Structure of the S4 class Arena
to represent the environment in which Organisms and Substances interact.
orgdat
A data frame collecting information about the accumulated biomass, 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. If true, bacteria move to random positions within the environment and substances have a uniform concentration value.
mflux
A vector containing highly used metabolic reactions within the arena
exchanges
A data.frame containing last exchanges of each organism.
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
removeM
A matrix indicating grid cells from which organisms are removed (i.e. killed) after each time step
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