Acetogens               Acetogens dataframe
Bacteroides             Bacteroides dataframe
ButyrateProducers1      ButyrateProducers1 dataframe
ButyrateProducers2      ButyrateProducers2 dataframe
ButyrateProducers3      ButyrateProducers3 dataframe
LactateProducers        LactateProducers dataframe
MFG                     Microbial Functional Group (MFG) dataframes
Methanogens             Methanogens dataframe
NoButyFibreDeg          NoButyFibreDeg dataframe
NoButyStarchDeg         NoButyStarchDeg dataframe
PropionateProducers     PropionateProducers dataframe
Xaa                     Xaa dataframe
Xh2                     Xh2 dataframe
Xsu                     Xsu 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
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
combineGrowthLimFuncDefault
                        combines the growth limitation functions and
                        max growth rates to get the growth rate of
                        strain
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' 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
getStrainPHcorners      get stochastically generated pH corners for
                        each strain
getStrainParamsFromFile
                        get strain parameter values from a csv file
getVNPlotObject         getVNPlotObject
getValues               get system quantity (e.g. startValue,
                        inflowRate, washOut) for all state variables
                        (convention is that microbes are before
                        resources)
growthLimFuncDefault    growth rate limitation function
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
massBalanceFuncDefault
                        mass balance Function
meanTraitFunc           calculate the mean trait at the end of the
                        model run
microPop-package        Microbial Population modelling
microPopModel           Runs the microbial population model
microbeSysInfo          microbeSysInfo
microbeSysInfoHuman     microbeSysInfoHuman dataframe
microbeSysInfoRumen     microbeSysInfoRumen dataframe
networkDFfromMPinput    networkDFfromMPinput
networkDFfromMPoutput   networkDFfromMPoutput
pHFuncDefault           pH Function
pHLimFuncDefault        pH Limitation Function
pHcentreOfMass          Find the pH value which is the centre of mass
                        of the pH limitation function (used for the pH
                        trait)
plotMicrobes            Generic plotting of microbes over time
plotResources           Generic plotting of resources over time
plotTraitChange         plot changes in trait over time
productionFuncDefault   Production Function
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.
rateFuncsDefault        List of functions that are used by the ODE
                        solver these functions can be changed by the
                        user but all must be listed.
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
uptakeFuncDefault       Uptake Function
