uptakeFuncDefault {microPop}

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

strainName

Name of the strain that is being looped through in the ODE solver

groupName

Name of microbial group that is being looped through in the ODE solver

pathName

Name of metabolic path (e.g. path1) that is being looped through in the ODE solver

varName

(string). Calculate uptake of this variable

keyResName

(string). Name of the key resource on this pathway

subst

Vector of strings giving the names of the substitutable resources for given strain, pathway

ess

Vector of strings giving the names of the essential resources for given strain, pathway

boost

Vector of strings giving the names of the boosting resources for given strain, pathway

maxGrowthRate

Vector containing maximum growth rate on each resource (named by resourceNames). If a resource is not on the pathway the value is NA

growthLim

Vector containing the growth limitation from each resource (named by resourceNames). If a resource is not on the pathway the value is NA

yield

Named vector (names are resourceNames) giving the mass yield of biomass on each resource (mass microbe/mass resource)

nonBoostFrac

(scalar) Fraction of max growth achievable if boosting resource is not present but is required on this pathway

stoichiom

Named vector (names are resourceNames) giving the mass of each resource in the stoichiometry i.e. molar mass of resource multiplied by the number of moles in the stoichiometry

parms

List containing all system parameters

Value

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