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 |
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