Structure of the S4 class Arena to represent the environment in which Organisms and Substances interact.
orgdatA data frame collecting information about the accumulated biomass, type, phenotype, x and y position for each individual in the environment.
specsA list of organism types and their associated parameters.
mediaA list of objects of class Substance-class for each compound in the environment.
phenotypesA list of unique phenotypes (metabolites consumed and produced), which occurred in the environment.
mediacA character vector containing the names of all substances in the environment.
tstepA number giving the time (in h) per iteration.
stirA 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.
mfluxA vector containing highly used metabolic reactions within the arena
exchangesA data.frame containing last exchanges of each organism.
shadowA vector containing shadow prices of metabolites present in the arena
nA number giving the horizontal size of the environment.
mA number giving the vertical size of the environment.
LxA number giving the horizontal grid size in cm.
LyA number giving the vertical grid size in cm.
gridgeometryA list containing grid geometry parameter
seedAn integer refering to the random number seed used to be reproducible
scaleA numeric defining the scale factor used for intern unit conversion.
modelsA list containing Objects of class sybil::modelorg which represent the genome scale metabolic models
occupyMA matrix indicating grid cells that are obstacles
sublbA data matrix containing positions with amounts of substance for all organism
removeMA matrix indicating grid cells from which organisms are removed (i.e. killed) after each time step