growthLimFuncDefault function

growth rate limitation function

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)

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

Returns

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