R/makeInflowFromSoln.R

In HelenKettle/microPop: Modelling Microbial Populations

#' Used for running microPop with multiple compartments

#' Takes the solution (state of system) from the previous compartment (out$solution)
#' and then finds the washout rate of each state variable using removalRateFunc
#' to find the inflow rate to the next downstream compartment 

#' @param out output from microPopModel()
#' @return matrix of flow rates (conc/time) with named columns (the same as out$solution) 
#' @export

makeInflowFromSoln = function(out) {
    
    soln = out$solution
    all.names = colnames(soln)
    washOutRate = out$parms$Smats$washOut
    resNames = out$parms$resourceNames
    
    mat = soln * NA
    mat[, 1] = soln[, "time"]
    
    for (i in 2:length(soln[1, ])) {
        xname = all.names[i]
        x = getGroupName(xname, out$parms$microbeNames)
        for (t in 1:length(soln[, "time"])) {
            mat[t, i] = out$parms$removalRateFunc(x, soln[t, xname], soln[t, ], soln[t, 
                "time"], washOutRate, out$parms)
        }
    }
    
    return(mat)
}