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)
assignNAsToMFGS         Assigns NA to the MFG data frames for parameter
                        values that are not used Even though these
                        values are not used it is important that they
                        are NAs when assigning random strain values It
                        alters the global variables that are the MFG
                        dataframes
assignStrainTraits      Internal function to assign stochastic strain
                        traits
checkResInfo            Checks whether the resource is 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
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'
getKeyRes               Finds the name of the key resource for each
                        path for each MFG
getMolarStoichiom       Read in the molar stoichiom values and put in
                        array array has form [group,resource,path]
                        reads in data from MFG dataframes
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
getValues               get quantity for all variables in 'Names' e.g.
                        get 'startValue' for all 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
makeParamMatrixG        generic function which assigns values to an
                        array called parameterName array has form
                        [group,resource,path] reads in data from MFG
                        dataframes
makeParamMatrixS        Gets parameter values for parameters halfSat,
                        yield and maxGrowthRate from the MFGs and puts
                        into a matrix also assigns strain traits since
                        traits are assigned to all strains at once for
                        one param they are stored in
                        Mat[strain,res,path], this is then rearranged
                        to make a matrix for each strain
                        (mat[path,res]).
massBalanceFuncDefault
                        mass balance Function
microPop-package        Microbial Population modelling
microPopModel           microPopModel
microbeSysInfo          microbeSysInfo
microbeSysInfoHuman     microbeSysInfoHuman dataframe
microbeSysInfoRumen     microbeSysInfoRumen dataframe
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)
plotTraitChange         plot changes in trait over time
productionFuncDefault   Production Function
quickPlot               Generic plotting showing results of microPop
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
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 subsets
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
