Microbial Population modelling

Description

microPop can be used to model the dynamics and interactions of microbial populations.

Author(s)

Helen Kettle

References

To be done

Acetogens dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

Acetogens

Format

dataframe

See Also

MFG

Bacteroides dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

Bacteroides

Format

dataframe

See Also

MFG

ButyrateProducers1 dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

ButyrateProducers1

Format

dataframe

See Also

MFG

ButyrateProducers2 dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

ButyrateProducers2

Format

dataframe

See Also

MFG

ButyrateProducers3 dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

ButyrateProducers3

Format

dataframe

See Also

MFG

LactateProducers dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

LactateProducers

Format

dataframe

See Also

MFG

Microbial Functional Group (MFG) dataframes

Description

This is a generic description of the dataframes describing the pathways and parameters of each microbial functional group. Each resource (substrate, metabolic product or biomass (if microbial production is included in the chemical stoichiometry)) has a column. The first column can be used for describing the units of each parameter. This is optional and just for clarity - it is not used within microPop (note, the units column must be labelled 'units' and it can not contain NAs). The row names and their details are given below:

• Rtype Describes the type of resource. Can be S (substitutable substrate), Se (essential substrate), Sb (boosting substrate), Sm (microbial substrate), Sw (water as a substrate), P (product), Pb (biomass product) or X (not used)

• halfSat Half-saturation constant for Monod Equation growth. Units must match the units of the resources. Resources that aren't used for growth will have entry NA.

• yield This is the biomass yield i.e. mass of microbes/mass of substrate consumed. Note this is NOT a mol/mol yield! Resources that aren't used for growth will have entry NA.

• maxGrowthRate Maximum growth rate of the group. Units are per unit time where time has the same units as those used for the microPopModel input arguments 'times'. Resources that aren't used for growth must have entry NA.

• stoichiom The chemical stoichiometry in moles of each resource (note that this may also include biomass (see Xsu)).

• keyResource If the stoichiometry is specified and all resources are essential then stoichiom will be used to determine rates of production and uptake and now 'yield' is the biomass produced per gram of the key resource specified here.

• pHcorners Specified using 4 values in the first 4 columns. The pH limitation on growth is described by a trapezium. For increasing pH values the limitation goes from 0,1,1,0 at the points specified by the pHcorners.

• numPathways The number of metabolic pathways the group has. If this is greater than 1 see details below for naming conventions.

Usage

MFG

Format

A dataframe with the row names in the itemised list below and a column for units (optional) and for each resource required by the microbial group.

Details

If there is more than one pathway the row names are as above but followed by .2 for second pathway, .3 for third pathway and so on. E.g. halfSat.2, yield.2

Note, when constructing new dataframes for new microbial functional groups (MFGs), the order of the rows does not matter but the names of the rows must be the same as those above. Also, the order of the resources columns does not matter (although if there is a 'units' column it must be the first column). The resources may be different for each MFG (e.g. See Bacteroides and Xsu).

When the user tells microPop which groups to use via the microbeNames input argument, the package will determine the names of all the resources and MFGs in the system and then check they are also in the system information files.

Note that the optional units column can not contain NAs. For entries without units put 'none'.

Methanogens dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

Methanogens

Format

dataframe

See Also

MFG

NoButyFibreDeg dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

NoButyFibreDeg

Format

dataframe

See Also

MFG

NoButyStarchDeg dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

NoButyStarchDeg

Format

dataframe

See Also

MFG

PropionateProducers dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

PropionateProducers

Format

dataframe

See Also

MFG

Xaa dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

Xaa

Format

dataframe

See Also

MFG

Xh2 dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

Xh2

Format

dataframe

See Also

MFG

Xsu dataframe

Description

Table of information describing the behaviour of the microbial functional group. See help(MFG) or ?MFG for explanation of the contents of the microbial functional groups dataframes

Usage

Xsu

Format

dataframe

See Also

MFG

Internal function to trade off one trait against another (used when assigning randomly generated strain traits)

Description

works by finding the values for each strain for par1 and par2 and then sorting them in opposite orders. This means the parameter values don't change number but they are assigned to different strains.

Usage

applyTraitTradeOffs(
  microbeNames,
  tradeOffParams,
  numPaths,
  numStrains,
  Pmats,
  resourceNames
)

Arguments

Value

new version of Pmats where parameter values are traded off

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

Description

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

Usage

assignNAsToMFGs(microbeNames, numPaths, keyRes, resourceNames)

Arguments

Value

nothing

Internal function to assign stochastic strain traits

Description

Produces a random distribution of trait values where the mean is groupVal and the range is determined by strainOptions$percentTraitRange (if not pHtrait) and by maxPHshift if it is the pHtrait (see strainOptions)

Usage

assignStrainTraits(
  numStrains,
  groupVal,
  strainOptions,
  parName = "unspecified param",
  pHtrait = FALSE,
  gname = "None"
)

Arguments

Value

vector of values for each strain for one parameter

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

Description

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

Usage

checkResInfo(resNames, sys.data)

Arguments

Value

nothing

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

Description

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

Usage

checkSolution(soln, tol = -0.1)

Arguments

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

Description

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

Usage

checkStoichiom(
  stoichiom,
  Rtype,
  microbeNames,
  numPaths,
  stoiTol,
  reBalanceStoichiom = FALSE
)

Arguments

Value

new stoichiom matrix

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

Description

Returns the specific growth rate in units of inverse time

Usage

combineGrowthLimFuncDefault(
  strainName,
  groupName,
  pathName,
  subst,
  ess,
  boost,
  bio.sub,
  maxGrowthRate,
  growthLim,
  keyResName,
  nonBoostFrac
)

Arguments

Value

(scalar) specific growth rate in units of inverse time

Combine microbial growth on different pathways by one microbe

Description

Returns a vector specifying the fraction of the total microbial growth on each pathway. This function is needed to ensure that groups which have the most paths do not automatically have the most growth - i.e. need to weight the growth on each pathway.

Usage

combinePathsFuncDefault(
  strainName,
  groupName,
  growthRate,
  num.paths,
  pathNames
)

Arguments

Value

vector specifying the fraction of the total microbial growth on each pathway

convertFlowsToMoles

Description

convert network flows from mass to moles

Usage

convertFlowsToMoles(allStrainNames, flow, molarMass)

Arguments

convertStatesToMoles

Description

convert network nodes from mass to moles for resources (microbes remain as mass)

Usage

convertStatesToMoles(nodeMass, MolarMass)

Arguments

Create a dataframe from a CSV file

Description

Create a dataframe from a CSV file

Usage

createDF(filename)

Arguments

Value

A dataframe

Differential Equations called by ODE solver

Description

Differential Equations called by ODE solver

Usage

derivsDefault(t, y, parms)

Arguments

entry Rate Function

Description

Return the rate of entry to the system for any state variable

Usage

entryRateFuncDefault(
  varName,
  varValue,
  stateVarValues,
  time,
  inflowRate,
  parms
)

Arguments

Value

(scalar) rate of entry (quantity per unit time) for any state variable

Extra Growth Limitation Function

Description

Return the value of extraGrowthLim (number between 0 and 1)

Usage

extraGrowthLimFuncDefault(
  strainName,
  groupName,
  pathName,
  stateVarValues,
  stateVarNames,
  time,
  parms
)

Arguments

Value

(scalar) limitation on growth (between 0 and 1)

Makes vector of unique resource names

Description

Makes vector of unique resource names

Usage

getAllResources(microbeNames, gutModel = FALSE, myPars = NULL)

Arguments

Value

vector of resource names

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

Description

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

Usage

getGroupName(xname, microbeNames)

Arguments

Value

group name (string) if xname is a strain name. If xname is not a the name of a strain it will simply return xname unchanged.

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

Description

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

Usage

getKeyRes(microbeNames, numPaths)

Arguments

Value

list of vectors where the names are microbeNames

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

Description

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

Usage

getNonBoostFrac(microbeNames, resourceNames, numPaths)

Arguments

Value

an array with format [group,resource,path]

get the number of metabolic pathways for the given group

Description

get the number of metabolic pathways for the given group

Usage

getNumPaths(microbeNames)

Arguments

Value

a named vector of the number of paths for each group if numPathways is not in dataframe then it is set to 1.

get pH corners Function

Description

Returns the values of the pH values of the limit function i.e. where the limit is c(0,1,1,0) Reads these in from the microbe group dataframes

Usage

getPHcorners(microbeNames, pHLimit)

Arguments

Value

(matrix) values of the pH values of the limit function i.e. where the limit is c(0,1,1,0). Row names are microbeNames

get stochastically generated pH corners for each strain

Description

Returns the values of the pH values of the limit function i.e. where the limit is c(0,1,1,0) Reads these in from the microbe group dataframes

Usage

getStrainPHcorners(
  microbeNames,
  allStrainNames,
  numStrains,
  pHcorners,
  pHLimit,
  strainOptions,
  oneStrainRandomParams
)

Arguments

Value

(matrix) values of the pH values of the limit function i.e. where the limit is c(0,1,1,0) for each strain

get strain parameter values from a csv file

Description

get strain parameter values from a csv file

Usage

getStrainParamsFromFile(Pmats, strainPHcorners, strainOptions)

Arguments

Value

(list) - first entry is new version of Pmats, second is new version of strainPHcorners

getVNPlotObject

Description

uses visNetwork to produce an interactive network plot based on the links and edges dataframes

Usage

getVNPlotObject(
  nodes,
  edges,
  addLegend = FALSE,
  addExport = TRUE,
  figType = "png",
  mainTitle = NULL,
  subTitle = NULL,
  layoutSeed = NA,
  scaleNodes = FALSE,
  scaleEdges = FALSE,
  microbeCol = "gold",
  resourceCol = "lightblue",
  productionCol = "magenta",
  uptakeCol = "darkgrey",
  figWidth = 700,
  figHeight = 700
)

Arguments

Value

a visNetwork object that can be shown using print() function.

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

Description

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

Usage

getValues(
  sysInfoMicrobes,
  sysInfoRes,
  stateVarNames,
  quantity,
  strainNames,
  microbeNames,
  resourceNames,
  numStrains
)

Arguments

growth rate limitation function

Description

Returns the value of growthLim (must lie in interval [0,1] i.e. unitless) of strainName on varName which is used to scale the maximum growth rate Contains two options - one for essential resources and one for substitutable resources (based on Ballyk and Wolkowicz, 1993)

Usage

growthLimFuncDefault(
  strainName,
  groupName,
  pathName,
  varName,
  resourceValues,
  allSubType,
  strainHalfSat,
  stateVarValues,
  parms
)

Arguments

Value

scalar giving limitation on growth rate - must be >=0 and <=1

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

Description

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

Usage

makeInflowFromSoln(out)

Arguments

Value

matrix of flow rates (conc/time) with named columns (the same as out$solution)

makeNetworkMatrices

Description

make links and nodes matrices for use in network plotting software

Usage

makeNetworkMatrices(
  chosen.time,
  out,
  convertToMoles = TRUE,
  sumOverStrains = TRUE
)

Arguments

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

Description

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

Usage

makeParamMatrixG(
  microbeNames,
  parameterName,
  numPaths,
  resData,
  microbeMolarMass,
  resNames
)

Arguments

Value

array of form: parameterName [gname,rname,pname]

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]).

Description

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]).

Usage

makeParamMatrixS(
  resNames,
  microbeNames,
  parameterName,
  numPaths,
  numStrains,
  strainOptions,
  oneStrainRandomParams
)

Arguments

Value

A list called parameterName which contains matrices for all strains (in all groups) with paths on rows and resources on columns

mass balance Function

Description

Doesn't return anything but prints to screen if mass does not balance after the equations for biological growth have been derived This is only run if checkMassConv is TRUE

Usage

massBalanceFuncDefault(uptake, production, growthRate, balanceTol, strainName)

Arguments

calculate the mean trait at the end of the model run

Description

calculate the mean trait at the end of the model run

Usage

meanTraitFunc(out, trait.name, gname, resource.name, path)

Arguments

Runs the microbial population model

Description

creates a system of ordinary differential equations and solves them

Usage

microPopModel(
  microbeNames,
  times,
  resourceSysInfo,
  microbeSysInfo,
  rateFuncs = rateFuncsDefault,
  odeFunc = derivsDefault,
  numStrains = 1,
  oneStrainRandomParams = FALSE,
  pHLimit = FALSE,
  pHVal = NA,
  plotOptions = list(),
  odeOptions = list(),
  strainOptions = list(),
  checkingOptions = list(),
  microbeMolarMass = 113,
  bacCutOff = 1e-14,
  networkAnalysis = FALSE,
  myPars = NULL,
  ...
)

Arguments

Value

The output is a list containing a matrix called 'solution' where rows are points in time and the columns are the state variables, and another list called parms which contains all the information needed to run the model. Within parms there are a number of other lists (e.g. Pmats for parameter values and Smats for system settings etc - try names(out$parms)).

Examples

#simplest example - define one microbial group (Archea) with 4 resources and
#simulate growth over 50 days
#make microbial group data frame:
MFG=matrix(NA,ncol=4,nrow=6,dimnames=list(c('Rtype','halfSat','yield',
'maxGrowthRate','stoichiom','keyResource'),c('H2','CO2','CH4','H2O')))
MFG['Rtype',]=c('Se','Se','P','P')
MFG['halfSat',c('H2','CO2')]=1e-6
MFG['yield','H2']=0.2
MFG['maxGrowthRate','H2']=2
MFG['keyResource',1]='H2'
MFG['stoichiom',]=c(4,1,1,2)
Archea=data.frame(MFG,stringsAsFactors=FALSE)

#make resourceSysInfo data frame
Rmat=matrix(NA,ncol=4,nrow=4,dimnames=list(c('startValue','inflowRate',
'washOut','molarMass'),c('H2','CO2','CH4','H2O')))
Rmat['startValue',]=c(1,1,0,0)
Rmat['inflowRate',]=c(1,5,0,0)
Rmat['washOut',]=c(0.1,0.1,0.1,0.1)
Rmat['molarMass',]=c(2,44,16,18)

#make microbeSysInfo data frame
Mmat=matrix(NA,ncol=1,nrow=3,dimnames=list(c('startValue','inflowRate',
'washOut'),c('Archea')))
Mmat['startValue',]=1
Mmat['inflowRate',]=0
Mmat['washOut',]=0.1

out=microPopModel(
    microbeNames='Archea',
    times=seq(0,50,0.1),
    resourceSysInfo=data.frame(Rmat,stringsAsFactors=FALSE),
    microbeSysInfo=data.frame(Mmat,stringsAsFactors=FALSE)
)

microbeSysInfo

Description

Data frame describing the system information for the microbial state variables

Usage

microbeSysInfo

Format

A dataframe with the row names in the itemised list below and a column for units (optional) and for each microbial functional group (MFG) in the system to be simulated.

Details

Each MFG has a column. The first column can be used for describing the units of each variable. This is optional and just for clarity - it is not used within microPop (note, the units column must be labelled 'units'). The data frame must contain the following rows:

• startValue The value of each MFG at the start time of the simulation (e.g. units are g/l)

• inflowRate The value of the rate of inflow of each MFG (e.g. units are g/l/d)

• washOut The specific washout rate of each MFG (e.g. units are /d)

microbeSysInfoHuman dataframe

Description

Table of information describing the inflows, outflows, start values of each microbial group for the R script microPop/inst/DemoFiles/human*.R See help(microbeSysInfo) or for an explanation of the contents

Usage

microbeSysInfoHuman

Format

dataframe

See Also

microbeSysInfo

microbeSysInfoRumen dataframe

Description

Table of information describing the inflows, outflows, start values of each microbial group for the R script microPop/inst/DemoFiles/rumen.R See help(microbeSysInfo) or for an explanation of the contents

Usage

microbeSysInfoRumen

Format

dataframe

See Also

microbeSysInfo

networkDFfromMPinput

Description

make node and edge data frames to use in visNetwork from microPop microbial data frames

Usage

networkDFfromMPinput(microbeNames)

Arguments

Value

a list containing the edges and nodes

networkDFfromMPoutput

Description

make node and edge data frames from microPop output to use in visNetwork

Usage

networkDFfromMPoutput(
  chosen.time,
  MPoutput,
  groupNames = NULL,
  sumOverPaths = TRUE,
  sumOverStrains = TRUE,
  convertToMoles = TRUE
)

Arguments

Value

a list containing the edges and nodes

pH Function

Description

Return the value of pH in pH units

Usage

pHFuncDefault(time, parms, stateVarValues = NULL)

Arguments

Value

(scalar) pH at the given time

pH Limitation Function

Description

Return the value of pHLim (must lie in interval [0,1])

Usage

pHLimFuncDefault(strainName, groupName, pH, parms)

Arguments

Value

(scalar) pH limitation (0 to 1)

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

Description

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

Usage

pHcentreOfMass(strainName, groupName, pHLimFunc, parms)

Arguments

Value

pH value at centre of mass

Generic plotting of microbes over time

Description

Generic plotting of microbes over time

Usage

plotMicrobes(
  out,
  sumOverStrains = TRUE,
  yLabel = "Concentration",
  xLabel = "Time",
  legendPosition = "topleft",
  cex.title = 1,
  cex.ax = 1,
  cex.legend = 1
)

Arguments

Value

Nothing just generates a plot

Generic plotting of resources over time

Description

Generic plotting of resources over time

Usage

plotResources(
  out,
  yLabel = "Concentration",
  xLabel = "Time",
  legendPosition = "topleft",
  cex.title = 1,
  cex.ax = 1,
  cex.legend = 1
)

Arguments

Value

Nothing just generates a plot

plot changes in trait over time

Description

plot changes in trait over time

Usage

plotTraitChange(
  out,
  trait.name,
  group.names,
  resource.name = NULL,
  path = NULL,
  xlabel = "Time (days)",
  saveFig = FALSE,
  figType = "eps",
  figName = "Traits"
)

Arguments

Production Function

Description

Production rate of resource (units are resource mass/time)

Usage

productionFuncDefault(
  strainName,
  groupName,
  pathName,
  varName,
  all.substrates,
  keyResName,
  stoichiom,
  products,
  bio.products,
  uptake,
  growthRate,
  yield,
  parms,
  water
)

Arguments

Value

(scalar) production rate of given resource (units are resource mass/time)

Generic plotting showing results of microPop

Description

Generic plotting showing results of microPop

Usage

quickPlot(
  soln,
  numR,
  numStrains,
  microbeNames,
  yLabel,
  xLabel,
  sumOverStrains,
  resourceLegendPosition = "topleft",
  microbeLegendPosition = "topleft",
  saveFig = FALSE,
  figType = "eps",
  figName = "microPopFig"
)

Arguments

Value

Nothing just generates a plot

Generic plotting showing results of microPop

Description

Generic plotting showing results of microPop

Usage

quickPlot1(
  soln,
  numR,
  numStrains,
  microbeNames,
  yLabel,
  xLabel,
  sumOverStrains,
  resourceLegendPosition = "topleft",
  microbeLegendPosition = "topleft",
  saveFig = FALSE,
  figType = "eps",
  figName = "microPopFig"
)

Arguments

Value

Nothing just generates a plot

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

Description

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

Usage

quickPlot2(
  soln,
  numR,
  numStrains,
  microbeNames,
  yLabel = "Concentration (g/L)",
  xLabel = "Time",
  sumOverStrains = TRUE,
  resourceLegendPosition = "topleft",
  microbeLegendPosition = "topleft",
  saveFig = FALSE,
  figType = "eps",
  figName = "microPopFig",
  cex.plot = 1,
  cex.legend = 0.7
)

Arguments

Value

Nothing just generates a plot

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

Description

rateFuncsDefault=list(pHFunc=pHFuncDefault, pHLimFunc=pHLimFuncDefault, extraGrowthLimFunc=extraGrowthLimFuncDefault, growthLimFunc=growthLimFuncDefault, combineGrowthLimFunc=combineGrowthLimFuncDefault, uptakeFunc=uptakeFuncDefault, productionFunc=productionFuncDefault, combinePathsFunc=combinePathsFuncDefault, massBalanceFunc=massBalanceFuncDefault, entryRateFunc=entryRateFuncDefault, removalRateFunc=removalRateFuncDefault)

Usage

rateFuncsDefault

Format

An object of class list of length 11.

Removal Rate Function

Description

Return the rate of removal of any state variable from the system This is called in the ODE derivs func

Usage

removalRateFuncDefault(varName, varValue, stateVarValues, time, washOut, parms)

Arguments

Value

(scalar) rate of removal (quantity per unit time) for the state variable varName

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

Description

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

Usage

replaceListItems(list.in, list.default)

Arguments

Value

list.default updated with entries from list.in

reshapeFlowMat

Description

reshapes the flow matrices out$flow.uptake or out$flow.production into a list elements of the list are the microbeNames and then there is a matrix [path,res]

Usage

reshapeFlowMat(time.step, flow.direction, out)

Arguments

Value

a list with microbeNames as elements and a matrix of [path,resource] showing the chosen flow direction (eg. uptake or production). Note theses flows have not been converted to moles.

resourceSysInfo

Description

Data frame describing the system information for the state variables that are resources (i.e. substrates or metabolic products).

Usage

resourceSysInfo

Format

A dataframe with the row names in the itemised list below and a column for units (optional) and for each resource in the system to be simulated.

Details

Each resource (substrate, metabolic product or biomass if microbes are a resource e.g. in the case of viruses) has a column. The first column can be used for describing the units of each variable. This is optional and just for clarity - it is not used within microPop (note, the units column must be labelled 'units'). The data frame must contain the following rows:

• startValue The value of each resource at the start time of the simulation (e.g. units are g/l)

• inflowRate The value of the rate of inflow of each resource (e.g. units are g/l/d)

• washOut The specific washout rate of each resource (e.g. units are /d)

• molarMass The mass in grams of one mole of the resource (units are g/mol)

resourceSysInfoHuman dataframe

Description

Table of information describing the inflows, outflows, start values and molar masses of each resource for the R script microPop/inst/DemoFiles/human*.R See help(resourceSysInfo) or for an explanation of the contents

Usage

resourceSysInfoHuman

Format

dataframe

See Also

resourceSysInfo

resourceSysInfoRumen dataframe

Description

Table of information describing the inflows, outflows, start values and molar masses of each resource for the R script microPop/inst/DemoFiles/rumen*.R See help(resourceSysInfo) or for an explanation of the contents

Usage

resourceSysInfoRumen

Format

dataframe

See Also

resourceSysInfo

runMicroPopExample

Description

This function is similar to the demo() function but requires less interaction It is used to run the canned examples from the microPop package.

Usage

runMicroPopExample(name = NULL)

Arguments

strainParams dataframe

Description

Table containing some parameter values for specific strains for the R script microPop/inst/DemoFiles/human4.R The file must have colnames c(strainName, paramName, paramVal, paramUnit, resource,path) where strainName is in format 'groupName.i' where i is the strain number.

Usage

strainParams

Format

dataframe

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

Description

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

Usage

subsetFunc(array.in, gname, path)

Arguments

Value

named vector or array

sumConcOverStrains

Description

sum concentration of each strain into the group it is in

Usage

sumConcOverStrains(
  concentration.orig,
  allStrainNames,
  groupNames,
  resourceNames
)

Arguments

sumFlowOverStrains

Description

make links and nodes matrices for use in network plotting software

Usage

sumFlowOverStrains(flowList, allStrainNames, groupNames)

Arguments

sumFlowsOverPaths

Description

sum flows over links between the same nodes i.e. if the link has more than one metabolic path

Usage

sumFlowsOverPaths(links)

Arguments

Value

matrix of links

systemInfoMicrobesPhyto dataframe

Description

Table of information describing the inflows, outflows, start values of each microbial group for the R script microPop/inst/DemoFiles/phyto.R See help(microbeSysInfo) or for an explanation of the contents

Usage

systemInfoMicrobesPhyto

Format

dataframe

See Also

microbeSysInfo

systemInfoMicrobesVirus dataframe

Description

Table of information describing the inflows, outflows, start values of each microbial group for the R script microPop/inst/DemoFiles/phages.R See help(microbeSysInfo) or for an explanation of the contents

Usage

systemInfoMicrobesVirus

Format

dataframe

See Also

microbeSysInfo

systemInfoResourcesPhyto dataframe

Description

Table of information describing the inflows, outflows, start values and molar masses of each resource for the R script microPop/inst/DemoFiles/phyto.R See help(resourceSysInfo) or for an explanation of the contents

Usage

systemInfoResourcesPhyto

Format

dataframe

See Also

resourceSysInfo

systemInfoResourcesVirus dataframe

Description

Table of information describing the inflows, outflows, start values and molar masses of each resource for the R script microPop/inst/DemoFiles/phages.R See help(resourceSysInfo) or for an explanation of the contents

Usage

systemInfoResourcesVirus

Format

dataframe

See Also

resourceSysInfo

Uptake Function

Description

Return the value of resource uptake per biomass (i.e. resource quantity per unit time per mass unit of biomass) for given resource

Usage

uptakeFuncDefault(
  strainName,
  groupName,
  pathName,
  varName,
  keyResName,
  subst,
  ess,
  boost,
  maxGrowthRate,
  growthLim,
  yield,
  nonBoostFrac,
  stoichiom,
  parms
)

Arguments

Value

(scalar) uptake of resource per mass unit of biomass (units are resource mass/biomass/time)

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

Description

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

Usage

waterUptakeRatio(microbeNames, stoichiom, Rtype, numPaths)

Arguments

Value

water mass ratio matrix [gname,pathName] with names.