALG  = expression(-1)))            # gDM/gDM

# Growth of zooplankton:
# ----------------------

gro.ZOO   <- new(Class  = "process",
                 name   = "Growth of zooplankton",
                 rate   = expression(k.gro.ZOO
                                     *C.ALG
                                     *C.ZOO),
                 stoich = list(C.ZOO  = expression(1),              # gDM/gDM
                               C.ALG  = expression(-1/Y.ZOO)))      # gP/gDM

# Death of zooplankton:
# ---------------------

death.ZOO <- new(Class  = "process",
                 name   = "Death of zooplankton",
                 rate   = expression(k.death.ZOO*C.ZOO),
                 stoich = list(C.ZOO  = expression(-1)))            # gDM/gDM

# Definition of reactor:
# ======================

# Epilimnion:
# -----------

epilimnion <- 
   new(Class            = "reactor",
       name             = "Epilimnion",
       volume.ini       = expression(A*h.epi),
       conc.pervol.ini  = list(C.HPO4 = expression(C.HPO4.ini),     # gP/m3
                               C.ALG  = expression(C.ALG.ini),      # gDM/m3
                               C.ZOO  = expression(C.ZOO.ini)),     # gDM/m3
       inflow           = expression(Q.in*86400),                   # m3/d
       inflow.conc      = list(C.HPO4 = expression(C.HPO4.in),
                               C.ALG  = 0,
                               C.ZOO  = 0),
       outflow          = expression(Q.in*86400),
       processes        = list(gro.ALG,death.ALG,gro.ZOO,death.ZOO))

# Definition of system:
# =====================

# Lake system:
# ------------

system <- new(Class    = "system",
              name     = "Lake",
              reactors = list(epilimnion),
              param    = param,
              t.out    = seq(0,365,by=1))

# Perform simulation:
# ===================

res <- calcres(system)

# Plot results:
# =============
                 
plotres(res)              # plot to screen

plotres(res,file="ecosim_example_plot1.pdf")  # plot to pdf file

plotres(res, colnames=c("C.ALG", "C.ZOO"))  # plot selected variables

plotres(res, colnames=list("C.HPO4",c("C.ALG", "C.ZOO")))

plotres(res[1:100,], colnames=list("C.HPO4",c("C.ALG", "C.ZOO"))) # plot selected time steps

plotres(res      = res,    # plot to pdf file
        colnames = list("C.HPO4",c("C.ALG","C.ZOO")),
        file     = "ecosim_example_plot2.pdf",
        width    = 8,
        height   = 4)