| 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 |
| chemotaxis |
Function for chemotaxis of bacteria to their prefered substrate |
| chemotaxis-method |
Function for chemotaxis of bacteria to their prefered substrate |
| 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 |
| 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 |
| getSublb |
Function for calculated the substrate concentration for every organism |
| getSublb-method |
Function for calculated the substrate concentration for every organism |
| 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 |
| 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 |
| simBac |
Function for one simulation iteration for objects of Bac class |
| simBac-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 |
| 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' |