From 3aa5fb86772c28402047c7ebd07841061dbcdbba Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 11 Jun 2015 15:23:22 +0200 Subject: Add facilities to calculate decline curves --- pkg/R/pfm_degradation.R | 48 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 pkg/R/pfm_degradation.R (limited to 'pkg/R/pfm_degradation.R') diff --git a/pkg/R/pfm_degradation.R b/pkg/R/pfm_degradation.R new file mode 100644 index 0000000..d1d2f9d --- /dev/null +++ b/pkg/R/pfm_degradation.R @@ -0,0 +1,48 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +#' 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 +#' pfm_degradation("SFO", DT50 = 10) +pfm_degradation <- function(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = 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) +} -- cgit v1.2.1