Substance-class

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

Can be used for simulation of organisms living in
communities (Bauer and Zimmermann (2017) <doi:10.1371/journal.pcbi.1005544>).
Each organism is represented individually and genome scale
metabolic models determine the uptake and release of compounds. Biological
processes such as movement, diffusion, chemotaxis and kinetics are available
along with data analysis techniques.

Johannes Zimmermann

BacArena

Modeling Framework for Cellular Communities in their
Environments

Eugen Bauer

Substance-class function

<dl class="dl-horizontal">
<dt><code>smax</code></dt><dd>A number representing the start concentration of the substance for each grid cell in the environment.</dd></dl><dt><code>diffmat</code></dt><dd>A sparse matrix containing all concentrations of the substance in the environment.</dd><dt><code>name</code></dt><dd>A character vector representing the name of the substance.</dd><dt><code>id</code></dt><dd>A character vector representing the identifier of the substance.</dd><dt><code>difunc</code></dt><dd>A character vector ("pde","cpp" or "r") describing the function for diffusion.</dd><dt><code>difspeed</code></dt><dd>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 ).</dd><dt><code>advspeed</code></dt><dd>A number indicating the advection rate in x direction (given by cm/h).</dd><dt><code>diffgeometry</code></dt><dd>Diffusion coefficient defined on all grid cells (initially set by constructor).</dd><dt><code>pde</code></dt><dd>Choose diffusion transport reaction to be used (default is diffusion only)</dd><dt><code>boundS</code></dt><dd>A number defining the attached amount of substance at the boundary (Warning: boundary-function must be set in pde!)</dd>

Substance-class: Structure of the S4 class "Substance"

Description

Arguments

Slots