# SCOC: A Sediment Model of Oxygen Consumption In deSolve: Solvers for Initial Value Problems of Differential Equations ('ODE', 'DAE', 'DDE')

## 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

 1 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 <[email protected]>

## References

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

ccl4model, the CCl4 inhalation model.
aquaphy, the algal growth model.
  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 ## 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")