growthLimFuncDefault: 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

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) Name of variable (resource) of interest

resourceValues

State vector of resources (with names)

allSubType

Vector of strings (with names corresponding to the resourceNames) which describes the type of each resource ('Rtype') - Rtypes are S (substitutable resource), Se (essential resource), Sb (booster resource), Sm (microbial resource), P (product) and Pb (biomass product)

strainHalfSat

Vector (with names corresponding to the resourceNames) of half-saturation constants for the given strain. If resource is not a substrate for the given strain, the value is NA

stateVarValues

State vector (resources and microbes) (with names)

parms

list of parameter values

Value

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