Man pages for microPop
Process-Based Modelling of Microbial Populations

AcetogensAcetogens dataframe
applyTraitTradeOffsInternal function to trade off one trait against another...
assignNAsToMFGsAssigns NA to the MFG data frames for parameter values that...
assignStrainTraitsInternal function to assign stochastic strain traits
BacteroidesBacteroides dataframe
ButyrateProducers1ButyrateProducers1 dataframe
ButyrateProducers2ButyrateProducers2 dataframe
ButyrateProducers3ButyrateProducers3 dataframe
checkResInfoChecks whether the all the resources needed are included in...
checkSolutionChecks whether the solution generated by the ODE solver...
checkStoichiomChecks whether the stoichiometries in each MFG conserve mass...
combineGrowthLimFuncDefaultcombines the growth limitation functions and max growth rates...
combinePathsFuncDefaultCombine microbial growth on different pathways by one microbe
createDFCreate a dataframe from a CSV file
derivsDefaultDifferential Equations called by ODE solver
entryRateFuncDefaultentry Rate Function
extraGrowthLimFuncDefaultExtra Growth Limitation Function
getAllResourcesMakes vector of unique resource names
getGroupNameConvert strain name to its group name e.g. 'Bacteroides.1'...
getKeyResFinds the name of the key resource for each path for each MFG
getNonBoostFracobtains the none boosting fraction of growth for given MFG if...
getNumPathsget the number of metabolic pathways for the given group
getPHcornersget pH corners Function
getStrainParamsFromFileget strain parameter values from a csv file
getStrainPHcornersget stochastically generated pH corners for each strain
getValuesget system quantity (e.g. startValue, inflowRate, washOut)...
growthLimFuncDefaultgrowth rate limitation function
LactateProducersLactateProducers dataframe
makeInflowFromSolnUsed for running microPop with multiple compartments Takes...
makeParamMatrixGgeneric function which assigns values for Rtype or stoichiom...
makeParamMatrixSGets parameter values for parameters halfSat, yield and...
massBalanceFuncDefaultmass balance Function
meanTraitFunccalculate the mean trait at the end of the model run
MethanogensMethanogens dataframe
MFGMicrobial Functional Group (MFG) dataframes
microbeSysInfoHumanmicrobeSysInfoHuman dataframe
microbeSysInfoRumenmicrobeSysInfoRumen dataframe
microPopModelRuns the microbial population model
microPop-packageMicrobial Population modelling
NoButyFibreDegNoButyFibreDeg dataframe
NoButyStarchDegNoButyStarchDeg dataframe
pHcentreOfMassFind the pH value which is the centre of mass of the pH...
pHFuncDefaultpH Function
pHLimFuncDefaultpH Limitation Function
plotMicrobesGeneric plotting of microbes over time
plotResourcesGeneric plotting of resources over time
plotTraitChangeplot changes in trait over time
productionFuncDefaultProduction Function
PropionateProducersPropionateProducers dataframe
quickPlotGeneric plotting showing results of microPop
quickPlot1Generic plotting showing results of microPop
quickPlot2Generic plotting showing results of microPop Now shows...
rateFuncsDefaultList of functions that are used by the ODE solver these...
removalRateFuncDefaultRemoval Rate Function
replaceListItemsused to replace items in in list.default needed for...
resourceSysInfoHumanresourceSysInfoHuman dataframe
resourceSysInfoRumenresourceSysInfoRumen dataframe
strainParamsstrainParams dataframe
subsetFuncthis function is needed due to R dropping the names when it...
systemInfoMicrobesPhytosystemInfoMicrobesPhyto dataframe
systemInfoMicrobesVirussystemInfoMicrobesVirus dataframe
systemInfoResourcesPhytosystemInfoResourcesPhyto dataframe
systemInfoResourcesVirussystemInfoResourcesVirus dataframe
uptakeFuncDefaultUptake Function
waterUptakeRatioComputes the mass ratio of water uptake to substrate uptake...
XaaXaa dataframe
Xh2Xh2 dataframe
XsuXsu dataframe
microPop documentation built on Feb. 3, 2022, 5:07 p.m.