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' |