Man pages for microPop
Process-Based Modelling of Microbial Populations
| Acetogens | Acetogens dataframe |
| applyTraitTradeOffs | Internal function to trade off one trait against another... |
| assignNAsToMFGs | Assigns NA to the MFG data frames for parameter values that... |
| assignStrainTraits | Internal function to assign stochastic strain traits |
| Bacteroides | Bacteroides dataframe |
| ButyrateProducers1 | ButyrateProducers1 dataframe |
| ButyrateProducers2 | ButyrateProducers2 dataframe |
| ButyrateProducers3 | ButyrateProducers3 dataframe |
| checkResInfo | Checks whether the all the resources needed are included in... |
| checkSolution | Checks whether the solution generated by the ODE solver... |
| checkStoichiom | Checks whether the stoichiometries in each MFG conserve mass... |
| combineGrowthLimFuncDefault | combines the growth limitation functions and max growth rates... |
| combinePathsFuncDefault | Combine microbial growth on different pathways by one microbe |
| convertFlowsToMoles | convertFlowsToMoles |
| convertStatesToMoles | convertStatesToMoles |
| createDF | Create a dataframe from a CSV file |
| derivsDefault | Differential Equations called by ODE solver |
| entryRateFuncDefault | entry Rate Function |
| extraGrowthLimFuncDefault | Extra Growth Limitation Function |
| getAllResources | Makes vector of unique resource names |
| getGroupName | Convert strain name to its group name e.g. 'Bacteroides.1'... |
| getKeyRes | Finds the name of the key resource for each path for each MFG |
| getNonBoostFrac | obtains the none boosting fraction of growth for given MFG if... |
| getNumPaths | get the number of metabolic pathways for the given group |
| getPHcorners | get pH corners Function |
| getStrainParamsFromFile | get strain parameter values from a csv file |
| getStrainPHcorners | get stochastically generated pH corners for each strain |
| getValues | get system quantity (e.g. startValue, inflowRate, washOut)... |
| getVNPlotObject | getVNPlotObject |
| growthLimFuncDefault | growth rate limitation function |
| LactateProducers | LactateProducers dataframe |
| makeInflowFromSoln | Used for running microPop with multiple compartments Takes... |
| makeNetworkMatrices | makeNetworkMatrices |
| makeParamMatrixG | generic function which assigns values for Rtype or stoichiom... |
| makeParamMatrixS | Gets parameter values for parameters halfSat, yield and... |
| massBalanceFuncDefault | mass balance Function |
| meanTraitFunc | calculate the mean trait at the end of the model run |
| Methanogens | Methanogens dataframe |
| MFG | Microbial Functional Group (MFG) dataframes |
| microbeSysInfo | microbeSysInfo |
| microbeSysInfoHuman | microbeSysInfoHuman dataframe |
| microbeSysInfoRumen | microbeSysInfoRumen dataframe |
| microPopModel | Runs the microbial population model |
| microPop-package | Microbial Population modelling |
| networkDFfromMPinput | networkDFfromMPinput |
| networkDFfromMPoutput | networkDFfromMPoutput |
| NoButyFibreDeg | NoButyFibreDeg dataframe |
| NoButyStarchDeg | NoButyStarchDeg dataframe |
| pHcentreOfMass | Find the pH value which is the centre of mass of the pH... |
| pHFuncDefault | pH Function |
| pHLimFuncDefault | pH Limitation Function |
| plotMicrobes | Generic plotting of microbes over time |
| plotResources | Generic plotting of resources over time |
| plotTraitChange | plot changes in trait over time |
| productionFuncDefault | Production Function |
| PropionateProducers | PropionateProducers dataframe |
| quickPlot | Generic plotting showing results of microPop |
| quickPlot1 | Generic plotting showing results of microPop |
| quickPlot2 | Generic plotting showing results of microPop Now shows... |
| rateFuncsDefault | List of functions that are used by the ODE solver these... |
| removalRateFuncDefault | Removal Rate Function |
| replaceListItems | used to replace items in list.in in list.default needed for... |
| reshapeFlowMat | reshapeFlowMat |
| resourceSysInfo | resourceSysInfo |
| resourceSysInfoHuman | resourceSysInfoHuman dataframe |
| resourceSysInfoRumen | resourceSysInfoRumen dataframe |
| runMicroPopExample | runMicroPopExample |
| strainParams | strainParams dataframe |
| subsetFunc | this function is needed due to R dropping the names when it... |
| sumConcOverStrains | sumConcOverStrains |
| sumFlowOverStrains | sumFlowOverStrains |
| sumFlowsOverPaths | sumFlowsOverPaths |
| systemInfoMicrobesPhyto | systemInfoMicrobesPhyto dataframe |
| systemInfoMicrobesVirus | systemInfoMicrobesVirus dataframe |
| systemInfoResourcesPhyto | systemInfoResourcesPhyto dataframe |
| systemInfoResourcesVirus | systemInfoResourcesVirus dataframe |
| uptakeFuncDefault | Uptake Function |
| waterUptakeRatio | Computes the mass ratio of water uptake to substrate uptake... |
| Xaa | Xaa dataframe |
| Xh2 | Xh2 dataframe |
| Xsu | Xsu dataframe |
