BacArena: Modeling Framework for Cellular Communities in their Environments
Version 1.6

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 publication2017-05-23 17:28:04 UTC
MaintainerJohannes Zimmermann <j.zimmermann@iem.uni-kiel.de>
LicenseGPL-3
Version1.6
URL https://github.com/euba/BacArena
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BacArena")

Getting started

README.md
BacArena - An Agent-Based Modeling Framework for Cellular Communities

Popular man pages

addEval: Function for adding a simulation step
BacArena: BacArena: An Agent-Based Modeling Framework for Cellular...
changeFobj: Function for changing the objective function of the model
createGradient: Change substance concentration patterns in the environment...
getArena: Function for re-constructing an Arena object from a...
growLin: Function for letting organisms grow linearly
Organism-constructor: Constructor of the S4 class 'Organism-class'
See all...

All man pages Function index File listing

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
findFeeding3rep: Function for investigation of cross feeding patterns of...
findInArena: Function for searching a keyword in arena organisms and media
findRxnFlux: Function to get all reactions fluxes that are associated with...
flushSubs: Remove all substances in the environment
fluxVarSim: Function to compute flux variability analysis on an...
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: Structure of the S4 class "Organism"
Organism-constructor: Constructor of the S4 class 'Organism-class'
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
plotFVA: Function to plot population level minimum and maximum flux...
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
plotReaActivity: Function to plot reaction activity for every species
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
plotSubDist: Function to overview the spatial distribution of a substance...
plotSubDist2: Function to overview the spatial distribution of a substance...
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'
unit_conversion: Function for unit conversion
usd: Computer standard deviation upper bound

Functions

AdvecDiff2d Source code
AdvecDiffConserv2d Source code
Arena Man page Source code
Arena-class Man page
Arena-constructor Man page
Bac Man page Source code
Bac-Constructor Man page
Bac-class Man page
BacArena Man page
BacArena-package Man page
ConstBoundAdvecDiff2d Source code
ConstBoundDiff2d Source code
Diff2d Source code
Eval Man page Source code
Eval-class Man page
Eval-constructor Man page
Human Man page Source code
Human-class Man page
Human-constructor Man page
InfluxBoundDiff2d Source code
NemptyHood Man page
NemptyHood,Organism-method Man page
Organism Man page Source code
Organism-class Man page
Organism-constructor Man page
Substance Man page Source code
Substance-class Man page
Substance-constructor Man page
addBacCpp Source code
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
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
diffuseGrajdeanuCpp Source code
diffuseNaiveCpp Source code
diffusePDE Man page
diffusePDE,Substance-method Man page
diffuseR Man page
diffuseR,Substance-method Man page
diffuseSteveCpp Source code
diffuse_par Man page
diffuse_par,Arena-method Man page
duplicateCpp Source code
emptyHood Man page
emptyHood,Organism-method Man page
estimate_lrw Source code
evalArena Man page
evalArena,Eval-method Man page
extractMed Man page
extractMed,Eval-method Man page
findFeeding Man page
findFeeding,Eval-method Man page
findFeeding2 Man page
findFeeding2,Eval-method Man page
findFeeding3 Man page
findFeeding3,Eval-method Man page
findFeeding3rep Man page Source code
findInArena Man page
findInArena,Arena-method Man page
findRxnFlux Man page
findRxnFlux,Eval-method Man page
flushSubs Man page
flushSubs,Arena-method Man page
fluxVarSim Man page
fluxVarSim,Eval-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
lsd Man page Source code
lysis Man page
lysis,Organism-method Man page
minePheno Man page
minePheno,Eval-method Man page
move Man page
move,Organism-method Man page
movementCpp Source code
onAttach Source code
openArena Man page Source code
optimizeLP Man page
optimizeLP,Organism-method Man page
plotAbundance Man page Source code
plotCurves Man page
plotCurves,Eval-method Man page
plotCurves2 Man page
plotCurves2,Eval-method Man page
plotFVA Man page Source code
plotFluxVar Man page Source code
plotGrowthCurve Man page Source code
plotInterNum Man page Source code
plotPhenCurve Man page Source code
plotPhenNum Man page Source code
plotReaActivity Man page Source code
plotShadowCost Man page
plotShadowCost,Eval-method Man page
plotSpecActivity Man page Source code
plotSubCurve Man page Source code
plotSubDist Man page
plotSubDist,Eval-method Man page
plotSubDist2 Man page
plotSubDist2,Eval-method Man page
plotSubUsage Man page Source code
plotSubVar Man page Source code
plotTotFlux Man page
plotTotFlux,Eval-method Man page
redEval Man page
redEval,Eval-method Man page
reset_screen Man page Source code
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
unit_conversion Man page
unit_conversion,Arena-method Man page
updateSubmat Source code
usd Man page Source code

Files

inst
inst/doc
inst/doc/BacArena-Introduction.R
inst/doc/BacArena-Introduction.Rmd
inst/doc/BacArena-Introduction.pdf
src
src/diff.cpp
src/move.cpp
src/addBac.cpp
src/duplicate.cpp
src/RcppExports.cpp
NAMESPACE
NEWS
data
data/colpal.rda
data/sihumi_test.rda
data/datalist
R
R/data.R
R/BacArena.R
R/Substance.R
R/RcppExports.R
R/Stuff.R
R/Organism.R
R/Arena.R
vignettes
vignettes/BacArena-Introduction.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/changeDiff.Rd
man/checkPhen.Rd
man/growExp.Rd
man/getPhenoMat.Rd
man/extractMed.Rd
man/diffusePDE.Rd
man/colpal1.Rd
man/lsd.Rd
man/Arena-constructor.Rd
man/getVarSubs.Rd
man/findFeeding.Rd
man/Human.Rd
man/addSubs.Rd
man/Human-constructor.Rd
man/createGradient.Rd
man/setKinetics.Rd
man/plotFluxVar.Rd
man/growLin.Rd
man/usd.Rd
man/findRxnFlux.Rd
man/colpal5.Rd
man/Eval-class.Rd
man/simEnv_par.Rd
man/plotAbundance.Rd
man/emptyHood.Rd
man/rmSubs.Rd
man/minePheno.Rd
man/plotCurves.Rd
man/chemotaxis.Rd
man/findInArena.Rd
man/Substance-constructor.Rd
man/colpal3.Rd
man/dat2mat.Rd
man/plotPhenNum.Rd
man/getSublb.Rd
man/flushSubs.Rd
man/findFeeding3.Rd
man/selPheno.Rd
man/consume.Rd
man/plotInterNum.Rd
man/fluxVarSim.Rd
man/cellgrowth.Rd
man/simEnv.Rd
man/constrain.Rd
man/Bac-Constructor.Rd
man/plotFVA.Rd
man/optimizeLP.Rd
man/checkPhen_par.Rd
man/plotGrowthCurve.Rd
man/plotSubCurve.Rd
man/plotTotFlux.Rd
man/findFeeding2.Rd
man/colpal2.Rd
man/simHum.Rd
man/plotSubDist2.Rd
man/lysis.Rd
man/evalArena.Rd
man/plotPhenCurve.Rd
man/growth_par.Rd
man/colpal4.Rd
man/getPhenotype.Rd
man/plotSpecActivity.Rd
man/simBac.Rd
man/addOrg.Rd
man/getSubHist.Rd
man/growth.Rd
man/Organism-constructor.Rd
man/changeFobj.Rd
man/findFeeding3rep.Rd
man/NemptyHood.Rd
man/changeSub.Rd
man/changeOrg.Rd
man/plotSubVar.Rd
man/plotSubDist.Rd
man/addEssentialMed.Rd
man/addDefaultMed.Rd
man/Organism.Rd
man/checkCorr.Rd
man/diffuse_par.Rd
man/diffuse.Rd
man/simBac_par.Rd
man/statPheno.Rd
man/diffuseR.Rd
man/openArena.Rd
man/redEval.Rd
man/getCorrM.Rd
man/colpal6.Rd
man/plotShadowCost.Rd
man/reset_screen.Rd
man/move.Rd
man/BacArena.Rd
man/stirEnv.Rd
man/getArena.Rd
man/plotSubUsage.Rd
man/Eval-constructor.Rd
man/Substance.Rd
man/plotCurves2.Rd
man/plotReaActivity.Rd
man/unit_conversion.Rd
man/sihumi_test.Rd
man/Bac.Rd
man/Arena-class.Rd
man/addEval.Rd
BacArena documentation built on May 24, 2017, 1:02 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.