Substance-class {BacArena}R Documentation

Structure of the S4 class "Substance"

Description

Structure of the S4 class Substance representing substances in the environment which can be produced or consumed.

Slots

smax

A number representing the start concentration of the substance for each grid cell in the environment.

diffmat

A sparse matrix containing all concentrations of the substance in the environment.

name

A character vector representing the name of the substance.

id

A character vector representing the identifier of the substance.

difunc

A character vector ("pde","cpp" or "r") describing the function for diffusion.

difspeed

A number indicating the diffusion rate (given by cm^2/h). Default is set to glucose diffusion in a aqueous solution (6.7e-6 cm^2/s * 3600 s/h = 0.02412 cm^2/h ).

advspeed

A number indicating the advection rate in x direction (given by cm/h).

diffgeometry

Diffusion coefficient defined on all grid cells (initially set by constructor).

pde

Choose diffusion transport reaction to be used (default is diffusion only)

boundS

A number defining the attached amount of substance at the boundary (Warning: boundary-function must be set in pde!)


[Package BacArena version 1.8.2 Index]