R/combineGrowthLimFuncDefault.R

In microPop: Process-Based Modelling of Microbial Populations

#' combines the growth limitation functions and max growth rates to get the growth rate of strain
#' 
#' Returns the specific growth rate in units of inverse time 
#'
#' @aliases combineGrowthLimFunc

#' @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 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 bio.sub Vector of strings giving the names of the microbial 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 keyResName String giving the name of the key resource on this pathway
#' @param nonBoostFrac (scalar) Fraction of max growth achievable if boosting resource is not present but is required on this pathway

#' @return (scalar) specific growth rate in units of inverse time 
#'
#' @export
combineGrowthLimFuncDefault = function(strainName, groupName, pathName, subst, ess, 
    boost, bio.sub, maxGrowthRate, growthLim, keyResName, nonBoostFrac) {
    
    if (length(subst) > 0) {
        # sum growth limitations for substitutable resources
        subst.growth = sum(maxGrowthRate[subst] * growthLim[subst])
    }
    
    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)
    }
    
    if (length(ess) > 0 & length(subst) == 0 & length(boost) == 0) {
        # all res are essential res
        v = maxGrowthRate[keyResName] * ess.lim
    }
    
    if (length(subst) > 0 & length(ess) == 0 & length(boost) == 0) {
        # all res are subst res
        v = subst.growth
    }
    
    if (length(subst) > 0 & length(ess) > 0 & length(boost) == 0) {
        # res are a mix of subst and ess
        v = subst.growth * ess.lim
    }
    
    if (length(subst) > 0 & length(boost) > 0 & length(ess) == 0) {
        # res are a mix of subst and boost
        v = subst.growth * (nonBoostFrac[boost] + (1 - nonBoostFrac[boost]) * boost.lim)
    }
    
    if (length(subst) == 0 & length(boost) > 0 & length(ess) > 0) {
        # res are a mix of ess and boost
        v = maxGrowthRate[keyResName] * ess.lim * (nonBoostFrac[boost] + (1 - nonBoostFrac[boost]) * 
            boost.lim)
    }
    
    
    if (!exists("v")) {
        stop("MICROPOP ERROR: An unaccounted for combination of resource types in combineGrowthLimFunc")
    }
    
    return(v)
    
}