API for euba/BacArena
Modeling Framework for Cellular Communities in their Environments
| Global functions | |
|---|---|
| .onAttach | 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 |
| 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 |
| 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 |
| ecoInteract | 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 |
| getLPstat | Source code |
| 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 |
| 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 |
| readMATmod | Man page Source code |
| 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 |
