# Modeling Framework for Cellular Communities in their Environments

## Documentation for package ‘BacArena’ version 1.8.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H L M N O P R S U

## -- A --

addDefaultMed | Add default medium of an organism to arena.
addDefaultMed-method | Add default medium of an organism to arena.
addEssentialMed | Add minimal medium of an organism to arena.
addEssentialMed-method | Add minimal medium of an organism to arena.
addEval | Function for adding a simulation step
addEval-method | Function for adding a simulation step
addOrg | Add individuals to the environment
addOrg-method | Add individuals to the environment
addSubs | Add substances to the environment
addSubs-method | Add substances to the environment
Arena | Constructor of the S4 class 'Arena-class'
Arena-class | Structure of the S4 class "Arena"
Arena-constructor | Constructor of the S4 class 'Arena-class'

## -- B --

Bac | Constructor of the S4 class 'Bac-class'
Bac-class | Structure of the S4 class "Bac"
Bac-Constructor | Constructor of the S4 class 'Bac-class'
BacArena | BacArena: An Agent-Based Modeling Framework for Cellular Communities

## -- C --

cellgrowth | Function implementing a growth model of a human cell
cellgrowth-method | Function implementing a growth model of a human cell
changeDiff | Change substance concentration patterns in the environment
changeDiff-method | Change substance concentration patterns in the environment
changeFobj | Function for changing the objective function of the model
changeFobj-method | Function for changing the objective function of the model
changeOrg | Change organisms in the environment
changeOrg-method | Change organisms in the environment
changeSub | Change substances in the environment
changeSub-method | Change substances in the environment
checkCorr | Function to show correlations of a simulated organism or substrate
checkCorr-method | Function to show correlations of a simulated organism or substrate
checkPhen | Function for checking phenotypes in the environment
checkPhen-method | Function for checking phenotypes in the environment
checkPhen_par | Function for checking phenotypes in the environment
checkPhen_par-method | Function for checking phenotypes in the environment
chemotaxis | Function for chemotaxis of bacteria to their prefered substrate
chemotaxis-method | 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
constrain-method | Function for constraining the models based on metabolite concentrations
consume | Function to account for the consumption and production of substances
consume-method | Function to account for the consumption and production of substances
createGradient | Change substance concentration patterns in the environment according to a gradient
createGradient-method | Change substance concentration patterns in the environment according to a gradient

## -- D --

dat2mat | Function for transforming the organism data frame to a presence/absence matrix of organisms
dat2mat-method | Function for transforming the organism data frame to a presence/absence matrix of organisms
diffuse | Function for diffusion
diffuse-method | Function for diffusion
diffusePDE | Function for diffusion of the Substance matrix
diffusePDE-method | Function for diffusion of the Substance matrix
diffuseR | Function for naive diffusion (neighbourhood) of the Substance matrix
diffuseR-method | Function for naive diffusion (neighbourhood) of the Substance matrix
diffuse_par | Function for parallelzied diffusion
diffuse_par-method | Function for parallelzied diffusion

## -- E --

emptyHood | Function to check if the there is a free place in the Moore neighbourhood
emptyHood-method | Function to check if the there is a free place in the Moore neighbourhood
Eval | Constructor of the S4 class 'Eval-class'
Eval-class | Structure of the S4 class "Eval"
Eval-constructor | Constructor of the S4 class 'Eval-class'
evalArena | Function for plotting spatial and temporal change of populations and/or concentrations
evalArena-method | Function for plotting spatial and temporal change of populations and/or concentrations
extractMed | Function for re-constructing a medium concentrations from simulations
extractMed-method | Function for re-constructing a medium concentrations from simulations

## -- F --

findFeeding | Function for investigation of feeding between phenotypes
findFeeding-method | Function for investigation of feeding between phenotypes
findFeeding2 | Function for investigation of feeding between phenotypes
findFeeding2-method | Function for investigation of feeding between phenotypes
findFeeding3 | Function for investigation of feeding between phenotypes
findFeeding3-method | 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
findInArena-method | 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 the metabolite of a given exchange reactions
findRxnFlux-method | Function to get all reactions fluxes that are associated with the metabolite of a given exchange reactions
flushSubs | Remove all substances in the environment
flushSubs-method | Remove all substances in the environment
fluxVarSim | Function to compute flux variability analysis on an simulation object to get min/max of substance usage
fluxVarSim-method | Function to compute flux variability analysis on an simulation object to get min/max of substance usage

## -- G --

getArena | Function for re-constructing an Arena object from a simulation step
getArena-method | Function for re-constructing an Arena object from a simulation step
getCorrM | Function to compute and return correlation matrix
getCorrM-method | Function to compute and return correlation matrix
getPhenoMat | Function for getting a matrix of phenotypes from the dataset
getPhenoMat-method | Function for getting a matrix of phenotypes from the dataset
getPhenotype | Function to extract the phenotype of an organism object
getPhenotype-method | Function to extract the phenotype of an organism object
getSubHist | Function to get timeline of a substance
getSubHist-method | Function to get timeline of a substance
getSublb | Function for calculated the substrate concentration for every organism
getSublb-method | Function for calculated the substrate concentration for every organism
getVarSubs | Function to get varying substances
getVarSubs-method | Function to get varying substances
growExp | Function for letting organisms grow exponentially
growExp-method | Function for letting organisms grow exponentially
growLin | Function for letting organisms grow linearly
growLin-method | Function for letting organisms grow linearly
growth | Function implementing a growth model of a bacterium
growth-method | Function implementing a growth model of a bacterium
growth_par | Function implementing a growth model of a bacterium
growth_par-method | Function implementing a growth model of a bacterium

## -- H --

Human | Constructor of the S4 class 'Human-class'
Human-class | Structure of the S4 class "Human"
Human-constructor | Constructor of the S4 class 'Human-class'

## -- L --

lsd | Computer standard deviation lower bound
lysis | Lysis function of organismal cells by adding biomass_compounds to the medium
lysis-method | Lysis function of organismal cells by adding biomass_compounds to the medium

## -- M --

minePheno | Function for mining/analyzing phenotypes which occured on the arena
minePheno-method | Function for mining/analyzing phenotypes which occured on the arena
move | Function for random movement of organisms
move-method | Function for random movement of organisms

## -- N --

NemptyHood | Function to check if the there is a free place in the Moore neighbourhood
NemptyHood-method | Function to check if the there is a free place in the Moore neighbourhood

## -- O --

openArena | Start simulation
optimizeLP | Function for computing the linear programming according to the model structure
optimizeLP-method | Function for computing the linear programming according to the model structure
Organism | Constructor of the S4 class 'Organism-class'
Organism-class | Structure of the S4 class "Organism"
Organism-constructor | Constructor of the S4 class 'Organism-class'

## -- P --

plotAbundance | Plot abundances of species
plotCurves | Function for plotting the overall change as curves
plotCurves-method | Function for plotting the overall change as curves
plotCurves2 | Function for plotting the overall change as curves with maximally distinct colors
plotCurves2-method | Function for plotting the overall change as curves with maximally distinct colors
plotFluxVar | Plot population flux variations
plotFVA | Function to plot population level minimum and maximum flux from alternative optimal solutions obtained by FVA
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
plotShadowCost-method | 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.
plotSubDist-method | Function to overview the spatial distribution of a substance over time.
plotSubDist2 | Function to overview the spatial distribution of a substance over time.
plotSubDist2-method | 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
plotTotFlux-method | Function for plotting the overall change in reaction activity

## -- R --

readMATmod | Read matlab model
redEval | Function for reducing the size of an Eval object by collapsing the medium concentrations
redEval-method | Function for reducing the size of an Eval object by collapsing the medium concentrations
reset_screen | Reset plotting screen
rmSubs | Remove substances
rmSubs-method | Remove substances

## -- S --

selPheno | Function for selecting phenotypes which occured on the arena from specific iterations and species
selPheno-method | 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
setKinetics-method | 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-method | Function for one simulation iteration for objects of Bac class
simBac_par | Function for one simulation iteration for objects of Bac class
simBac_par-method | Function for one simulation iteration for objects of Bac class
simEnv | Main function for simulating all processes in the environment
simEnv-method | Main function for simulating all processes in the environment
simEnv_par | Main function for simulating in parallel all processes in the environment
simEnv_par-method | Main function for simulating in parallel all processes in the environment
simHum | Function for one simulation iteration for objects of Human class
simHum-method | Function for one simulation iteration for objects of Human class
statPheno | Function for investigating a specific phenotype of an organism
statPheno-method | Function for investigating a specific phenotype of an organism
stirEnv | Function for stirring/mixing the complete evironment
stirEnv-method | Function for stirring/mixing the complete evironment
Substance | Constructor of the S4 class 'Substance'
Substance-class | Structure of the S4 class "Substance"
Substance-constructor | Constructor of the S4 class 'Substance'

## -- U --

unit_conversion | Function for unit conversion
unit_conversion-method | Function for unit conversion
usd | Computer standard deviation upper bound