Structure of the S4 class
Arena to represent the environment in which Organisms and Substances interact.
A data frame collecting information about the accumulated biomass, type, phenotype, x and y position for each individual in the environment.
A list of organism types and their associated parameters.
A list of objects of class
Substance-class for each compound in the environment.
A list of unique phenotypes (metabolites consumed and produced), which occurred in the environment.
A character vector containing the names of all substances in the environment.
A number giving the time (in h) per iteration.
A boolean variable indicating if environment should be stirred. If true, bacteria move to random positions within the environment and substances have a uniform concentration value.
A vector containing highly used metabolic reactions within the arena
A vector containing shadow prices of metabolites present in the arena
A number giving the horizontal size of the environment.
A number giving the vertical size of the environment.
A number giving the horizontal grid size in cm.
A number giving the vertical grid size in cm.
A list containing grid geometry parameter
An integer refering to the random number seed used to be reproducible
A numeric defining the scale factor used for intern unit conversion.
A list containing Objects of class sybil::modelorg which represent the genome scale metabolic models
A matrix indicating grid cells that are obstacles
A data matrix containing positions with amounts of substance for all organism
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