| 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 |
| checkPhen_par |
Function for checking phenotypes in the environment |
| checkPhen_par-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 |
| 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 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 |
| 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 |
| findFeeding |
Function for investigation of feeding between phenotypes |
| findFeeding-method |
Function for investigation of feeding between phenotypes |
| findFeeding2 |
Function for investigation of feeding between phenotypes |
| findFeeding2-method |
Function for investigation of feeding between phenotypes |
| findFeeding3 |
Function for investigation of feeding between phenotypes |
| findFeeding3-method |
Function for investigation of feeding between phenotypes |
| findFeeding3rep |
Function for investigation of cross feeding patterns of replicate simulations |
| findInArena |
Function for searching a keyword in arena organisms and media |
| findInArena-method |
Function for searching a keyword in arena organisms and media |
| findrBiomass |
Find biomass reaction in model |
| findRxnFlux |
Function to get all reactions fluxes that are associated with the metabolite of a given exchange reactions |
| findRxnFlux-method |
Function to get all reactions fluxes that are associated with the metabolite of a given exchange reactions |
| flushSubs |
Remove all substances in the environment |
| flushSubs-method |
Remove all substances in the environment |
| fluxVarSim |
Function to compute flux variability analysis on an simulation object to get min/max of substance usage |
| fluxVarSim-method |
Function to compute flux variability analysis on an simulation object to get min/max of substance usage |
| 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 |
| getSubHist |
Function to get timeline of a substance |
| getSubHist-method |
Function to get timeline of a substance |
| getSublb |
Function for calculated the substrate concentration for every organism |
| getSublb-method |
Function for calculated the substrate concentration for every organism |
| getVarSubs |
Function to get varying substances |
| getVarSubs-method |
Function to get varying substances |
| 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 |
| growth_par |
Function implementing a growth model of a bacterium |
| growth_par-method |
Function implementing a growth model of a bacterium |
| plotAbundance |
Plot abundances of species |
| 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 |
| plotFluxVar |
Plot population flux variations |
| plotFVA |
Function to plot population level minimum and maximum flux from alternative optimal solutions obtained by FVA |
| plotGrowthCurve |
Plot growth curve for several simulations |
| plotInterNum |
Plot number of variation in number of interactions for several simulations |
| 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 |
| plotShadowCost-method |
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 over time. |
| plotSubDist-method |
Function to overview the spatial distribution of a substance over time. |
| plotSubDist2 |
Function to overview the spatial distribution of a substance over time. |
| plotSubDist2-method |
Function to overview the spatial distribution of a substance over time. |
| plotSubUsage |
Function to plot usage of substances species wise |
| plotSubVar |
Plot substance variations |
| plotTotFlux |
Function for plotting the overall change in reaction activity |
| plotTotFlux-method |
Function for plotting the overall change in reaction activity |
| 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 |
| setKinetics |
Function to set Michaelis-Menten kinetics for uptake of a substance |
| setKinetics-method |
Function to set Michaelis-Menten kinetics for uptake of a substance |
| sihumi_test |
Multi-species test data set |
| simBac |
Function for one simulation iteration for objects of Bac class |
| simBac-method |
Function for one simulation iteration for objects of Bac class |
| simBac_par |
Function for one simulation iteration for objects of Bac class |
| simBac_par-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 |
| simEnv_par |
Main function for simulating in parallel all processes in the environment |
| simEnv_par-method |
Main function for simulating in parallel 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' |