Arena-class


Structure of the S4 class <code>Arena</code> to represent the environment in which Organisms and Substances interact.


Can be used for simulation of organisms living in
communities. 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

Arena-class function

 <dl>
<dt><code>orgdat</code></dt><dd>A data frame collecting information about the accumulated growth, type, phenotype, x and y position for each individual in the environment.</dd> <dt><code>specs</code></dt><dd>A list of organism types and their associated parameters.</dd> <dt><code>media</code></dt><dd>A list of objects of class <code><a rd-options="" href="/link/Substance-class?package=BacArena&version=1.0.1" data-mini-rdoc="BacArena::Substance-class">Substance-class</a></code> for each compound in the environment.</dd> <dt><code>phenotypes</code></dt><dd>A list of unique phenotypes (metabolites consumed and produced), which occurred in the environment.</dd> <dt><code>mediac</code></dt><dd>A character vector containing the names of all substances in the environment.</dd> <dt><code>tstep</code></dt><dd>A number giving the time (in h) per iteration.</dd> <dt><code>stir</code></dt><dd>A boolean variable indicating if environment should be stirred.</dd> <dt><code>mflux</code></dt><dd>A vector containing highly used metabolic reactions within the arena</dd> <dt><code>n</code></dt><dd>A number giving the horizontal size of the environment.</dd> <dt><code>m</code></dt><dd>A number giving the vertical size of the environment.</dd> <dt><code>Lx</code></dt><dd>A number giving the horizontal grid size in cm.</dd> <dt><code>Ly</code></dt><dd>A number giving the vertical grid size in cm.</dd> <dt><code>gridgeometry</code></dt><dd>A list containing grid geometry parameter</dd> <dt><code>seed</code></dt><dd>An integer refering to the random number seed used to be reproducible</dd> <dt><code>scale</code></dt><dd>A numeric defining the scale factor used for intern unit conversion.</dd> </dl>

State of Data and AI Literacy Report 2025

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

Description

Arguments

Slots