Eval-class

Structure of the S4 class <code>Eval</code> inheriting from class <code><a rd-options="" href="/link/Arena-class?package=BacArena&version=1.8.2" data-mini-rdoc="BacArena::Arena-class">Arena-class</a></code> for the analysis of simulations.

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

Eval-class function

<dl class="dl-horizontal">
<dt><code>medlist</code></dt><dd>A list of compressed medium concentrations (only changes of concentrations are stored) per time step.</dd></dl><dt><code>simlist</code></dt><dd>A list of the organism features per time step.</dd><dt><code>mfluxlist</code></dt><dd>A list of containing highly used metabolic reactions per time step.</dd><dt><code>shadowlist</code></dt><dd>A list of containing shadow prices per time step.</dd><dt><code>subchange</code></dt><dd>A vector of all substrates with numbers indicating the degree of change in the overall simulation.</dd><dt><code>exchangeslist</code></dt><dd>A list of containing exchanges per time step.</dd>

Slots

Structure of the S4 class <code>Eval</code> inheriting from class <code><a rd-options='' href='Arena-class'>Arena-class</a></code> for the analysis of simulations.

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

Description

Arguments

Slots