R/uptakeFuncDefault.R

In microPop: Process-Based Modelling of Microbial Populations

#' Uptake Function
#'
#' Return the value of resource uptake per biomass (i.e. resource quantity per unit time per mass unit of biomass) for given resource
#'
#' @aliases uptakeFunc
#' @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 uptake of this variable
#' @param keyResName (string). Name of the key resource on this pathway
#' @param subst Vector of strings giving the names of the substitutable resources  for given strain, pathway
#' @param ess Vector of strings giving the names of the essential resources  for given strain, pathway
#' @param boost Vector of strings giving the names of the boosting resources  for given strain, pathway
#' @param maxGrowthRate Vector containing maximum growth rate on each resource (named by resourceNames). If a resource is not on the pathway the value is NA
#' @param growthLim Vector containing the growth limitation from each resource (named by resourceNames). If a resource is not on the pathway the value is NA
#' @param yield Named vector (names are resourceNames) giving the mass yield of biomass on each resource (mass microbe/mass resource)
#' @param nonBoostFrac (scalar) Fraction of max growth achievable if boosting resource is not present but is required 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 parms List containing all system parameters
#'
#' @return (scalar) uptake of resource per mass unit of biomass (units are resource mass/biomass/time)
#' @export
uptakeFuncDefault = function(strainName, groupName, pathName, varName, keyResName, 
    subst, ess, boost, maxGrowthRate, growthLim, yield, nonBoostFrac, stoichiom, 
    parms) {
    
    if (length(ess) > 0) {
        # multiply growth lims for essential resources
        ess.lim = prod(growthLim[ess], na.rm = TRUE)
    }
    if (length(boost) > 0) {
        # multiply growth lims for essential resources
        boost.lim = prod(growthLim[boost], na.rm = TRUE)
        nbf = nonBoostFrac[boost]
    }
    
    if (varName %in% subst) {
        
        if (length(ess) == 0 & length(boost) == 0) {
            v = maxGrowthRate[varName] * growthLim[varName]/yield[varName]
        } else if (length(ess) > 0 & length(boost) == 0) {
            # include ess res
            v = ess.lim * maxGrowthRate[varName] * growthLim[varName]/yield[varName]
        } else if (length(ess) == 0 & length(boost) > 0) {
            # include boost res
            v = (nbf + (1 - nbf) * boost.lim) * maxGrowthRate[varName] * growthLim[varName]/yield[varName]
        }
        
    } else if (varName %in% ess) {
        
        if (length(subst) == 0) {
            # all res are ess - use key resource
            if (varName == keyResName) {
                v = maxGrowthRate[keyResName] * ess.lim/yield[keyResName]
            } else {
                v = (stoichiom[varName]/stoichiom[keyResName]) * maxGrowthRate[keyResName] * 
                  ess.lim/yield[keyResName]
            }
        } else {
            # mix of subst and ess res - do not use key resource
            subst.uptake = ess.lim * sum(maxGrowthRate[subst] * growthLim[subst]/yield[subst])
            v = (stoichiom[varName]/mean(stoichiom[subst])) * subst.uptake
        }
        
    } else if (varName %in% boost) {
        # compute uptake of substitutable resources due to booster - do not use key
        # resource
        subst.uptake = (1 - nbf) * boost.lim * sum(maxGrowthRate[subst] * growthLim[subst]/yield[subst])
        v = subst.uptake * stoichiom[boost]/mean(stoichiom[subst])
    } else {
        v = 0
    }
    
    return(max(v, 0))
}