productionFuncDefault {microPop}

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

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 production of this variable

all.substrates

Vector of strings giving the names of the all the substrates used on this pathway

keyResName

(string). Name of the key resource 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

products

Vector of strings giving the names of the all the metabolic products created on this pathway

bio.products

Vector of strings giving the names of the all the microbial products created on this pathway

uptake

Vector with names given by resourceNames which given mass uptake of each resource per unit time

growthRate

(scalar) microbial growth rate (mass per unit time) on the given pathway

yield

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

parms

List containing all system parameters

water

Name of resource with Rtype 'Sw' - i.e resource could be called 'water' or 'H2O' etc

Value

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