SCOC: A Sediment Model of Oxygen Consumption

Description

A model that describes oxygen consumption in a marine sediment.

One state variable:

sedimentary organic carbon,

Organic carbon settles on the sediment surface (forcing function Flux) and decays at a constant rate.

The equation is simple:

$\frac{d C}{d t} = F l u x - k C$

This model is written in FORTRAN.

Usage

SCOC(times, y = NULL, parms, Flux, ...)

Arguments

times: time sequence for which output is wanted; the first value of times must be the initial time,
y: the initial value of the state variable; if NULL it will be estimated based on Flux and parms,
parms: the model parameter, k,
Flux: a data set with the organic carbon deposition rates,
...: any other parameters passed to the integrator ode (which solves the model).

Author

Karline Soetaert <karline.soetaert@nioz.nl>

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.

References

Soetaert, K. and P.M.J. Herman, 2009. A Practical Guide to Ecological Modelling. Using R as a Simulation Platform. Springer, 372 pp.

Examples

Run this code


## Forcing function data
Flux <- matrix(ncol = 2, byrow = TRUE, data = c(
  1, 0.654, 11, 0.167,   21, 0.060, 41, 0.070, 73,0.277, 83,0.186,
  93,0.140,103, 0.255,  113, 0.231,123, 0.309,133,1.127,143,1.923,
  153,1.091,163,1.001,  173, 1.691,183, 1.404,194,1.226,204,0.767,
  214, 0.893,224,0.737, 234,0.772,244, 0.726,254,0.624,264,0.439,
  274,0.168,284 ,0.280, 294,0.202,304, 0.193,315,0.286,325,0.599,
  335, 1.889,345, 0.996,355,0.681,365,1.135))

parms <- c(k = 0.01)

times <- 1:365
out <- SCOC(times, parms = parms, Flux = Flux)

plot(out[,"time"], out[,"Depo"], type = "l", col = "red")
lines(out[,"time"], out[,"Mineralisation"], col = "blue")

## Constant interpolation of forcing function - left side of interval
fcontrol <- list(method = "constant")

out2 <- SCOC(times, parms = parms, Flux = Flux, fcontrol = fcontrol)

plot(out2[,"time"], out2[,"Depo"], type = "l",col = "red")
lines(out2[,"time"], out2[,"Mineralisation"], col = "blue")

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