- 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

16 files changed, 1635 insertions, 3 deletions

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
--- /dev/null
+++ b/vignettes/examples-FOCUS_2006_L3_2.pdf
diff --git a/vignettes/examples-FOCUS_2006_L4.pdf b/vignettes/examples-FOCUS_2006_L4.pdf
new file mode 100644
index 0000000..bd67e70
--- /dev/null
+++ b/vignettes/examples-FOCUS_2006_L4.pdf
diff --git a/vignettes/examples-L1_SFO_plot.pdf b/vignettes/examples-L1_SFO_plot.pdf
new file mode 100644
index 0000000..c44f903
--- /dev/null
+++ b/vignettes/examples-L1_SFO_plot.pdf
diff --git a/vignettes/examples-L1_SFO_residuals.pdf b/vignettes/examples-L1_SFO_residuals.pdf
new file mode 100644
index 0000000..66cc0a0
--- /dev/null
+++ b/vignettes/examples-L1_SFO_residuals.pdf
diff --git a/vignettes/examples-L2_plot.pdf b/vignettes/examples-L2_plot.pdf
new file mode 100644
index 0000000..d502cda
--- /dev/null
+++ b/vignettes/examples-L2_plot.pdf
diff --git a/vignettes/examples-L2_resplot.pdf b/vignettes/examples-L2_resplot.pdf
new file mode 100644
index 0000000..44a679e
--- /dev/null
+++ b/vignettes/examples-L2_resplot.pdf
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}
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diff --git a/vignettes/examples.out b/vignettes/examples.out
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@@ -0,0 +1,5 @@
+\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
diff --git a/vignettes/examples.pdf b/vignettes/examples.pdf
new file mode 100644
index 0000000..8bc6495
--- /dev/null
+++ b/vignettes/examples.pdf
diff --git a/vignettes/examples.tex b/vignettes/examples.tex
new file mode 100644
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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},