uptakeFuncDefault: Uptake Function

In microPop: Process-Based Modelling of Microbial Populations

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)

microPop documentation built on Feb. 3, 2022, 5:07 p.m.