Process-Based Modelling of Microbial Populations

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Documentation for package ‘microPop’ version 1.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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