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) |
assignNAsToMFGS |
Assigns NA to the MFG data frames for parameter values that are not used Even though these values are not used it is important that they are NAs when assigning random strain values It alters the global variables that are the MFG dataframes |
assignStrainTraits |
Internal function to assign stochastic strain traits |
Bacteroides |
Bacteroides dataframe |
ButyrateProducers1 |
ButyrateProducers1 dataframe |
ButyrateProducers2 |
ButyrateProducers2 dataframe |
ButyrateProducers3 |
ButyrateProducers3 dataframe |
checkResInfo |
Checks whether the resource is 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 |
getMolarStoichiom |
Read in the molar stoichiom values and put in array array has form [group,resource,path] reads in data from MFG dataframes |
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 |
getValues |
get quantity for all variables in 'Names' e.g. get 'startValue' for all 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 |
makeParamMatrixG |
generic function which assigns values to an array called parameterName array has form [group,resource,path] reads in data from MFG dataframes |
makeParamMatrixS |
Gets parameter values for parameters halfSat, yield and maxGrowthRate from the MFGs and puts into a matrix also assigns strain traits since traits are assigned to all strains at once for one param they are stored in Mat[strain,res,path], this is then rearranged to make a matrix for each strain (mat[path,res]). |
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 |
subsetFunc |
this function is needed due to R dropping the names when it subsets |
systemInfoMicrobesPhyto |
systemInfoMicrobesPhyto dataframe |
systemInfoMicrobesVirus |
systemInfoMicrobesVirus dataframe |
systemInfoResourcesPhyto |
systemInfoResourcesPhyto dataframe |
systemInfoResourcesVirus |
systemInfoResourcesVirus dataframe |
uptakeFunc |
Uptake Function |
uptakeFuncDefault |
Uptake Function |
waterUptakeRatio |
Computes the mass ratio of water uptake to substrate uptake |
Xaa |
Xaa dataframe |
Xh2 |
Xh2 dataframe |
Xsu |
Xsu dataframe |