R/productionFuncDefault.R

In HelenKettle/microPop: Modelling Microbial Populations

#' Production Function
#' 
#' Production rate of resource (units are resource mass/time)
#'
#' @aliases productionFunc
#' @param strainName Name of the strain that is being looped through in the ODE solver
#' @param groupName Name of microbial group that is being looped through in the ODE solver
#' @param pathName Name of metabolic path (e.g. path1) that is being looped through in the ODE solver
#' @param varName (string). Calculate production of this variable
#' @param all.substrates Vector of strings giving the names of the all the substrates used on this pathway
#' @param keyResName (string). Name of the key resource on this pathway
#' @param 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
#' @param products Vector of strings giving the names of the all the metabolic products created on this pathway
#' @param bio.products Vector of strings giving the names of the all the microbial products created on this pathway
#' @param uptake Vector with names given by resourceNames which given mass uptake of each resource per unit time
#' @param growthRate (scalar) microbial growth rate (mass per unit time) on the given pathway
#' @param yield Named vector (names are resourceNames) giving the mass yield of biomass on each resource (mass microbe/mass resource)
#' @param parms List containing all system parameters
#' @param water Name of resource with Rtype 'Sw' - i.e resource could be called 'water' or 'H2O' etc
#'
#' @return (scalar) production rate of given resource (units are resource mass/time)
#' @export 
productionFuncDefault = function(strainName, groupName, pathName,
                                 varName, all.substrates, keyResName, stoichiom, products,
                                 bio.products, uptake, growthRate, yield, parms, water) {
    
    if (growthRate > 0) {
        
        if (length(bio.products) > 0) {
            # biomass is in stoichiom so don't remove
            uptakeKeyRes = growthRate/yield[keyResName]
            v = stoichiom[varName]/stoichiom[keyResName] * uptakeKeyRes
            
        } else {
            # sum all uptakes and remove microbial growth to find mass available for products
            if (length(water) > 0) {#uptake rate of water
                waterUp = uptake[water]
            } else {
                waterUp = 0
            }

            v = (stoichiom[varName]/sum(stoichiom[products])) * (sum(uptake[all.substrates]) + 
                waterUp - growthRate)
        }
        
    } else {
        v = 0
    }
    
    return(max(v, 0))
}