Structure of the S4 class "Arena"

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Description

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

Slots

orgdat

A data frame collecting information about the accumulated growth, type, phenotype, x and y position for each individual in the environment.

specs

A list of organism types and their associated parameters.

media

A list of objects of class Substance-class for each compound in the environment.

phenotypes

A list of unique phenotypes (metabolites consumed and produced), which occurred in the environment.

mediac

A character vector containing the names of all substances in the environment.

tstep

A number giving the time (in h) per iteration.

stir

A boolean variable indicating if environment should be stirred.

mflux

A vector containing highly used metabolic reactions within the arena

shadow

A vector containing shadow prices of metabolites present in the arena

n

A number giving the horizontal size of the environment.

m

A number giving the vertical size of the environment.

Lx

A number giving the horizontal grid size in cm.

Ly

A number giving the vertical grid size in cm.

gridgeometry

A list containing grid geometry parameter

seed

An integer refering to the random number seed used to be reproducible

scale

A numeric defining the scale factor used for intern unit conversion.

models

A list containing Objects of class sybil::modelorg which represent the genome scale metabolic models

occupyM

A matrix indicating grid cells that are obstacles

sublb

A data matrix containing positions with amounts of substance for all organism

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