API for BacArena
Modeling Framework for Cellular Communities in their Environments

Global 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
HeatMapFeeding Man page
HeatMapFeeding,Eval-method 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
findrBiomass Man page Source code
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
BacArena documentation built on May 9, 2018, 5:04 p.m.