From 3715219923dca43dcc6f317f92099d512b0c4a64 Mon Sep 17 00:00:00 2001 From: jranke Date: Sun, 17 Feb 2013 20:18:28 +0000 Subject: - Added the examples vignette to the kinfit package - Added calls to utils::globalVariables to make R CMD check pass cleanly without NOTES git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/kinfit@62 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- DESCRIPTION | 4 +- R/kinplot.R | 3 +- vignettes/examples-FOCUS_2006_L3_2.pdf | Bin 0 -> 6609 bytes vignettes/examples-FOCUS_2006_L4.pdf | Bin 0 -> 6557 bytes vignettes/examples-L1_SFO_plot.pdf | Bin 0 -> 5572 bytes vignettes/examples-L1_SFO_residuals.pdf | Bin 0 -> 4718 bytes vignettes/examples-L2_plot.pdf | Bin 0 -> 5846 bytes vignettes/examples-L2_resplot.pdf | Bin 0 -> 4988 bytes vignettes/examples.Rnw | 224 +++++++++++ vignettes/examples.aux | 29 ++ vignettes/examples.bbl | 30 ++ vignettes/examples.blg | 46 +++ vignettes/examples.log | 617 ++++++++++++++++++++++++++++++ vignettes/examples.out | 5 + vignettes/examples.pdf | Bin 0 -> 155612 bytes vignettes/examples.tex | 657 ++++++++++++++++++++++++++++++++ vignettes/examples.toc | 5 + vignettes/references.bib | 25 +- 18 files changed, 1639 insertions(+), 6 deletions(-) create mode 100644 vignettes/examples-FOCUS_2006_L3_2.pdf create mode 100644 vignettes/examples-FOCUS_2006_L4.pdf create mode 100644 vignettes/examples-L1_SFO_plot.pdf create mode 100644 vignettes/examples-L1_SFO_residuals.pdf create mode 100644 vignettes/examples-L2_plot.pdf create mode 100644 vignettes/examples-L2_resplot.pdf create mode 100644 vignettes/examples.Rnw create mode 100644 vignettes/examples.aux create mode 100644 vignettes/examples.bbl create mode 100644 vignettes/examples.blg create mode 100644 vignettes/examples.log create mode 100644 vignettes/examples.out create mode 100644 vignettes/examples.pdf create mode 100644 vignettes/examples.tex create mode 100644 vignettes/examples.toc diff --git a/DESCRIPTION b/DESCRIPTION index 439800b..8850816 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: kinfit Type: Package Title: Routines for fitting kinetic models to chemical degradation data -Version: 1.1.10 -Date: 2012-08-23 +Version: 1.1.11 +Date: 2013-02-17 Author: Johannes Ranke and Katrin Lindenberger Maintainer: Johannes Ranke Description: Simple calculation routines based on the FOCUS Kinetics diff --git a/R/kinplot.R b/R/kinplot.R index 394e271..df21c13 100644 --- a/R/kinplot.R +++ b/R/kinplot.R @@ -1,6 +1,6 @@ # $Id: kinplot.R 117 2011-06-14 08:52:14Z kati $ -# Copyright (C) 2008-2010 Johannes Ranke +# Copyright (C) 2008-2013 Johannes Ranke # Contact: mkin-devel@lists.berlios.de # This file is part of the R package kinfit @@ -18,6 +18,7 @@ # You should have received a copy of the GNU General Public License along with # this program. If not, see +utils::globalVariables("x") kinplot <- function(kinobject, main = "", xlab = "Time [days]", ylab = "Parent [% of applied radioactivity]", diff --git a/vignettes/examples-FOCUS_2006_L3_2.pdf b/vignettes/examples-FOCUS_2006_L3_2.pdf new file mode 100644 index 0000000..84272c4 Binary files /dev/null and b/vignettes/examples-FOCUS_2006_L3_2.pdf differ diff --git a/vignettes/examples-FOCUS_2006_L4.pdf b/vignettes/examples-FOCUS_2006_L4.pdf new file mode 100644 index 0000000..bd67e70 Binary files /dev/null and b/vignettes/examples-FOCUS_2006_L4.pdf differ diff --git a/vignettes/examples-L1_SFO_plot.pdf b/vignettes/examples-L1_SFO_plot.pdf new file mode 100644 index 0000000..c44f903 Binary files /dev/null and b/vignettes/examples-L1_SFO_plot.pdf differ diff --git a/vignettes/examples-L1_SFO_residuals.pdf b/vignettes/examples-L1_SFO_residuals.pdf new file mode 100644 index 0000000..66cc0a0 Binary files /dev/null and b/vignettes/examples-L1_SFO_residuals.pdf differ diff --git a/vignettes/examples-L2_plot.pdf b/vignettes/examples-L2_plot.pdf new file mode 100644 index 0000000..d502cda Binary files /dev/null and b/vignettes/examples-L2_plot.pdf differ diff --git a/vignettes/examples-L2_resplot.pdf b/vignettes/examples-L2_resplot.pdf new file mode 100644 index 0000000..44a679e Binary files /dev/null and b/vignettes/examples-L2_resplot.pdf differ diff --git a/vignettes/examples.Rnw b/vignettes/examples.Rnw new file mode 100644 index 0000000..3807575 --- /dev/null +++ b/vignettes/examples.Rnw @@ -0,0 +1,224 @@ +% $Id: $ +%%\VignetteIndexEntry{Examples for kinetic evaluations using kinfit} +%%\usepackage{Sweave} +\documentclass[12pt,a4paper]{article} +\usepackage{a4wide} +%%\usepackage[lists,heads]{endfloat} +\input{header} +\hypersetup{ + pdftitle = {Examples for kinetic evaluations using kinfit}, + pdfsubject = {Manuscript}, + pdfauthor = {Johannes Ranke}, + colorlinks = {true}, + linkcolor = {blue}, + citecolor = {blue}, + urlcolor = {red}, + hyperindex = {true}, + linktocpage = {true}, +} +\SweaveOpts{engine=R, eps=FALSE, keep.source = TRUE} +<>= +options(prompt = "R> ") +options(SweaveHooks = list( + cex = function() par(cex.lab = 1.3, cex.axis = 1.3))) +@ +\begin{document} +\title{Examples for kinetic evaluations using kinfit} +\author{\textbf{Johannes Ranke} \\[0.5cm] +%EndAName +Eurofins Regulatory AG\\ +Weidenweg 15, CH--4310 Rheinfelden, Switzerland\\[0.5cm] +and\\[0.5cm] +University of Bremen\\ +} +\maketitle + +%\begin{abstract} +%\end{abstract} + +\thispagestyle{empty} \setcounter{page}{0} + +\clearpage + +\tableofcontents + +\textbf{Key words}: Kinetics, FOCUS, nonlinear optimisation + +\section{Kinetic evaluations for parent compounds} +\label{intro} + +These examples are also evaluated in a parallel vignette of the +\Rpackage{mkin} package \citep{pkg:mkin}. The datasets are from Appendix 3, +of the FOCUS kinetics report \citep{FOCUS2006, FOCUSkinetics2011}. + +\subsection{Laboratory Data L1} + +The following code defines an object containing the example dataset L1 from the +FOCUS kinetics report, p. 284 + +<>= +library("kinfit") +FOCUS_2006_L1 = kinobject("Parent", "Degradation data", "") +FOCUS_2006_L1$data = data.frame( + t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2), + parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6, + 72.0, 71.9, 50.3, 59.4, 47.0, 45.1, + 27.7, 27.3, 10.0, 10.4, 2.9, 4.0)) +@ + +The following two lines fit the model and produce the summary report +of the model fit. This covers the numerical analyses given in the +FOCUS report. + +<>= +FOCUS_2006_L1$fits <- kinfit(FOCUS_2006_L1$data, + kinmodels = c("SFO", "FOMC", "DFOP")) +FOCUS_2006_L1$results <- kinresults(FOCUS_2006_L1$fits) +kinreport(FOCUS_2006_L1) +@ + +Obviously, the FOMC model and the DFOP model were not fitted. As discussed in the +kinfit vignette of this package, this occurs when the SFO model fits very well. + +We can try to force the FOMC fit using the parameters obtained using mkin. + +<>= +FOCUS_2006_L1$fits <- kinfit(FOCUS_2006_L1$data, + kinmodels = c("SFO", "FOMC", "DFOP"), + start.FOMC = list(parent.0 = 92.47, alpha = 1.35e11, beta = 1.41e12)) +FOCUS_2006_L1$results <- kinresults(FOCUS_2006_L1$fits) +kinreport(FOCUS_2006_L1) +@ + +It still does not converge. As discussed in the kinfit vignette, the FOMC model usually +is not returned by kinfit when the SFO model fits very well. This should be seen as +a feature, not a bug, as the FOMC model is ill-defined in such cases. + +A plot of the fit is obtained with the kinplot function. + +<>= +kinplot(FOCUS_2006_L1, ylab = "Observed") +@ + +The residual plot can be easily obtained by + +<>= +kinresplot(FOCUS_2006_L1, "SFO", ylab = "Observed") +@ + +\subsection{Laboratory Data L2} + +The following code defines example dataset L2 from the FOCUS kinetics +report, p. 287 + +<>= +FOCUS_2006_L2 = kinobject("Parent", "Degradation data", "") +FOCUS_2006_L2$data = data.frame( + t = rep(c(0, 1, 3, 7, 14, 28), each = 2), + parent = c(96.1, 91.8, 41.4, 38.7, + 19.3, 22.3, 4.6, 4.6, + 2.6, 1.2, 0.3, 0.6)) +@ + +Again, the SFO, FOMC and DFOP models are fitted and a report is printed. + +<>= +FOCUS_2006_L2$fits <- kinfit(FOCUS_2006_L2$data, + kinmodels = c("SFO", "FOMC", "DFOP")) +FOCUS_2006_L2$results <- kinresults(FOCUS_2006_L2$fits) +kinreport(FOCUS_2006_L2) +@ + +Here, only the DFOP did not converge using default parameters. The DFOP fit can be +obtained using refined starting parameters: + +<>= +FOCUS_2006_L2$fits <- kinfit(FOCUS_2006_L2$data, + kinmodels = c("SFO", "FOMC", "DFOP"), + start.DFOP = list(parent.0 = 94, g = 0.4, k1 = 142, k2 = 0.34)) +FOCUS_2006_L2$results <- kinresults(FOCUS_2006_L2$fits) +kinreport(FOCUS_2006_L2) +@ + +Again, even with starting parameters very close to the optimum obtained using mkin, +there is no convergence with kinfit. However, when looking at the fit obtained using +mkin plotted in the mkin vignette, it is clear that the point where the break point +of the curve, caused by the large difference between k1 and k2, is not clearly defined +by the data. Therefore, it should be seen as a desirable feature of the +underlying nls() function that no solution is returned. + +Comparison of $\chi^2$ error levels of the two models shows that the FOMC model allows +for a better representation of the data. This is also obvious from the plot +of the fits. + +<>= +kinplot(FOCUS_2006_L2, ylab = "Observed") +@ + +Residual plots are obtained using kinresplot. + +<>= +par(mfrow=c(2,1)) +kinresplot(FOCUS_2006_L2, "SFO", ylab = "Observed") +kinresplot(FOCUS_2006_L2, "FOMC", ylab = "Observed") +@ + +\subsection{Laboratory Data L3} + +The following code defines example dataset L3 from the FOCUS kinetics +report, p. 290 and attempts to fit the SFO, FOMC and DFOP models. + +<>= +FOCUS_2006_L3 = kinobject("Parent", "Degradation data", "") +FOCUS_2006_L3$data = data.frame( + t = c(0, 3, 7, 14, 30, 60, 91, 120), + parent = c(97.8, 60, 51, 43, 35, 22, 15, 12)) +FOCUS_2006_L3$fits <- kinfit(FOCUS_2006_L3$data, + kinmodels = c("SFO", "FOMC", "DFOP")) +FOCUS_2006_L3$results <- kinresults(FOCUS_2006_L3$fits) +kinreport(FOCUS_2006_L3) +@ + +In this case, the FOMC model does not return a solution using kinfit. Trying with +closer starting parameters gives success this time. + +<>= +FOCUS_2006_L3$fits <- kinfit(FOCUS_2006_L3$data, + kinmodels = c("SFO", "FOMC", "DFOP"), + start.FOMC = list(parent.0 = 100, alpha = 0.5, beta = 2)) +FOCUS_2006_L3$results <- kinresults(FOCUS_2006_L3$fits) +kinreport(FOCUS_2006_L3) +kinplot(FOCUS_2006_L3, ylab = "Observed") +@ + +Based on the $\chi^2$ error level criterion and the visual analysis of the +fits, the DFOP model would be the best-fit model of choice for laboratory data +L3. + +\subsection{Laboratory Data L4} + +The following code defines example dataset L4 from the FOCUS kinetics +report, p. 293 and attempts to fit the SFO, FOMC and DFOP models. + +<>= +FOCUS_2006_L4 = kinobject("Parent", "Degradation data", "") +FOCUS_2006_L4$data = data.frame( + t = c(0, 3, 7, 14, 30, 60, 91, 120), + parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0)) +FOCUS_2006_L4$fits <- kinfit(FOCUS_2006_L4$data, + kinmodels = c("SFO", "FOMC", "DFOP")) +FOCUS_2006_L4$results <- kinresults(FOCUS_2006_L4$fits) +kinreport(FOCUS_2006_L4) +kinplot(FOCUS_2006_L4, ylab = "Observed") +@ + +Although the $\chi^2$ error level is slightly smaller for the DFOP model and also +for the FOMC model, the differences are small, and the SFO model may appear to +be a suitable choice. The better fit of the DFOP model depends very much on the +last three data points. + +\bibliographystyle{plainnat} +\bibliography{references} + +\end{document} +% vim: set foldmethod=syntax: diff --git a/vignettes/examples.aux b/vignettes/examples.aux new file mode 100644 index 0000000..b87a0c2 --- /dev/null +++ b/vignettes/examples.aux @@ -0,0 +1,29 @@ +\relax +\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument} +\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined +\global\let\oldcontentsline\contentsline +\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}} +\global\let\oldnewlabel\newlabel +\gdef\newlabel#1#2{\newlabelxx{#1}#2} +\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}} +\AtEndDocument{\ifx\hyper@anchor\@undefined +\let\contentsline\oldcontentsline +\let\newlabel\oldnewlabel +\fi} +\fi} +\global\let\hyper@last\relax +\gdef\HyperFirstAtBeginDocument#1{#1} +\providecommand\HyField@AuxAddToFields[1]{} +\citation{pkg:mkin} +\citation{FOCUS2006,FOCUSkinetics2011} +\@writefile{toc}{\contentsline {section}{\numberline {1}Kinetic evaluations for parent compounds}{1}{section.1}} +\newlabel{intro}{{1}{1}{Kinetic evaluations for parent compounds\relax }{section.1}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}Laboratory Data L1}{1}{subsection.1.1}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}Laboratory Data L2}{5}{subsection.1.2}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}Laboratory Data L3}{10}{subsection.1.3}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.4}Laboratory Data L4}{14}{subsection.1.4}} +\bibstyle{plainnat} +\bibdata{references} +\bibcite{FOCUS2006}{{1}{2006}{{FOCUS Work Group on Degradation Kinetics}}{{}}} +\bibcite{FOCUSkinetics2011}{{2}{2011}{{FOCUS Work Group on Degradation Kinetics}}{{}}} +\bibcite{pkg:mkin}{{3}{2013}{{mkin}}{{}}} diff --git a/vignettes/examples.bbl b/vignettes/examples.bbl new file mode 100644 index 0000000..29159ac --- /dev/null +++ b/vignettes/examples.bbl @@ -0,0 +1,30 @@ +\begin{thebibliography}{3} +\providecommand{\natexlab}[1]{#1} +\providecommand{\url}[1]{\texttt{#1}} +\expandafter\ifx\csname urlstyle\endcsname\relax + \providecommand{\doi}[1]{doi: #1}\else + \providecommand{\doi}{doi: \begingroup \urlstyle{rm}\Url}\fi + +\bibitem[{FOCUS Work Group on Degradation Kinetics}(2006)]{FOCUS2006} +{FOCUS Work Group on Degradation Kinetics}. +\newblock \emph{Guidance Document on Estimating Persistence and Degradation + Kinetics from Environmental Fate Studies on Pesticides in EU Registration. + Report of the FOCUS Work Group on Degradation Kinetics}, 2006. +\newblock URL \url{http://focus.jrc.ec.europa.eu/dk}. +\newblock EC Document Reference Sanco/10058/2005 version 2.0. + +\bibitem[{FOCUS Work Group on Degradation Kinetics}(2011)]{FOCUSkinetics2011} +{FOCUS Work Group on Degradation Kinetics}. +\newblock \emph{Generic guidance for estimating persistence and degradation + kinetics from environmental fate studies on pesticides in EU registration}, + 1.0 edition, November 2011. +\newblock URL \url{http://focus.jrc.ec.europa.eu/dk}. + +\bibitem[mkin(2013)]{pkg:mkin} +mkin. +\newblock \emph{mkin: {R}outines for fitting kinetic models with one or more + state variables to chemical degradation data}, 2013. +\newblock URL \url{http://CRAN.R-project.org}. +\newblock R package version 0.9-11. + +\end{thebibliography} diff --git a/vignettes/examples.blg b/vignettes/examples.blg new file mode 100644 index 0000000..bbb3b5c --- /dev/null +++ b/vignettes/examples.blg @@ -0,0 +1,46 @@ +This is BibTeX, Version 0.99d (TeX Live 2012/Debian) +Capacity: max_strings=35307, hash_size=35307, hash_prime=30011 +The top-level auxiliary file: examples.aux +The style file: plainnat.bst +Database file #1: references.bib +You've used 3 entries, + 2773 wiz_defined-function locations, + 610 strings with 5517 characters, +and the built_in function-call counts, 904 in all, are: += -- 84 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/dev/null +++ b/vignettes/examples.tex @@ -0,0 +1,657 @@ +% $Id: $ +%%\VignetteIndexEntry{Examples for kinetic evaluations using kinfit} +%%\usepackage{Sweave} +\documentclass[12pt,a4paper]{article} +\usepackage{a4wide} +%%\usepackage[lists,heads]{endfloat} +\input{header} +\hypersetup{ + pdftitle = {Examples for kinetic evaluations using kinfit}, + pdfsubject = {Manuscript}, + pdfauthor = {Johannes Ranke}, + colorlinks = {true}, + linkcolor = {blue}, + citecolor = {blue}, + urlcolor = {red}, + hyperindex = {true}, + linktocpage = {true}, +} + +\begin{document} +\title{Examples for kinetic evaluations using kinfit} +\author{\textbf{Johannes Ranke} \\[0.5cm] +%EndAName +Eurofins Regulatory AG\\ +Weidenweg 15, CH--4310 Rheinfelden, Switzerland\\[0.5cm] +and\\[0.5cm] +University of Bremen\\ +} +\maketitle + +%\begin{abstract} +%\end{abstract} + +\thispagestyle{empty} \setcounter{page}{0} + +\clearpage + +\tableofcontents + +\textbf{Key words}: Kinetics, FOCUS, nonlinear optimisation + +\section{Kinetic evaluations for parent compounds} +\label{intro} + +These examples are also evaluated in a parallel vignette of the +\Rpackage{mkin} package \citep{pkg:mkin}. The datasets are from Appendix 3, +of the FOCUS kinetics report \citep{FOCUS2006, FOCUSkinetics2011}. + +\subsection{Laboratory Data L1} + +The following code defines an object containing the example dataset L1 from the +FOCUS kinetics report, p. 284 + +\begin{Schunk} +\begin{Sinput} +R> library("kinfit") +R> FOCUS_2006_L1 = kinobject("Parent", "Degradation data", "") +R> FOCUS_2006_L1$data = data.frame( ++ t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2), ++ parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6, ++ 72.0, 71.9, 50.3, 59.4, 47.0, 45.1, ++ 27.7, 27.3, 10.0, 10.4, 2.9, 4.0)) +\end{Sinput} +\end{Schunk} + +The following two lines fit the model and produce the summary report +of the model fit. This covers the numerical analyses given in the +FOCUS report. + +\begin{Schunk} +\begin{Sinput} +R> FOCUS_2006_L1$fits <- kinfit(FOCUS_2006_L1$data, ++ kinmodels = c("SFO", "FOMC", "DFOP")) +R> FOCUS_2006_L1$results <- kinresults(FOCUS_2006_L1$fits) +R> kinreport(FOCUS_2006_L1) +\end{Sinput} +\begin{Soutput} +Parent compound: Parent +Study type: Degradation data +System: +kinfit version: 1.1.10 +R version: 2.15.2 +Report generated: Sun Feb 17 21:07:59 2013 + +Data: + t parent +1 0 88.3 +2 0 91.4 +3 1 85.6 +4 1 84.5 +5 2 78.9 +6 2 77.6 +7 3 72.0 +8 3 71.9 +9 5 50.3 +10 5 59.4 +11 7 47.0 +12 7 45.1 +13 14 27.7 +14 14 27.3 +15 21 10.0 +16 21 10.4 +17 30 2.9 +18 30 4.0 + + + +--- +Nonlinear least squares fit of the SFO model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 92.4710 1.36830 67.6 0.00e+00 +k 0.0956 0.00388 24.6 1.87e-14 + +Chi2 error estimation: 3.42 % + + + +--- +Endpoint estimates + + DT50 DT90 +SFO 7.2 24.1 +\end{Soutput} +\end{Schunk} + +Obviously, the FOMC model and the DFOP model were not fitted. As discussed in the +kinfit vignette of this package, this occurs when the SFO model fits very well. + +We can try to force the FOMC fit using the parameters obtained using mkin. + +\begin{Schunk} +\begin{Sinput} +R> FOCUS_2006_L1$fits <- kinfit(FOCUS_2006_L1$data, ++ kinmodels = c("SFO", "FOMC", "DFOP"), ++ start.FOMC = list(parent.0 = 92.47, alpha = 1.35e11, beta = 1.41e12)) +R> FOCUS_2006_L1$results <- kinresults(FOCUS_2006_L1$fits) +R> kinreport(FOCUS_2006_L1) +\end{Sinput} +\begin{Soutput} +Parent compound: Parent +Study type: Degradation data +System: +kinfit version: 1.1.10 +R version: 2.15.2 +Report generated: Sun Feb 17 21:08:00 2013 + +Data: + t parent +1 0 88.3 +2 0 91.4 +3 1 85.6 +4 1 84.5 +5 2 78.9 +6 2 77.6 +7 3 72.0 +8 3 71.9 +9 5 50.3 +10 5 59.4 +11 7 47.0 +12 7 45.1 +13 14 27.7 +14 14 27.3 +15 21 10.0 +16 21 10.4 +17 30 2.9 +18 30 4.0 + + + +--- +Nonlinear least squares fit of the SFO model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 92.4710 1.36830 67.6 0.00e+00 +k 0.0956 0.00388 24.6 1.87e-14 + +Chi2 error estimation: 3.42 % + + + +--- +Endpoint estimates + + DT50 DT90 +SFO 7.2 24.1 +\end{Soutput} +\end{Schunk} + +It still does not converge. As discussed in the kinfit vignette, the FOMC model usually +is not returned by kinfit when the SFO model fits very well. This should be seen as +a feature, not a bug, as the FOMC model is ill-defined in such cases. + +A plot of the fit is obtained with the kinplot function. + +\begin{Schunk} +\begin{Sinput} +R> kinplot(FOCUS_2006_L1, ylab = "Observed") +\end{Sinput} +\end{Schunk} +\includegraphics{examples-L1_SFO_plot} + +The residual plot can be easily obtained by + +\begin{Schunk} +\begin{Sinput} +R> kinresplot(FOCUS_2006_L1, "SFO", ylab = "Observed") +\end{Sinput} +\end{Schunk} +\includegraphics{examples-L1_SFO_residuals} + +\subsection{Laboratory Data L2} + +The following code defines example dataset L2 from the FOCUS kinetics +report, p. 287 + +\begin{Schunk} +\begin{Sinput} +R> FOCUS_2006_L2 = kinobject("Parent", "Degradation data", "") +R> FOCUS_2006_L2$data = data.frame( ++ t = rep(c(0, 1, 3, 7, 14, 28), each = 2), ++ parent = c(96.1, 91.8, 41.4, 38.7, ++ 19.3, 22.3, 4.6, 4.6, ++ 2.6, 1.2, 0.3, 0.6)) +\end{Sinput} +\end{Schunk} + +Again, the SFO, FOMC and DFOP models are fitted and a report is printed. + +\begin{Schunk} +\begin{Sinput} +R> FOCUS_2006_L2$fits <- kinfit(FOCUS_2006_L2$data, ++ kinmodels = c("SFO", "FOMC", "DFOP")) +R> FOCUS_2006_L2$results <- kinresults(FOCUS_2006_L2$fits) +R> kinreport(FOCUS_2006_L2) +\end{Sinput} +\begin{Soutput} +Parent compound: Parent +Study type: Degradation data +System: +kinfit version: 1.1.10 +R version: 2.15.2 +Report generated: Sun Feb 17 21:08:00 2013 + +Data: + t parent +1 0 96.1 +2 0 91.8 +3 1 41.4 +4 1 38.7 +5 3 19.3 +6 3 22.3 +7 7 4.6 +8 7 4.6 +9 14 2.6 +10 14 1.2 +11 28 0.3 +12 28 0.6 + + + +--- +Nonlinear least squares fit of the SFO model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 91.466 3.8065 24.03 1.77e-10 +k 0.663 0.0712 9.31 1.52e-06 + +Chi2 error estimation: 14.38 % + + + +--- +Nonlinear least squares fit of the FOMC model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 93.77 1.856 50.51 1.17e-12 +alpha 1.37 0.257 5.36 2.30e-04 +beta 1.23 0.363 3.40 3.95e-03 + +Chi2 error estimation: 6.2 % + + + +--- +Endpoint estimates + + DT50 DT90 +SFO 1.0 3.5 +FOMC 0.8 5.4 +\end{Soutput} +\end{Schunk} + +Here, only the DFOP did not converge using default parameters. The DFOP fit can be +obtained using refined starting parameters: + +\begin{Schunk} +\begin{Sinput} +R> FOCUS_2006_L2$fits <- kinfit(FOCUS_2006_L2$data, ++ kinmodels = c("SFO", "FOMC", "DFOP"), ++ start.DFOP = list(parent.0 = 94, g = 0.4, k1 = 142, k2 = 0.34)) +R> FOCUS_2006_L2$results <- kinresults(FOCUS_2006_L2$fits) +R> kinreport(FOCUS_2006_L2) +\end{Sinput} +\begin{Soutput} +Parent compound: Parent +Study type: Degradation data +System: +kinfit version: 1.1.10 +R version: 2.15.2 +Report generated: Sun Feb 17 21:08:00 2013 + +Data: + t parent +1 0 96.1 +2 0 91.8 +3 1 41.4 +4 1 38.7 +5 3 19.3 +6 3 22.3 +7 7 4.6 +8 7 4.6 +9 14 2.6 +10 14 1.2 +11 28 0.3 +12 28 0.6 + + + +--- +Nonlinear least squares fit of the SFO model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 91.466 3.8065 24.03 1.77e-10 +k 0.663 0.0712 9.31 1.52e-06 + +Chi2 error estimation: 14.38 % + + + +--- +Nonlinear least squares fit of the FOMC model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 93.77 1.856 50.51 1.17e-12 +alpha 1.37 0.257 5.36 2.30e-04 +beta 1.23 0.363 3.40 3.95e-03 + +Chi2 error estimation: 6.2 % + + + +--- +Endpoint estimates + + DT50 DT90 +SFO 1.0 3.5 +FOMC 0.8 5.4 +\end{Soutput} +\end{Schunk} + +Again, even with starting parameters very close to the optimum obtained using mkin, +there is no convergence with kinfit. However, when looking at the fit obtained using +mkin plotted in the mkin vignette, it is clear that the point where the break point +of the curve, caused by the large difference between k1 and k2, is not clearly defined +by the data. Therefore, it should be seen as a desirable feature of the +underlying nls() function that no solution is returned. + +Comparison of $\chi^2$ error levels of the two models shows that the FOMC model allows +for a better representation of the data. This is also obvious from the plot +of the fits. + +\begin{Schunk} +\begin{Sinput} +R> kinplot(FOCUS_2006_L2, ylab = "Observed") +\end{Sinput} +\end{Schunk} +\includegraphics{examples-L2_plot} + +Residual plots are obtained using kinresplot. + +\begin{Schunk} +\begin{Sinput} +R> par(mfrow=c(2,1)) +R> kinresplot(FOCUS_2006_L2, "SFO", ylab = "Observed") +R> kinresplot(FOCUS_2006_L2, "FOMC", ylab = "Observed") +\end{Sinput} +\end{Schunk} +\includegraphics{examples-L2_resplot} + +\subsection{Laboratory Data L3} + +The following code defines example dataset L3 from the FOCUS kinetics +report, p. 290 and attempts to fit the SFO, FOMC and DFOP models. + +\begin{Schunk} +\begin{Sinput} +R> FOCUS_2006_L3 = kinobject("Parent", "Degradation data", "") +R> FOCUS_2006_L3$data = data.frame( ++ t = c(0, 3, 7, 14, 30, 60, 91, 120), ++ parent = c(97.8, 60, 51, 43, 35, 22, 15, 12)) +R> FOCUS_2006_L3$fits <- kinfit(FOCUS_2006_L3$data, ++ kinmodels = c("SFO", "FOMC", "DFOP")) +R> FOCUS_2006_L3$results <- kinresults(FOCUS_2006_L3$fits) +R> kinreport(FOCUS_2006_L3) +\end{Sinput} +\begin{Soutput} +Parent compound: Parent +Study type: Degradation data +System: +kinfit version: 1.1.10 +R version: 2.15.2 +Report generated: Sun Feb 17 21:08:00 2013 + +Data: + t parent +1 0 97.8 +2 3 60.0 +3 7 51.0 +4 14 43.0 +5 30 35.0 +6 60 22.0 +7 91 15.0 +8 120 12.0 + + + +--- +Nonlinear least squares fit of the SFO model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 74.8718 8.45736 8.85 5.78e-05 +k 0.0253 0.00824 3.07 1.10e-02 + +Chi2 error estimation: 21.24 % + + + +--- +Nonlinear least squares fit of the DFOP model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 97.7460 1.438160 68.0 1.40e-07 +k1 0.5162 0.068841 7.5 8.46e-04 +k2 0.0138 0.000812 16.9 3.56e-05 +g 0.4566 0.017970 25.4 7.12e-06 + +Chi2 error estimation: 2.22 % + + + +--- +Endpoint estimates + + DT50 DT90 +SFO 27.4 91.1 +DFOP 7.5 123.0 +\end{Soutput} +\end{Schunk} + +In this case, the FOMC model does not return a solution using kinfit. Trying with +closer starting parameters gives success this time. + +\begin{Schunk} +\begin{Sinput} +R> FOCUS_2006_L3$fits <- kinfit(FOCUS_2006_L3$data, ++ kinmodels = c("SFO", "FOMC", "DFOP"), ++ start.FOMC = list(parent.0 = 100, alpha = 0.5, beta = 2)) +R> FOCUS_2006_L3$results <- kinresults(FOCUS_2006_L3$fits) +R> kinreport(FOCUS_2006_L3) +\end{Sinput} +\begin{Soutput} +Parent compound: Parent +Study type: Degradation data +System: +kinfit version: 1.1.10 +R version: 2.15.2 +Report generated: Sun Feb 17 21:08:00 2013 + +Data: + t parent +1 0 97.8 +2 3 60.0 +3 7 51.0 +4 14 43.0 +5 30 35.0 +6 60 22.0 +7 91 15.0 +8 120 12.0 + + + +--- +Nonlinear least squares fit of the SFO model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 74.8718 8.45736 8.85 5.78e-05 +k 0.0253 0.00824 3.07 1.10e-02 + +Chi2 error estimation: 21.24 % + + + +--- +Nonlinear least squares fit of the FOMC model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 96.974 4.550 21.31 2.11e-06 +alpha 0.422 0.072 5.87 1.02e-03 +beta 1.858 0.881 2.11 4.44e-02 + +Chi2 error estimation: 7.32 % + + + +--- +Nonlinear least squares fit of the DFOP model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 97.7460 1.438160 68.0 1.40e-07 +k1 0.5162 0.068841 7.5 8.46e-04 +k2 0.0138 0.000812 16.9 3.56e-05 +g 0.4566 0.017970 25.4 7.12e-06 + +Chi2 error estimation: 2.22 % + + + +--- +Endpoint estimates + + DT50 DT90 +SFO 27.4 91.1 +FOMC 7.7 431.2 +DFOP 7.5 123.0 +\end{Soutput} +\begin{Sinput} +R> kinplot(FOCUS_2006_L3, ylab = "Observed") +\end{Sinput} +\end{Schunk} +\includegraphics{examples-FOCUS_2006_L3_2} + +Based on the $\chi^2$ error level criterion and the visual analysis of the +fits, the DFOP model would be the best-fit model of choice for laboratory data +L3. + +\subsection{Laboratory Data L4} + +The following code defines example dataset L4 from the FOCUS kinetics +report, p. 293 and attempts to fit the SFO, FOMC and DFOP models. + +\begin{Schunk} +\begin{Sinput} +R> FOCUS_2006_L4 = kinobject("Parent", "Degradation data", "") +R> FOCUS_2006_L4$data = data.frame( ++ t = c(0, 3, 7, 14, 30, 60, 91, 120), ++ parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0)) +R> FOCUS_2006_L4$fits <- kinfit(FOCUS_2006_L4$data, ++ kinmodels = c("SFO", "FOMC", "DFOP")) +R> FOCUS_2006_L4$results <- kinresults(FOCUS_2006_L4$fits) +R> kinreport(FOCUS_2006_L4) +\end{Sinput} +\begin{Soutput} +Parent compound: Parent +Study type: Degradation data +System: +kinfit version: 1.1.10 +R version: 2.15.2 +Report generated: Sun Feb 17 21:08:00 2013 + +Data: + t parent +1 0 96.6 +2 3 96.3 +3 7 94.3 +4 14 88.8 +5 30 74.9 +6 60 59.9 +7 91 53.5 +8 120 49.0 + + + +--- +Nonlinear least squares fit of the SFO model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 96.44152 1.948781 49.5 2.28e-09 +k 0.00654 0.000523 12.5 8.01e-06 + +Chi2 error estimation: 3.29 % + + + +--- +Nonlinear least squares fit of the FOMC model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 99.143 1.680 59.02 1.32e-08 +alpha 0.704 0.262 2.68 2.18e-02 +beta 64.980 36.617 1.77 6.81e-02 + +Chi2 error estimation: 2.03 % + + + +--- +Nonlinear least squares fit of the DFOP model + +Parameter estimation: + Estimate Std. Error t value Pr(>t) +parent.0 98.7514 1.33707 73.857 1.01e-07 +k1 0.0105 0.00449 2.348 3.93e-02 +k2 -0.0112 0.01884 -0.596 7.08e-01 +g 0.9390 0.18530 5.068 3.57e-03 + +Chi2 error estimation: 1.63 % + + + +--- +Endpoint estimates + + DT50 DT90 +SFO 106.0 352.0 +FOMC 108.9 1644.1 +DFOP 118.7 122.8 +\end{Soutput} +\begin{Sinput} +R> kinplot(FOCUS_2006_L4, ylab = "Observed") +\end{Sinput} +\end{Schunk} +\includegraphics{examples-FOCUS_2006_L4} + +Although the $\chi^2$ error level is slightly smaller for the DFOP model and also +for the FOMC model, the differences are small, and the SFO model may appear to +be a suitable choice. The better fit of the DFOP model depends very much on the +last three data points. + +\bibliographystyle{plainnat} +\bibliography{references} + +\end{document} +% vim: set foldmethod=syntax: diff --git a/vignettes/examples.toc b/vignettes/examples.toc new file mode 100644 index 0000000..af3c624 --- /dev/null +++ b/vignettes/examples.toc @@ -0,0 +1,5 @@ +\contentsline {section}{\numberline {1}Kinetic evaluations for parent compounds}{1}{section.1} +\contentsline {subsection}{\numberline {1.1}Laboratory Data L1}{1}{subsection.1.1} +\contentsline {subsection}{\numberline {1.2}Laboratory Data L2}{5}{subsection.1.2} +\contentsline {subsection}{\numberline {1.3}Laboratory Data L3}{10}{subsection.1.3} +\contentsline {subsection}{\numberline {1.4}Laboratory Data L4}{14}{subsection.1.4} diff --git a/vignettes/references.bib b/vignettes/references.bib index 8cde4bd..443ed9d 100644 --- a/vignettes/references.bib +++ b/vignettes/references.bib @@ -1,8 +1,16 @@ @Manual{pkg:kinfit, title = {kinfit: {R}outines for fitting kinetic models to chemical degradation data}, author = {kinfit}, - year = {2009}, - note = {R package version 1.0-0}, + year = {2013}, + note = {R package version 1.1-10}, + url = {http://CRAN.R-project.org} +} + +@Manual{pkg:mkin, + title = {mkin: {R}outines for fitting kinetic models with one or more state variables to chemical degradation data}, + author = {mkin}, + year = {2013}, + note = {R package version 0.9-11}, url = {http://CRAN.R-project.org} } @@ -27,9 +35,20 @@ url = {http://focus.jrc.ec.europa.eu/dk} } +@MANUAL{FOCUSkinetics2011, + title = {Generic guidance for estimating persistence and degradation kinetics + from environmental fate studies on pesticides in EU registration}, + author = {{FOCUS Work Group on Degradation Kinetics}}, + edition = {1.0}, + month = {November}, + year = {2011}, + file = {FOCUS kinetics 2011 Generic guidance:/home/ranke/dok/orgs/focus/FOCUSkineticsvc_1_0_Nov23.pdf:PDF}, + url = {http://focus.jrc.ec.europa.eu/dk} +} + @Inproceedings{ schaefer2007, title = {{KinGUI}: a new kinetic software tool for evaluations according to {FOCUS} degradation kinetics}, - author = {D. Sch\"{a}fer and M. Mikolasch and P. Rainbird and B. Harvey}, + author = {D. Sch\"{a}fer and B. Mikolasch and P. Rainbird and B. Harvey}, booktitle = {Proceedings of the XIII Symposium Pesticide Chemistry}, editor = {Del Re A. A. M. and Capri E. and Fragoulis G. and Trevisan M.}, year = {2007}, -- cgit v1.2.1