Arena-class             Structure of the S4 class "Arena"
Arena-constructor       Constructor of the S4 class 'Arena-class'
Bac-Constructor         Constructor of the S4 class 'Bac-class'
Bac-class               Structure of the S4 class "Bac"
BacArena                BacArena: An Agent-Based Modeling Framework for
                        Cellular Communities
Eval-class              Structure of the S4 class "Eval"
Eval-constructor        Constructor of the S4 class 'Eval-class'
Human-class             Structure of the S4 class "Human"
Human-constructor       Constructor of the S4 class 'Human-class'
NemptyHood              Function to check if the there is a free place
                        in the Moore neighbourhood
Organism-class          Structure of the S4 class "Organism"
Organism-constructor    Constructor of the S4 class 'Organism-class'
Substance-class         Structure of the S4 class "Substance"
Substance-constructor   Constructor of the S4 class 'Substance'
addDefaultMed           Add default medium of an organism to arena.
addEssentialMed         Add minimal medium of an organism to arena.
addEval                 Function for adding a simulation step
addOrg                  Add individuals to the environment
addSubs                 Add substances to the environment
cellgrowth              Function implementing a growth model of a human
                        cell
changeDiff              Change substance concentration patterns in the
                        environment
changeFobj              Function for changing the objective function of
                        the model
changeOrg               Change organisms in the environment
changeSub               Change substances in the environment
checkCorr               Function to show correlations of a simulated
                        organism or substrate
checkPhen               Function for checking phenotypes in the
                        environment
checkPhen_par           Function for checking phenotypes in the
                        environment
chemotaxis              Function for chemotaxis of bacteria to their
                        prefered substrate
colpal1                 Color palette
colpal2                 Color palette
colpal3                 Color palette
colpal4                 Color palette
colpal5                 Color palette
colpal6                 Color palette
constrain               Function for constraining the models based on
                        metabolite concentrations
consume                 Function to account for the consumption and
                        production of substances
createGradient          Change substance concentration patterns in the
                        environment according to a gradient
dat2mat                 Function for transforming the organism data
                        frame to a presence/absence matrix of organisms
diffuse                 Function for diffusion
diffusePDE              Function for diffusion of the Substance matrix
diffuseR                Function for naive diffusion (neighbourhood) of
                        the Substance matrix
diffuse_par             Function for parallelzied diffusion
emptyHood               Function to check if the there is a free place
                        in the Moore neighbourhood
evalArena               Function for plotting spatial and temporal
                        change of populations and/or concentrations
extractMed              Function for re-constructing a medium
                        concentrations from simulations
findFeeding             Function for investigation of feeding between
                        phenotypes
findFeeding2            Function for investigation of feeding between
                        phenotypes
findFeeding3            Function for investigation of feeding between
                        phenotypes
findFeeding3rep         Function for investigation of cross feeding
                        patterns of replicate simulations
findInArena             Function for searching a keyword in arena
                        organisms and media
findRxnFlux             Function to get all reactions fluxes that are
                        associated with the metabolite of a given
                        exchange reactions
findrBiomass            Find biomass reaction in model
flushSubs               Remove all substances in the environment
fluxVarSim              Function to compute flux variability analysis
                        on an simulation object to get min/max of
                        substance usage
getArena                Function for re-constructing an Arena object
                        from a simulation step
getCorrM                Function to compute and return correlation
                        matrix
getPhenoMat             Function for getting a matrix of phenotypes
                        from the dataset
getPhenotype            Function to extract the phenotype of an
                        organism object
getSubHist              Function to get timeline of a substance
getSublb                Function for calculated the substrate
                        concentration for every organism
getVarSubs              Function to get varying substances
growExp                 Function for letting organisms grow
                        exponentially
growLin                 Function for letting organisms grow linearly
growth                  Function implementing a growth model of a
                        bacterium
growth_par              Function implementing a growth model of a
                        bacterium
lsd                     Computer standard deviation lower bound
lysis                   Lysis function of organismal cells by adding
                        biomass_compounds to the medium
minePheno               Function for mining/analyzing phenotypes which
                        occured on the arena
move                    Function for random movement of organisms
openArena               Start simulation
optimizeLP              Function for computing the linear programming
                        according to the model structure
plotAbundance           Plot abundances of species
plotCurves              Function for plotting the overall change as
                        curves
plotCurves2             Function for plotting the overall change as
                        curves with maximally distinct colors
plotFVA                 Function to plot population level minimum and
                        maximum flux from alternative optimal solutions
                        obtained by FVA
plotFluxVar             Plot population flux variations
plotGrowthCurve         Plot growth curve for several simulations
plotInterNum            Plot number of variation in number of
                        interactions for several simulations
plotPhenCurve           Plot growth curve for several simulations
plotPhenNum             Plot number of phenotypes curve for several
                        simulations
plotReaActivity         Function to plot reaction activity for every
                        species
plotShadowCost          Function to plot substance shadow costs for a
                        specie
plotSpecActivity        Function to plot substance usage for every
                        species
plotSubCurve            Plot substance curve for several simulations
plotSubDist             Function to overview the spatial distribution
                        of a substance over time.
plotSubDist2            Function to overview the spatial distribution
                        of a substance over time.
plotSubUsage            Function to plot usage of substances species
                        wise
plotSubVar              Plot substance variations
plotTotFlux             Function for plotting the overall change in
                        reaction activity
readMATmod              Read matlab model
redEval                 Function for reducing the size of an Eval
                        object by collapsing the medium concentrations
reset_screen            Reset plotting screen
rmSubs                  Remove substances
selPheno                Function for selecting phenotypes which occured
                        on the arena from specific iterations and
                        species
setKinetics             Function to set Michaelis-Menten kinetics for
                        uptake of a substance
sihumi_test             Multi-species test data set
simBac                  Function for one simulation iteration for
                        objects of Bac class
simBac_par              Function for one simulation iteration for
                        objects of Bac class
simEnv                  Main function for simulating all processes in
                        the environment
simEnv_par              Main function for simulating in parallel all
                        processes in the environment
simHum                  Function for one simulation iteration for
                        objects of Human class
statPheno               Function for investigating a specific phenotype
                        of an organism
stirEnv                 Function for stirring/mixing the complete
                        evironment
unit_conversion         Function for unit conversion
usd                     Computer standard deviation upper bound
