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... |
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 |
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 |
getMolarStoichiom | Read in the molar stoichiom values and put in array array has... |
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)... |
growthLimFuncDefault | growth rate limitation function |
LactateProducers | LactateProducers dataframe |
makeInflowFromSoln | Used for running microPop with multiple compartments Takes... |
makeParamMatrixG | generic function which assigns values for Rtype or stoichiom... |
makeParamMatrixS | Gets parameter values for parameters halfSat, yield and... |
massBalanceFuncDefault | mass balance Function |
Methanogens | Methanogens dataframe |
MFG | Microbial Functional Group (MFG) dataframes |
microbeSysInfo | microbeSysInfo |
microbeSysInfoHuman | microbeSysInfoHuman dataframe |
microbeSysInfoRumen | microbeSysInfoRumen dataframe |
microPopModel | microPopModel |
microPop-package | Microbial Population modelling |
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 |
plotTraitChange | plot changes in trait over time |
productionFuncDefault | Production Function |
PropionateProducers | PropionateProducers dataframe |
quickPlot | Generic plotting showing results of microPop |
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... |
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... |
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 |
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