- BacArena: Modeling Framework for Cellular Communities in their Environments
- plotFluxVar: Plot population flux variations
Plot population flux variations
plotFluxVar takes a list of simulations and metabolites, returning a plot with metabolite fluxes for each species
A list of simulations (eval objects).
A vector with the name of exchange reactions of interest
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- 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
- findInArena: Function for searching a keyword in arena organisms and media
- flushSubs: Remove all substances in the environment
- 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-class: Structure of the S4 class "Organism"
- Organism-constructor: Constructor of the S4 class 'Organism'
- 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
- 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
- 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
- plotSubUsage: Function to plot usage of substances species wise
- plotSubVar: Plot substance variations
- plotTotFlux: Function for plotting the overall change in reaction activity
- 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'
- usd: Computer standard deviation upper bound