Man pages for BacArena
Modeling Framework for Cellular Communities in their Environments

addDefaultMedAdd default medium of an organism to arena.
addEssentialMedAdd minimal medium of an organism to arena.
addEvalFunction for adding a simulation step
addOrgAdd individuals to the environment
addSubsAdd substances to the environment
Arena-classStructure of the S4 class "Arena"
Arena-constructorConstructor of the S4 class 'Arena-class'
BacStructure of the S4 class "Bac"
BacArenaBacArena: An Agent-Based Modeling Framework for Cellular...
Bac-ConstructorConstructor of the S4 class 'Bac-class'
cellgrowthFunction implementing a growth model of a human cell
changeDiffChange substance concentration patterns in the environment
changeFobjFunction for changing the objective function of the model
changeOrgChange organisms in the environment
changeSubChange substances in the environment
checkCorrFunction to show correlations of a simulated organism or...
checkPhenFunction for checking phenotypes in the environment
checkPhen_parFunction for checking phenotypes in the environment
chemotaxisFunction for chemotaxis of bacteria to their prefered...
colpal1Color palette
colpal2Color palette
colpal3Color palette
colpal4Color palette
colpal5Color palette
colpal6Color palette
constrainFunction for constraining the models based on metabolite...
consumeFunction to account for the consumption and production of...
createGradientChange substance concentration patterns in the environment...
dat2matFunction for transforming the organism data frame to a...
diffuseFunction for diffusion
diffuse_parFunction for parallelzied diffusion
diffusePDEFunction for diffusion of the Substance matrix
diffuseRFunction for naive diffusion (neighbourhood) of the Substance...
emptyHoodFunction to check if the there is a free place in the Moore...
evalArenaFunction for plotting spatial and temporal change of...
Eval-classStructure of the S4 class "Eval"
Eval-constructorConstructor of the S4 class 'Eval-class'
extractMedFunction for re-constructing a medium concentrations from...
findFeedingFunction for investigation of feeding between phenotypes
findFeeding2Function for investigation of feeding between phenotypes
findFeeding3Function for investigation of feeding between phenotypes
findFeeding3repFunction for investigation of cross feeding patterns of...
findInArenaFunction for searching a keyword in arena organisms and media
findrBiomassFind biomass reaction in model
findRxnFluxFunction to get all reactions fluxes that are associated with...
flushSubsRemove all substances in the environment
fluxVarSimFunction to compute flux variability analysis on an...
getArenaFunction for re-constructing an Arena object from a...
getCorrMFunction to compute and return correlation matrix
getPhenoMatFunction for getting a matrix of phenotypes from the dataset
getPhenotypeFunction to extract the phenotype of an organism object
getSubHistFunction to get timeline of a substance
getSublbFunction for calculated the substrate concentration for every...
getVarSubsFunction to get varying substances
growExpFunction for letting organisms grow exponentially
growLinFunction for letting organisms grow linearly
growthFunction implementing a growth model of a bacterium
growth_parFunction implementing a growth model of a bacterium
HeatMapFeedingFunction for plotting heatmap of feeding between two selected...
HumanStructure of the S4 class "Human"
Human-constructorConstructor of the S4 class 'Human-class'
lsdComputer standard deviation lower bound
lysisLysis function of organismal cells by adding...
minePhenoFunction for mining/analyzing phenotypes which occured on the...
moveFunction for random movement of organisms
NemptyHoodFunction to check if the there is a free place in the Moore...
openArenaStart simulation
optimizeLPFunction for computing the linear programming according to...
OrganismStructure of the S4 class "Organism"
Organism-constructorConstructor of the S4 class 'Organism-class'
plotAbundancePlot abundances of species
plotCurvesFunction for plotting the overall change as curves
plotCurves2Function for plotting the overall change as curves with...
plotFluxVarPlot population flux variations
plotFVAFunction to plot population level minimum and maximum flux...
plotGrowthCurvePlot growth curve for several simulations
plotInterNumPlot number of variation in number of interactions for...
plotPhenCurvePlot growth curve for several simulations
plotPhenNumPlot number of phenotypes curve for several simulations
plotReaActivityFunction to plot reaction activity for every species
plotShadowCostFunction to plot substance shadow costs for a specie
plotSpecActivityFunction to plot substance usage for every species
plotSubCurvePlot substance curve for several simulations
plotSubDistFunction to overview the spatial distribution of a substance...
plotSubDist2Function to overview the spatial distribution of a substance...
plotSubUsageFunction to plot usage of substances species wise
plotSubVarPlot substance variations
plotTotFluxFunction for plotting the overall change in reaction activity
redEvalFunction for reducing the size of an Eval object by...
reset_screenReset plotting screen
rmSubsRemove substances
selPhenoFunction for selecting phenotypes which occured on the arena...
setKineticsFunction to set Michaelis-Menten kinetics for uptake of a...
sihumi_testMulti-species test data set
simBacFunction for one simulation iteration for objects of Bac...
simBac_parFunction for one simulation iteration for objects of Bac...
simEnvMain function for simulating all processes in the environment
simEnv_parMain function for simulating in parallel all processes in the...
simHumFunction for one simulation iteration for objects of Human...
statPhenoFunction for investigating a specific phenotype of an...
stirEnvFunction for stirring/mixing the complete evironment
SubstanceStructure of the S4 class "Substance"
Substance-constructorConstructor of the S4 class 'Substance'
unit_conversionFunction for unit conversion
usdComputer standard deviation upper bound
BacArena documentation built on May 9, 2018, 5:04 p.m.