BacArena: Modeling Framework for Cellular Communities in their Environments

Can be used for simulation of organisms living in communities. Each organism is represented individually and genome scale metabolic models determine the uptake and release of compounds. Biological processes such as movement, diffusion, chemotaxis and kinetics are available along with data analysis techniques.

AuthorEugen Bauer [aut], Johannes Zimmermann [aut, cre]
Date of publication2016-12-05 18:28:46
MaintainerJohannes Zimmermann <j.zimmermann@iem.uni-kiel.de>
LicenseGPL-3
Version1.5.1
https://github.com/euba/BacArena

View on CRAN

Man pages

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

Functions

addDefaultMed Man page
addDefaultMed,Arena-method Man page
addEssentialMed Man page
addEssentialMed,Arena-method Man page
addEval Man page
addEval,Eval-method Man page
addOrg Man page
addOrg,Arena-method Man page
addSubs Man page
addSubs,Arena-method Man page
Arena Man page
Arena-class Man page
Arena-constructor Man page
Bac Man page
BacArena Man page
BacArena-package Man page
Bac-class Man page
Bac-Constructor Man page
cellgrowth Man page
cellgrowth,Human-method Man page
changeDiff Man page
changeDiff,Arena-method Man page
changeFobj Man page
changeFobj,Human-method Man page
changeOrg Man page
changeOrg,Arena-method Man page
changeSub Man page
changeSub,Arena-method Man page
checkCorr Man page
checkCorr,Eval-method Man page
checkPhen Man page
checkPhen,Arena-method Man page
checkPhen_par Man page
checkPhen_par,Arena-method Man page
chemotaxis Man page
chemotaxis,Bac-method Man page
colpal1 Man page
colpal2 Man page
colpal3 Man page
colpal4 Man page
colpal5 Man page
colpal6 Man page
constrain Man page
constrain,Organism-method Man page
consume Man page
consume,Organism-method Man page
createGradient Man page
createGradient,Arena-method Man page
dat2mat Man page
dat2mat,Arena-method Man page
diffuse Man page
diffuse,Arena-method Man page
diffuse_par Man page
diffuse_par,Arena-method Man page
diffusePDE Man page
diffusePDE,Substance-method Man page
diffuseR Man page
diffuseR,Substance-method Man page
emptyHood Man page
emptyHood,Organism-method Man page
Eval Man page
evalArena Man page
evalArena,Eval-method Man page
Eval-class Man page
Eval-constructor Man page
extractMed Man page
extractMed,Eval-method Man page
findFeeding Man page
findFeeding2 Man page
findFeeding2,Eval-method Man page
findFeeding3 Man page
findFeeding3,Eval-method Man page
findFeeding,Eval-method Man page
findInArena Man page
findInArena,Arena-method Man page
flushSubs Man page
flushSubs,Arena-method Man page
getArena Man page
getArena,Eval-method Man page
getCorrM Man page
getCorrM,Eval-method Man page
getPhenoMat Man page
getPhenoMat,Eval-method Man page
getPhenotype Man page
getPhenotype,Organism-method Man page
getSubHist Man page
getSubHist,Eval-method Man page
getSublb Man page
getSublb,Arena-method Man page
getVarSubs Man page
getVarSubs,Eval-method Man page
growExp Man page
growExp,Organism-method Man page
growLin Man page
growLin,Organism-method Man page
growth Man page
growth,Bac-method Man page
growth_par Man page
growth_par,Bac-method Man page
Human Man page
Human-class Man page
Human-constructor Man page
lsd Man page
lysis Man page
lysis,Organism-method Man page
minePheno Man page
minePheno,Eval-method Man page
move Man page
move,Organism-method Man page
NemptyHood Man page
NemptyHood,Organism-method Man page
openArena Man page
optimizeLP Man page
optimizeLP,Organism-method Man page
Organism Man page
Organism-class Man page
Organism-constructor Man page
plotAbundance Man page
plotCurves Man page
plotCurves2 Man page
plotCurves2,Eval-method Man page
plotCurves,Eval-method Man page
plotFluxVar Man page
plotGrowthCurve Man page
plotInterNum Man page
plotPhenCurve Man page
plotPhenNum Man page
plotShadowCost Man page
plotShadowCost,Eval-method Man page
plotSpecActivity Man page
plotSubCurve Man page
plotSubUsage Man page
plotSubVar Man page
plotTotFlux Man page
plotTotFlux,Eval-method Man page
redEval Man page
redEval,Eval-method Man page
reset_screen Man page
rmSubs Man page
rmSubs,Arena-method Man page
selPheno Man page
selPheno,Eval-method Man page
setKinetics Man page
setKinetics,Organism-method Man page
sihumi_test Man page
simBac Man page
simBac,Bac-method Man page
simBac_par Man page
simBac_par,Bac-method Man page
simEnv Man page
simEnv,Arena-method Man page
simEnv_par Man page
simEnv_par,Arena-method Man page
simHum Man page
simHum,Human-method Man page
statPheno Man page
statPheno,Eval-method Man page
stirEnv Man page
stirEnv,Arena-method Man page
Substance Man page
Substance-class Man page
Substance-constructor Man page
usd Man page

Files

BacArena
BacArena/inst
BacArena/inst/doc
BacArena/inst/doc/BacArena-Introduction.R
BacArena/inst/doc/BacArena-Introduction.Rmd
BacArena/inst/doc/BacArena-Introduction.pdf
BacArena/src
BacArena/src/diff.cpp
BacArena/src/move.cpp
BacArena/src/addBac.cpp
BacArena/src/duplicate.cpp
BacArena/src/RcppExports.cpp
BacArena/NAMESPACE
BacArena/NEWS
BacArena/data
BacArena/data/colpal.rda
BacArena/data/sihumi_test.rda
BacArena/data/datalist
BacArena/R
BacArena/R/data.R BacArena/R/BacArena.R BacArena/R/Substance.R BacArena/R/RcppExports.R BacArena/R/Stuff.R BacArena/R/Organism.R BacArena/R/Arena.R
BacArena/vignettes
BacArena/vignettes/BacArena-Introduction.Rmd
BacArena/README.md
BacArena/MD5
BacArena/build
BacArena/build/vignette.rds
BacArena/DESCRIPTION
BacArena/man
BacArena/man/changeDiff.Rd BacArena/man/checkPhen.Rd BacArena/man/growExp.Rd BacArena/man/getPhenoMat.Rd BacArena/man/extractMed.Rd BacArena/man/diffusePDE.Rd BacArena/man/colpal1.Rd BacArena/man/lsd.Rd BacArena/man/Arena-constructor.Rd BacArena/man/getVarSubs.Rd BacArena/man/findFeeding.Rd BacArena/man/Human.Rd BacArena/man/addSubs.Rd BacArena/man/Human-constructor.Rd BacArena/man/createGradient.Rd BacArena/man/setKinetics.Rd BacArena/man/plotFluxVar.Rd BacArena/man/growLin.Rd BacArena/man/usd.Rd BacArena/man/colpal5.Rd BacArena/man/Eval-class.Rd BacArena/man/simEnv_par.Rd BacArena/man/plotAbundance.Rd BacArena/man/emptyHood.Rd BacArena/man/rmSubs.Rd BacArena/man/minePheno.Rd BacArena/man/plotCurves.Rd BacArena/man/chemotaxis.Rd BacArena/man/findInArena.Rd BacArena/man/Substance-constructor.Rd BacArena/man/colpal3.Rd BacArena/man/dat2mat.Rd BacArena/man/plotPhenNum.Rd BacArena/man/getSublb.Rd BacArena/man/flushSubs.Rd BacArena/man/findFeeding3.Rd BacArena/man/selPheno.Rd BacArena/man/consume.Rd BacArena/man/plotInterNum.Rd BacArena/man/cellgrowth.Rd BacArena/man/simEnv.Rd BacArena/man/constrain.Rd BacArena/man/Bac-Constructor.Rd BacArena/man/optimizeLP.Rd BacArena/man/checkPhen_par.Rd BacArena/man/plotGrowthCurve.Rd BacArena/man/plotSubCurve.Rd BacArena/man/Organism-class.Rd BacArena/man/plotTotFlux.Rd BacArena/man/findFeeding2.Rd BacArena/man/colpal2.Rd BacArena/man/simHum.Rd BacArena/man/lysis.Rd BacArena/man/evalArena.Rd BacArena/man/plotPhenCurve.Rd BacArena/man/growth_par.Rd BacArena/man/colpal4.Rd BacArena/man/getPhenotype.Rd BacArena/man/plotSpecActivity.Rd BacArena/man/simBac.Rd BacArena/man/addOrg.Rd BacArena/man/getSubHist.Rd BacArena/man/growth.Rd BacArena/man/Organism-constructor.Rd BacArena/man/changeFobj.Rd BacArena/man/NemptyHood.Rd BacArena/man/changeSub.Rd BacArena/man/changeOrg.Rd BacArena/man/plotSubVar.Rd BacArena/man/addEssentialMed.Rd BacArena/man/addDefaultMed.Rd BacArena/man/checkCorr.Rd BacArena/man/diffuse_par.Rd BacArena/man/diffuse.Rd BacArena/man/simBac_par.Rd BacArena/man/statPheno.Rd BacArena/man/diffuseR.Rd BacArena/man/openArena.Rd BacArena/man/redEval.Rd BacArena/man/getCorrM.Rd BacArena/man/colpal6.Rd BacArena/man/plotShadowCost.Rd BacArena/man/reset_screen.Rd BacArena/man/move.Rd BacArena/man/BacArena.Rd BacArena/man/stirEnv.Rd BacArena/man/getArena.Rd BacArena/man/plotSubUsage.Rd BacArena/man/Eval-constructor.Rd BacArena/man/Substance.Rd BacArena/man/plotCurves2.Rd BacArena/man/sihumi_test.Rd BacArena/man/Bac.Rd BacArena/man/Arena-class.Rd BacArena/man/addEval.Rd

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