From 12a31f4c130c551f82232d9ef7dfb608bd52c53f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 27 Sep 2016 23:00:48 +0200 Subject: Reorganise repository using standard package layout --- pkg/R/pfm_degradation.R | 48 ------------------------------------------------ 1 file changed, 48 deletions(-) delete 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 deleted file mode 100644 index 6c8610e..0000000 --- a/pkg/R/pfm_degradation.R +++ /dev/null @@ -1,48 +0,0 @@ -# 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 -#' head(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