R: Process-Based Modelling of Microbial Populations

# Process-Based Modelling of Microbial Populations

## 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