R: A Sediment Model of Oxygen Consumption

SCOC {deSolve} | R Documentation

## 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{dC}{dt} = Flux - 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).

### 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

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

### See Also

`ccl4model`, the CCl4 inhalation model.

`aquaphy`, the algal growth model.

### Examples

    ## 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")

[Package deSolve version 1.28 Index]