path: root/R/pfm_degradation.R

#' Calculate a time course of relative concentrations based on an mkinmod model
#'
#' @import mkin
#' @param model The degradation model to be used. Either a parent only model like
#'   'SFO' or 'FOMC', or an mkinmod object
#' @param DT50 The half-life. This is only used when simple exponential decline
#'   is calculated (SFO model).
#' @param parms The parameters used for the degradation model
#' @param years For how many years should the degradation be predicted?
#' @param step_days What step size in days should the output have?
#' @param times The output times
#' @export
#' @author Johannes Ranke
#' @examples
#' head(pfm_degradation("SFO", DT50 = 10))
pfm_degradation <- function(model = "SFO",
  DT50 = 1000, parms = c(k_parent = log(2)/DT50),
  years = 1, step_days = 1,
  times = seq(0, years * 365, by = step_days))
{
  if (model %in% c("SFO", "FOMC", "DFOP", "HS", "IORE")) {
    model <- mkinmod(parent = list(type = model))
  }
  initial_state = c(1, rep(0, length(model$diffs) - 1))
  names(initial_state) <- names(model$diffs)
  time_course <- mkinpredict(model, odeparms = parms, 
    odeini = initial_state,
    outtimes = times,
    solution_type = ifelse(length(model$spec) == 1, "analytical", "deSolve"))
  invisible(time_course)
}