| 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 |
| Arena-class | Structure of the S4 class "Arena" |
| Arena-constructor | Constructor of the S4 class 'Arena-class' |
| Bac | Structure of the S4 class "Bac" |
| BacArena | BacArena: An Agent-Based Modeling Framework for Cellular... |
| Bac-Constructor | Constructor of the S4 class 'Bac-class' |
| 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... |
| 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... |
| 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... |
| consume | Function to account for the consumption and production of... |
| createGradient | Change substance concentration patterns in the environment... |
| dat2mat | Function for transforming the organism data frame to a... |
| diffuse | Function for diffusion |
| diffuse_par | Function for parallelzied diffusion |
| diffusePDE | Function for diffusion of the Substance matrix |
| diffuseR | Function for naive diffusion (neighbourhood) of the Substance... |
| emptyHood | Function to check if the there is a free place in the Moore... |
| evalArena | Function for plotting spatial and temporal change of... |
| Eval-class | Structure of the S4 class "Eval" |
| Eval-constructor | Constructor of the S4 class 'Eval-class' |
| extractMed | Function for re-constructing a medium concentrations from... |
| 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... |
| findInArena | Function for searching a keyword in arena organisms and media |
| findrBiomass | Find biomass reaction in model |
| findRxnFlux | Function to get all reactions fluxes that are associated with... |
| flushSubs | Remove all substances in the environment |
| fluxVarSim | Function to compute flux variability analysis on an... |
| getArena | Function for re-constructing an Arena object from a... |
| 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... |
| 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 |
| Human | Structure of the S4 class "Human" |
| Human-constructor | Constructor of the S4 class 'Human-class' |
| lsd | Computer standard deviation lower bound |
| lysis | Lysis function of organismal cells by adding... |
| minePheno | Function for mining/analyzing phenotypes which occured on the... |
| move | Function for random movement of organisms |
| NemptyHood | Function to check if the there is a free place in the Moore... |
| openArena | Start simulation |
| optimizeLP | Function for computing the linear programming according to... |
| Organism | Structure of the S4 class "Organism" |
| Organism-constructor | Constructor of the S4 class 'Organism-class' |
| plotAbundance | Plot abundances of species |
| plotCurves | Function for plotting the overall change as curves |
| plotCurves2 | Function for plotting the overall change as curves with... |
| plotFluxVar | Plot population flux variations |
| plotFVA | Function to plot population level minimum and maximum flux... |
| plotGrowthCurve | Plot growth curve for several simulations |
| plotInterNum | Plot number of variation in number of interactions for... |
| 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... |
| plotSubDist2 | Function to overview the spatial distribution of a substance... |
| 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... |
| reset_screen | Reset plotting screen |
| rmSubs | Remove substances |
| selPheno | Function for selecting phenotypes which occured on the arena... |
| setKinetics | Function to set Michaelis-Menten kinetics for uptake of a... |
| sihumi_test | Multi-species test data set |
| simBac | Function for one simulation iteration for objects of Bac... |
| simBac_par | Function for one simulation iteration for objects of Bac... |
| simEnv | Main function for simulating all processes in the environment |
| simEnv_par | Main function for simulating in parallel all processes in the... |
| simHum | Function for one simulation iteration for objects of Human... |
| statPheno | Function for investigating a specific phenotype of an... |
| stirEnv | Function for stirring/mixing the complete evironment |
| Substance | Structure of the S4 class "Substance" |
| Substance-constructor | Constructor of the S4 class 'Substance' |
| unit_conversion | Function for unit conversion |
| usd | Computer standard deviation upper bound |
