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 |