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microPop (version 1.6)

Process-Based Modelling of Microbial Populations

Description

Modelling interacting microbial populations - example applications include human gut microbiota, rumen microbiota and phytoplankton. Solves a system of ordinary differential equations to simulate microbial growth and resource uptake over time. This version contains network visualisation functions.

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Version

Install

install.packages('microPop')

Monthly Downloads

217

Version

1.6

License

GPL-3 | file LICENSE

Maintainer

Helen Kettle

Last Published

February 3rd, 2022

Functions in microPop (1.6)

Methanogens dataframe

Acetogens dataframe

NoButyFibreDeg dataframe

Bacteroides dataframe

ButyrateProducers2

ButyrateProducers2 dataframe

ButyrateProducers1

ButyrateProducers1 dataframe

NoButyStarchDeg

NoButyStarchDeg dataframe

ButyrateProducers3

ButyrateProducers3 dataframe

Microbial Functional Group (MFG) dataframes

PropionateProducers

PropionateProducers dataframe

LactateProducers

LactateProducers dataframe

Differential Equations called by ODE solver

Create a dataframe from a CSV file

extraGrowthLimFuncDefault

Extra Growth Limitation Function

entryRateFuncDefault

entry Rate Function

assignStrainTraits

Internal function to assign stochastic strain traits

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

getVNPlotObject

getVNPlotObject

get system quantity (e.g. startValue, inflowRate, washOut) for all state variables (convention is that microbes are before resources)

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]).

Checks whether the solution generated by the ODE solver contains negative values

Runs the microbial population model

getAllResources

Makes vector of unique resource names

Finds the name of the key resource for each path for each MFG

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

Checks whether the all the resources needed are included in the system information file (e.g. start value, washout rate etc)

combinePathsFuncDefault

Combine microbial growth on different pathways by one microbe

combineGrowthLimFuncDefault

combines the growth limitation functions and max growth rates to get the growth rate of strain

Find the pH value which is the centre of mass of the pH limitation function (used for the pH trait)

massBalanceFuncDefault

mass balance Function

convertStatesToMoles

convertStatesToMoles

convertFlowsToMoles

convertFlowsToMoles

get pH corners Function

rateFuncsDefault

List of functions that are used by the ODE solver these functions can be changed by the user but all must be listed.

growthLimFuncDefault

growth rate limitation function

get the number of metabolic pathways for the given group

removalRateFuncDefault

Removal Rate Function

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

Generic plotting of resources over time

plotTraitChange

plot changes in trait over time

makeNetworkMatrices

makeNetworkMatrices

Generic plotting showing results of microPop Now shows resources and microbes on one plot.

networkDFfromMPinput

networkDFfromMPinput

microbeSysInfoHuman

microbeSysInfoHuman dataframe

Generic plotting showing results of microPop

replaceListItems

used to replace items in list.in in list.default needed for processing microPop input args like plotOptions

networkDFfromMPoutput

networkDFfromMPoutput

getNonBoostFrac

obtains the none boosting fraction of growth for given MFG if there is a boosting resource

Generic plotting of microbes over time

microbeSysInfoRumen

microbeSysInfoRumen dataframe

Convert strain name to its group name e.g. 'Bacteroides.1' becomes 'Bacteroides' updated (Dec 2019) so that MFG names can contain dots

sumConcOverStrains

sumConcOverStrains

makeParamMatrixG

generic function which assigns values for Rtype or stoichiom to an array of the same name array has form [group,resource,path] reads in data from MFG dataframes

sumFlowOverStrains

sumFlowOverStrains

getStrainPHcorners

get stochastically generated pH corners for each strain

strainParams dataframe

waterUptakeRatio

Computes the mass ratio of water uptake to substrate uptake (i.e. mass uptake of water divided by total mass uptake)

this function is needed due to R dropping the names when it subsets

runMicroPopExample

runMicroPopExample

Generic plotting showing results of microPop

productionFuncDefault

Production Function

sumFlowsOverPaths

sumFlowsOverPaths

resourceSysInfoRumen

resourceSysInfoRumen dataframe

calculate the mean trait at the end of the model run

getStrainParamsFromFile

get strain parameter values from a csv file

systemInfoMicrobesVirus

systemInfoMicrobesVirus dataframe

resourceSysInfo

resourceSysInfo

microPop-package

Microbial Population modelling

pHLimFuncDefault

pH Limitation Function

systemInfoResourcesPhyto

systemInfoResourcesPhyto dataframe

systemInfoMicrobesPhyto

systemInfoMicrobesPhyto dataframe

systemInfoResourcesVirus

systemInfoResourcesVirus dataframe

uptakeFuncDefault

Uptake Function

resourceSysInfoHuman

resourceSysInfoHuman dataframe