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#' 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
#' @return A data frame containing the output times and the concentrations
#' assuming initial concentrations of 1 for the parent and zero for
#' metabolites, if any.
#' @export
#' @author Johannes Ranke
#' @examples
#' # Simple example of an SFO decline curve
#' sfo_out <- pfm_degradation("SFO", DT50 = 10)
#' head(sfo_out)
#'
#' # Fictive example with a metabolite where we first generate an SFO-SFO model
#' sfo_sfo <- mkinmod(
#' parent = mkinsub("SFO", to = "metabolite"),
#' metabolite = mkinsub("SFO"))
#'
#' sfo_sfo_out <- pfm_degradation(sfo_sfo,
#' parms = c(k_parent = 0.1, f_parent_to_metabolite = 0.5, k_metabolite = 0.02))
#'
#' plot(
#' sfo_sfo_out[, "time"],
#' sfo_sfo_out[, "parent"], type = "l",
#' xlab = "Time", ylab = "Relative concentration",
#' xlim = c(0, 100))
#' lines(
#' sfo_sfo_out[, "time"],
#' sfo_sfo_out[, "metabolite"], lty = 2)
#'
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 (!inherits(model, "mkinmod")) {
if (model[1] %in% c("SFO", "FOMC", "DFOP", "HS", "IORE")) {
model <- mkinmod(parent = list(type = model))
} else {
stop("Please specify the model with a suitable name or an mkinmod object")
}
}
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)
}
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