R/makeInflowFromSoln.R

In microPop: Process-Based Modelling of 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$solution
    washOutRate = out$parms$Smats$washOut

    mat = soln * NA
    mat[, 1] = soln[, "time"]

    for (i in 2:ncol(soln)) {
        xname = colnames(soln)[i]
        x = getGroupName(xname, out$parms$microbeNames)
         for (t in 1:nrow(soln)) {
            mat[t, i] = soln[t,xname]*washOutRate[x]
        }
    }
    return(mat)
}
#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)
#}