Modeling Framework for Cellular Communities in their Environments


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Documentation for package ‘BacArena’ version 1.0.1

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

BacArena-package BacArena: An Agent-Based Modeling Framework for Cellular Communities

-- A --

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
chemotaxis Function for chemotaxis of bacteria to their prefered substrate
chemotaxis-method Function for chemotaxis of bacteria to their prefered substrate
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
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

-- 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
flushSubs Remove all substances in the environment
flushSubs-method Remove all substances in the environment

-- 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
getSublb Function for calculated the substrate concentration for every organism
getSublb-method Function for calculated the substrate concentration for every organism
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

-- 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 --

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'
Organism-class Structure of the S4 class "Organism"
Organism-constructor Constructor of the S4 class 'Organism'

-- P --

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
plotTotFlux Function for plotting the overall change in reaction activity
plotTotFlux-method Function for plotting the overall change in reaction activity

-- 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
simBac Function for one simulation iteration for objects of Bac class
simBac-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
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'