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Diffstat (limited to 'R/nafta.R')
| -rw-r--r-- | R/nafta.R | 79 |
1 files changed, 61 insertions, 18 deletions
@@ -1,21 +1,40 @@ -# Copyright (C) 2019 Johannes Ranke -# Contact: jranke@uni-bremen.de - -# This file is part of the R package mkin - -# mkin 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 <http://www.gnu.org/licenses/> - +#' Evaluate parent kinetics using the NAFTA guidance +#' +#' The function fits the SFO, IORE and DFOP models using \code{\link{mmkin}} +#' and returns an object of class \code{nafta} that has methods for printing +#' and plotting. +#' +#' @param ds A dataframe that must contain one variable called "time" with the +#' time values specified by the \code{time} argument, one column called +#' "name" with the grouping of the observed values, and finally one column of +#' observed values called "value". +#' @param title Optional title of the dataset +#' @param quiet Should the evaluation text be shown? +#' @param \dots Further arguments passed to \code{\link{mmkin}} (not for the +#' printing method). +#' @importFrom stats qf +#' @return An list of class \code{nafta}. The list element named "mmkin" is the +#' \code{\link{mmkin}} object containing the fits of the three models. The +#' list element named "title" contains the title of the dataset used. The +#' list element "data" contains the dataset used in the fits. +#' @author Johannes Ranke +#' @source NAFTA (2011) Guidance for evaluating and calculating degradation +#' kinetics in environmental media. NAFTA Technical Working Group on +#' Pesticides +#' \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation} +#' accessed 2019-02-22 +#' +#' US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to +#' Calculate Representative Half-life Values and Characterizing Pesticide +#' Degradation +#' \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance} +#' @examples +#' +#' nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1) +#' print(nafta_evaluation) +#' plot(nafta_evaluation) +#' +#' @export nafta <- function(ds, title = NA, quiet = FALSE, ...) { if (length(levels(ds$name)) > 1) { stop("The NAFTA procedure is only defined for decline data for a single compound") @@ -56,6 +75,20 @@ nafta <- function(ds, title = NA, quiet = FALSE, ...) { return(result) } +#' Plot the results of the three models used in the NAFTA scheme. +#' +#' The plots are ordered with increasing complexity of the model in this +#' function (SFO, then IORE, then DFOP). +#' +#' Calls \code{\link{plot.mmkin}}. +#' +#' @param x An object of class \code{\link{nafta}}. +#' @param legend Should a legend be added? +#' @param main Possibility to override the main title of the plot. +#' @param \dots Further arguments passed to \code{\link{plot.mmkin}}. +#' @return The function is called for its side effect. +#' @author Johannes Ranke +#' @export plot.nafta <- function(x, legend = FALSE, main = "auto", ...) { if (main == "auto") { if (is.na(x$title)) main = "" @@ -64,6 +97,16 @@ plot.nafta <- function(x, legend = FALSE, main = "auto", ...) { plot(x$mmkin, ..., legend = legend, main = main) } +#' Print nafta objects +#' +#' Print nafta objects. The results for the three models are printed in the +#' order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP. +#' +#' @param x An \code{\link{nafta}} object. +#' @param digits Number of digits to be used for printing parameters and +#' dissipation times. +#' @rdname nafta +#' @export print.nafta <- function(x, quiet = TRUE, digits = 3, ...) { cat("Sums of squares:\n") print(x$S) |