| microPop-package | Microbial Population modelling |
| Acetogens | Acetogens dataframe |
| applyTraitTradeOffs | Internal function to trade off one trait against another (used when assigning randomly generated strain traits) |
| 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 the system information file (e.g. start value, washout rate etc) |
| checkSolution | Checks whether the solution generated by the ODE solver contains negative values |
| checkStoichiom | Checks whether the stoichiometries in each MFG conserve mass within a specified tolerance If they do not then if reBalanceStoichiom=TRUE the stoichiometry will be adjusted |
| combineGrowthLimFunc | combines the growth limitation functions and max growth rates to get the growth rate of strain |
| combineGrowthLimFuncDefault | combines the growth limitation functions and max growth rates to get the growth rate of strain |
| combinePathsFunc | Combine microbial growth on different pathways by one microbe |
| 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 |
| entryRateFunc | entry Rate Function |
| entryRateFuncDefault | entry Rate Function |
| extraGrowthLimFunc | Extra Growth Limitation 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' becomes 'Bacteroides' updated (Dec 2019) so that MFG names can contain dots |
| 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 there is a boosting resource |
| 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) for all state variables (convention is that microbes are before resources) |
| getVNPlotObject | getVNPlotObject |
| growthLimFunc | growth rate limitation function |
| growthLimFuncDefault | growth rate limitation function |
| LactateProducers | LactateProducers dataframe |
| makeInflowFromSoln | Used for running microPop with multiple compartments Takes the solution (state of system) from the previous compartment (out$solution) and then finds the washout rate of each state variable using removalRateFunc to find the inflow rate to the next downstream compartment |
| makeNetworkMatrices | makeNetworkMatrices |
| massBalanceFunc | mass balance Function |
| 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 |
| microPop | Microbial Population modelling |
| microPopModel | Runs the microbial population model |
| networkDFfromMPinput | networkDFfromMPinput |
| networkDFfromMPoutput | networkDFfromMPoutput |
| NoButyFibreDeg | NoButyFibreDeg dataframe |
| NoButyStarchDeg | NoButyStarchDeg dataframe |
| pHcentreOfMass | Find the pH value which is the centre of mass of the pH limitation function (used for the pH trait) |
| pHFunc | pH Function |
| pHFuncDefault | pH Function |
| pHLimFunc | pH Limitation 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 |
| productionFunc | Production Function |
| 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 resources and microbes on one plot. |
| rateFuncs | List of functions that are used by the ODE solver these functions can be changed by the user but all must be listed. |
| rateFuncsDefault | List of functions that are used by the ODE solver these functions can be changed by the user but all must be listed. |
| removalRateFunc | Removal Rate Function |
| removalRateFuncDefault | Removal Rate Function |
| replaceListItems | used to replace items in list.in in list.default needed for processing microPop input args like plotOptions |
| reshapeFlowMat | reshapeFlowMat |
| resourceSysInfo | resourceSysInfo |
| resourceSysInfoHuman | resourceSysInfoHuman dataframe |
| resourceSysInfoRumen | resourceSysInfoRumen dataframe |
| runMicroPopExample | runMicroPopExample |
| strainParams | strainParams dataframe |
| sumConcOverStrains | sumConcOverStrains |
| sumFlowOverStrains | sumFlowOverStrains |
| sumFlowsOverPaths | sumFlowsOverPaths |
| systemInfoMicrobesPhyto | systemInfoMicrobesPhyto dataframe |
| systemInfoMicrobesVirus | systemInfoMicrobesVirus dataframe |
| systemInfoResourcesPhyto | systemInfoResourcesPhyto dataframe |
| systemInfoResourcesVirus | systemInfoResourcesVirus dataframe |
| uptakeFunc | Uptake Function |
| uptakeFuncDefault | Uptake Function |
| Xaa | Xaa dataframe |
| Xh2 | Xh2 dataframe |
| Xsu | Xsu dataframe |