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 |
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' |
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) |
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 |
massBalanceFunc | mass balance Function |
massBalanceFuncDefault | mass balance Function |
Methanogens | Methanogens dataframe |
MFG | Microbial Functional Group (MFG) dataframes |
microbeSysInfo | microbeSysInfo |
microbeSysInfoHuman | microbeSysInfoHuman dataframe |
microbeSysInfoRumen | microbeSysInfoRumen dataframe |
microPop | Microbial Population modelling |
microPopModel | microPopModel |
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 |
plotTraitChange | plot changes in trait over time |
productionFunc | Production Function |
productionFuncDefault | Production Function |
PropionateProducers | PropionateProducers dataframe |
quickPlot | Generic plotting showing results of microPop |
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 |
resourceSysInfo | resourceSysInfo |
resourceSysInfoHuman | resourceSysInfoHuman dataframe |
resourceSysInfoRumen | resourceSysInfoRumen dataframe |
runMicroPopExample | runMicroPopExample |
strainParams | strainParams dataframe |
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 |