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authorjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2013-02-17 20:18:28 +0000
committerjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2013-02-17 20:18:28 +0000
commit3715219923dca43dcc6f317f92099d512b0c4a64 (patch)
tree515083e5ee8111e94fe6da673b11dd4ce94c9cab
parentc175bfe010b42c8052b819eaabf0a08ee61e3b35 (diff)
- 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
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-rw-r--r--DESCRIPTION4
-rw-r--r--R/kinplot.R3
-rw-r--r--vignettes/examples-FOCUS_2006_L3_2.pdfbin0 -> 6609 bytes
-rw-r--r--vignettes/examples-FOCUS_2006_L4.pdfbin0 -> 6557 bytes
-rw-r--r--vignettes/examples-L1_SFO_plot.pdfbin0 -> 5572 bytes
-rw-r--r--vignettes/examples-L1_SFO_residuals.pdfbin0 -> 4718 bytes
-rw-r--r--vignettes/examples-L2_plot.pdfbin0 -> 5846 bytes
-rw-r--r--vignettes/examples-L2_resplot.pdfbin0 -> 4988 bytes
-rw-r--r--vignettes/examples.Rnw224
-rw-r--r--vignettes/examples.aux29
-rw-r--r--vignettes/examples.bbl30
-rw-r--r--vignettes/examples.blg46
-rw-r--r--vignettes/examples.log617
-rw-r--r--vignettes/examples.out5
-rw-r--r--vignettes/examples.pdfbin0 -> 155612 bytes
-rw-r--r--vignettes/examples.tex657
-rw-r--r--vignettes/examples.toc5
-rw-r--r--vignettes/references.bib25
18 files changed, 1639 insertions, 6 deletions
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 <jranke@uni-bremen.de>
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 <http://www.gnu.org/licenses/>
+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
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diff --git a/vignettes/examples-FOCUS_2006_L4.pdf b/vignettes/examples-FOCUS_2006_L4.pdf
new file mode 100644
index 0000000..bd67e70
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diff --git a/vignettes/examples-L1_SFO_plot.pdf b/vignettes/examples-L1_SFO_plot.pdf
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diff --git a/vignettes/examples-L1_SFO_residuals.pdf b/vignettes/examples-L1_SFO_residuals.pdf
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diff --git a/vignettes/examples-L2_plot.pdf b/vignettes/examples-L2_plot.pdf
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diff --git a/vignettes/examples-L2_resplot.pdf b/vignettes/examples-L2_resplot.pdf
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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}
+<<setup, echo = FALSE, results = hide>>=
+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
+
+<<FOCUS_2006_L1_data, echo=TRUE, eval=TRUE>>=
+library("kinfit")
+FOCUS_2006_L1 = kinobject("Parent", "Degradation data", "")
+FOCUS_2006_L1$data = data.frame(
+ t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
+ parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6,
+ 72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
+ 27.7, 27.3, 10.0, 10.4, 2.9, 4.0))
+@
+
+The following two lines fit the model and produce the summary report
+of the model fit. This covers the numerical analyses given in the
+FOCUS report.
+
+<<L1, echo=TRUE>>=
+FOCUS_2006_L1$fits <- kinfit(FOCUS_2006_L1$data,
+ kinmodels = c("SFO", "FOMC", "DFOP"))
+FOCUS_2006_L1$results <- kinresults(FOCUS_2006_L1$fits)
+kinreport(FOCUS_2006_L1)
+@
+
+Obviously, the FOMC model and the DFOP model were not fitted. As discussed in the
+kinfit vignette of this package, this occurs when the SFO model fits very well.
+
+We can try to force the FOMC fit using the parameters obtained using mkin.
+
+<<L1_2, echo=TRUE>>=
+FOCUS_2006_L1$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$fits)
+kinreport(FOCUS_2006_L1)
+@
+
+It still does not converge. As discussed in the kinfit vignette, the FOMC model usually
+is not returned by kinfit when the SFO model fits very well. This should be seen as
+a feature, not a bug, as the FOMC model is ill-defined in such cases.
+
+A plot of the fit is obtained with the kinplot function.
+
+<<L1_SFO_plot, fig=TRUE, echo=TRUE>>=
+kinplot(FOCUS_2006_L1, ylab = "Observed")
+@
+
+The residual plot can be easily obtained by
+
+<<L1_SFO_residuals, fig=TRUE, echo=TRUE>>=
+kinresplot(FOCUS_2006_L1, "SFO", ylab = "Observed")
+@
+
+\subsection{Laboratory Data L2}
+
+The following code defines example dataset L2 from the FOCUS kinetics
+report, p. 287
+
+<<FOCUS_2006_L2_data, echo=TRUE, eval=TRUE>>=
+FOCUS_2006_L2 = kinobject("Parent", "Degradation data", "")
+FOCUS_2006_L2$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.
+
+<<L2, echo=TRUE>>=
+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:
+
+<<L2_2, echo=TRUE>>=
+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.
+
+<<L2_plot, fig=TRUE, echo=TRUE>>=
+kinplot(FOCUS_2006_L2, ylab = "Observed")
+@
+
+Residual plots are obtained using kinresplot.
+
+<<L2_resplot, fig=TRUE, echo=TRUE>>=
+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, echo=TRUE, eval=TRUE>>=
+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$fits)
+kinreport(FOCUS_2006_L3)
+@
+
+In this case, the FOMC model does not return a solution using kinfit. Trying with
+closer starting parameters gives success this time.
+
+<<FOCUS_2006_L3_2, echo=TRUE, eval=TRUE, fig=TRUE>>=
+FOCUS_2006_L3$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, echo=TRUE, eval=TRUE, fig=TRUE>>=
+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
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@@ -0,0 +1,46 @@
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+Capacity: max_strings=35307, hash_size=35307, hash_prime=30011
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+Database file #1: references.bib
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diff --git a/vignettes/examples.log b/vignettes/examples.log
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+\BOOKMARK [1][-]{section.1}{Kinetic evaluations for parent compounds}{}% 1
+\BOOKMARK [2][-]{subsection.1.1}{Laboratory Data L1}{section.1}% 2
+\BOOKMARK [2][-]{subsection.1.2}{Laboratory Data L2}{section.1}% 3
+\BOOKMARK [2][-]{subsection.1.3}{Laboratory Data L3}{section.1}% 4
+\BOOKMARK [2][-]{subsection.1.4}{Laboratory Data L4}{section.1}% 5
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+% $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},

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