Modeling Framework for Cellular Communities in their Environments


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Documentation for package ‘BacArena’ version 1.8.2

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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