summaryrefslogtreecommitdiff
path: root/vignettes
diff options
context:
space:
mode:
Diffstat (limited to 'vignettes')
-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
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files 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}
+<<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
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
+> -- 30
+< -- 3
++ -- 12
+- -- 9
+* -- 57
+:= -- 153
+add.period$ -- 11
+call.type$ -- 3
+change.case$ -- 10
+chr.to.int$ -- 3
+cite$ -- 6
+duplicate$ -- 51
+empty$ -- 76
+format.name$ -- 12
+if$ -- 175
+int.to.chr$ -- 1
+int.to.str$ -- 1
+missing$ -- 0
+newline$ -- 25
+num.names$ -- 12
+pop$ -- 18
+preamble$ -- 1
+purify$ -- 9
+quote$ -- 0
+skip$ -- 39
+stack$ -- 0
+substring$ -- 6
+swap$ -- 7
+text.length$ -- 0
+text.prefix$ -- 0
+top$ -- 0
+type$ -- 33
+warning$ -- 0
+while$ -- 9
+width$ -- 0
+write$ -- 48
diff --git a/vignettes/examples.log b/vignettes/examples.log
new file mode 100644
index 0000000..727935a
--- /dev/null
+++ b/vignettes/examples.log
@@ -0,0 +1,617 @@
+This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) (format=pdflatex 2012.11.5) 17 FEB 2013 21:08
+entering extended mode
+ restricted \write18 enabled.
+ %&-line parsing enabled.
+**examples.tex
+(./examples.tex
+LaTeX2e <2011/06/27>
+Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ng
+erman, german, swissgerman, ngerman-x-2012-05-30, german-x-2012-05-30, loaded.
+(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
+Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
+(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo
+File: size12.clo 2007/10/19 v1.4h Standard LaTeX file (size option)
+)
+\c@part=\count79
+\c@section=\count80
+\c@subsection=\count81
+\c@subsubsection=\count82
+\c@paragraph=\count83
+\c@subparagraph=\count84
+\c@figure=\count85
+\c@table=\count86
+\abovecaptionskip=\skip41
+\belowcaptionskip=\skip42
+\bibindent=\dimen102
+)
+(/usr/share/texlive/texmf-dist/tex/latex/a4wide/a4wide.sty
+Package: a4wide 1994/08/30
+
+(/usr/share/texlive/texmf-dist/tex/latex/ntgclass/a4.sty
+Package: a4 2004/04/15 v1.2g A4 based page layout
+)) (./header.tex
+(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty
+Package: booktabs 2005/04/14 v1.61803 publication quality tables
+\heavyrulewidth=\dimen103
+\lightrulewidth=\dimen104
+\cmidrulewidth=\dimen105
+\belowrulesep=\dimen106
+\belowbottomsep=\dimen107
+\aboverulesep=\dimen108
+\abovetopsep=\dimen109
+\cmidrulesep=\dimen110
+\cmidrulekern=\dimen111
+\defaultaddspace=\dimen112
+\@cmidla=\count87
+\@cmidlb=\count88
+\@aboverulesep=\dimen113
+\@belowrulesep=\dimen114
+\@thisruleclass=\count89
+\@lastruleclass=\count90
+\@thisrulewidth=\dimen115
+)
+(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty
+Package: amsfonts 2009/06/22 v3.00 Basic AMSFonts support
+\@emptytoks=\toks14
+\symAMSa=\mathgroup4
+\symAMSb=\mathgroup5
+LaTeX Font Info: Overwriting math alphabet `\mathfrak' in version `bold'
+(Font) U/euf/m/n --> U/euf/b/n on input line 96.
+)
+(/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty
+Package: latexsym 1998/08/17 v2.2e Standard LaTeX package (lasy symbols)
+\symlasy=\mathgroup6
+LaTeX Font Info: Overwriting symbol font `lasy' in version `bold'
+(Font) U/lasy/m/n --> U/lasy/b/n on input line 47.
+)
+(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
+Package: amsmath 2000/07/18 v2.13 AMS math features
+\@mathmargin=\skip43
+
+For additional information on amsmath, use the `?' option.
+(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
+Package: amstext 2000/06/29 v2.01
+
+(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty
+File: amsgen.sty 1999/11/30 v2.0
+\@emptytoks=\toks15
+\ex@=\dimen116
+))
+(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty
+Package: amsbsy 1999/11/29 v1.2d
+\pmbraise@=\dimen117
+)
+(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty
+Package: amsopn 1999/12/14 v2.01 operator names
+)
+\inf@bad=\count91
+LaTeX Info: Redefining \frac on input line 211.
+\uproot@=\count92
+\leftroot@=\count93
+LaTeX Info: Redefining \overline on input line 307.
+\classnum@=\count94
+\DOTSCASE@=\count95
+LaTeX Info: Redefining \ldots on input line 379.
+LaTeX Info: Redefining \dots on input line 382.
+LaTeX Info: Redefining \cdots on input line 467.
+\Mathstrutbox@=\box26
+\strutbox@=\box27
+\big@size=\dimen118
+LaTeX Font Info: Redeclaring font encoding OML on input line 567.
+LaTeX Font Info: Redeclaring font encoding OMS on input line 568.
+\macc@depth=\count96
+\c@MaxMatrixCols=\count97
+\dotsspace@=\muskip10
+\c@parentequation=\count98
+\dspbrk@lvl=\count99
+\tag@help=\toks16
+\row@=\count100
+\column@=\count101
+\maxfields@=\count102
+\andhelp@=\toks17
+\eqnshift@=\dimen119
+\alignsep@=\dimen120
+\tagshift@=\dimen121
+\tagwidth@=\dimen122
+\totwidth@=\dimen123
+\lineht@=\dimen124
+\@envbody=\toks18
+\multlinegap=\skip44
+\multlinetaggap=\skip45
+\mathdisplay@stack=\toks19
+LaTeX Info: Redefining \[ on input line 2666.
+LaTeX Info: Redefining \] on input line 2667.
+)
+(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
+Package: amssymb 2009/06/22 v3.00
+)
+(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
+Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)
+
+(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty
+Package: keyval 1999/03/16 v1.13 key=value parser (DPC)
+\KV@toks@=\toks20
+)
+(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
+Package: graphics 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR)
+
+(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty
+Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
+)
+(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg
+File: graphics.cfg 2010/04/23 v1.9 graphics configuration of TeX Live
+)
+Package graphics Info: Driver file: pdftex.def on input line 91.
+
+(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
+File: pdftex.def 2011/05/27 v0.06d Graphics/color for pdfTeX
+
+(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty
+Package: infwarerr 2010/04/08 v1.3 Providing info/warning/error messages (HO)
+)
+(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty
+Package: ltxcmds 2011/11/09 v1.22 LaTeX kernel commands for general use (HO)
+)
+\Gread@gobject=\count103
+))
+\Gin@req@height=\dimen125
+\Gin@req@width=\dimen126
+)
+(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty
+Package: parskip 2001/04/09 non-zero parskip adjustments
+)
+(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty
+Package: natbib 2010/09/13 8.31b (PWD, AO)
+\bibhang=\skip46
+\bibsep=\skip47
+LaTeX Info: Redefining \cite on input line 694.
+\c@NAT@ctr=\count104
+)
+(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
+Package: hyperref 2012/05/13 v6.82q Hypertext links for LaTeX
+
+(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
+Package: hobsub-hyperref 2012/05/28 v1.13 Bundle oberdiek, subset hyperref (HO)
+
+
+(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty
+Package: hobsub-generic 2012/05/28 v1.13 Bundle oberdiek, subset generic (HO)
+Package: hobsub 2012/05/28 v1.13 Construct package bundles (HO)
+Package hobsub Info: Skipping package `infwarerr' (already loaded).
+Package hobsub Info: Skipping package `ltxcmds' (already loaded).
+Package: ifluatex 2010/03/01 v1.3 Provides the ifluatex switch (HO)
+Package ifluatex Info: LuaTeX not detected.
+Package: ifvtex 2010/03/01 v1.5 Detect VTeX and its facilities (HO)
+Package ifvtex Info: VTeX not detected.
+Package: intcalc 2007/09/27 v1.1 Expandable calculations with integers (HO)
+Package: ifpdf 2011/01/30 v2.3 Provides the ifpdf switch (HO)
+Package ifpdf Info: pdfTeX in PDF mode is detected.
+Package: etexcmds 2011/02/16 v1.5 Avoid name clashes with e-TeX commands (HO)
+Package etexcmds Info: Could not find \expanded.
+(etexcmds) That can mean that you are not using pdfTeX 1.50 or
+(etexcmds) that some package has redefined \expanded.
+(etexcmds) In the latter case, load this package earlier.
+Package: kvsetkeys 2012/04/25 v1.16 Key value parser (HO)
+Package: kvdefinekeys 2011/04/07 v1.3 Define keys (HO)
+Package: pdftexcmds 2011/11/29 v0.20 Utility functions of pdfTeX for LuaTeX (HO
+)
+Package pdftexcmds Info: LuaTeX not detected.
+Package pdftexcmds Info: \pdf@primitive is available.
+Package pdftexcmds Info: \pdf@ifprimitive is available.
+Package pdftexcmds Info: \pdfdraftmode found.
+Package: pdfescape 2011/11/25 v1.13 Implements pdfTeX's escape features (HO)
+Package: bigintcalc 2012/04/08 v1.3 Expandable calculations on big integers (HO
+)
+Package: bitset 2011/01/30 v1.1 Handle bit-vector datatype (HO)
+Package: uniquecounter 2011/01/30 v1.2 Provide unlimited unique counter (HO)
+)
+Package hobsub Info: Skipping package `hobsub' (already loaded).
+Package: letltxmacro 2010/09/02 v1.4 Let assignment for LaTeX macros (HO)
+Package: hopatch 2012/05/28 v1.2 Wrapper for package hooks (HO)
+Package: xcolor-patch 2011/01/30 xcolor patch
+Package: atveryend 2011/06/30 v1.8 Hooks at the very end of document (HO)
+Package atveryend Info: \enddocument detected (standard20110627).
+Package: atbegshi 2011/10/05 v1.16 At begin shipout hook (HO)
+Package: refcount 2011/10/16 v3.4 Data extraction from label references (HO)
+Package: hycolor 2011/01/30 v1.7 Color options for hyperref/bookmark (HO)
+)
+(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty
+Package: ifxetex 2010/09/12 v0.6 Provides ifxetex conditional
+)
+(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
+Package: kvoptions 2011/06/30 v3.11 Key value format for package options (HO)
+)
+\@linkdim=\dimen127
+\Hy@linkcounter=\count105
+\Hy@pagecounter=\count106
+
+(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def
+File: pd1enc.def 2012/05/13 v6.82q Hyperref: PDFDocEncoding definition (HO)
+)
+\Hy@SavedSpaceFactor=\count107
+
+(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg
+File: hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive
+)
+Package hyperref Info: Hyper figures OFF on input line 4062.
+Package hyperref Info: Link nesting OFF on input line 4067.
+Package hyperref Info: Hyper index ON on input line 4070.
+Package hyperref Info: Plain pages OFF on input line 4077.
+Package hyperref Info: Backreferencing OFF on input line 4082.
+Package hyperref Info: Implicit mode ON; LaTeX internals redefined.
+Package hyperref Info: Bookmarks ON on input line 4300.
+\c@Hy@tempcnt=\count108
+
+(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty
+\Urlmuskip=\muskip11
+Package: url 2006/04/12 ver 3.3 Verb mode for urls, etc.
+)
+LaTeX Info: Redefining \url on input line 4653.
+\Fld@menulength=\count109
+\Field@Width=\dimen128
+\Fld@charsize=\dimen129
+Package hyperref Info: Hyper figures OFF on input line 5773.
+Package hyperref Info: Link nesting OFF on input line 5778.
+Package hyperref Info: Hyper index ON on input line 5781.
+Package hyperref Info: backreferencing OFF on input line 5788.
+Package hyperref Info: Link coloring OFF on input line 5793.
+Package hyperref Info: Link coloring with OCG OFF on input line 5798.
+Package hyperref Info: PDF/A mode OFF on input line 5803.
+LaTeX Info: Redefining \ref on input line 5843.
+LaTeX Info: Redefining \pageref on input line 5847.
+\Hy@abspage=\count110
+\c@Item=\count111
+\c@Hfootnote=\count112
+)
+
+Package hyperref Message: Driver (autodetected): hpdftex.
+
+(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
+File: hpdftex.def 2012/05/13 v6.82q Hyperref driver for pdfTeX
+\Fld@listcount=\count113
+\c@bookmark@seq@number=\count114
+
+(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty
+Package: rerunfilecheck 2011/04/15 v1.7 Rerun checks for auxiliary files (HO)
+Package uniquecounter Info: New unique counter `rerunfilecheck' on input line 2
+82.
+)
+\Hy@SectionHShift=\skip48
+)
+(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
+Package: inputenc 2008/03/30 v1.1d Input encoding file
+\inpenc@prehook=\toks21
+\inpenc@posthook=\toks22
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def
+File: latin1.def 2008/03/30 v1.1d Input encoding file
+))
+(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
+Package: fontenc 2005/09/27 v1.99g Standard LaTeX package
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def
+File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file
+LaTeX Font Info: Redeclaring font encoding T1 on input line 43.
+))
+(/usr/share/texlive/texmf-dist/tex/latex/ae/ae.sty
+Package: ae 2001/02/12 1.3 Almost European Computer Modern
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
+Package: fontenc 2005/09/27 v1.99g Standard LaTeX package
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def
+File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file
+LaTeX Font Info: Redeclaring font encoding T1 on input line 43.
+)
+LaTeX Font Info: Try loading font information for T1+aer on input line 100.
+
+(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aer.fd
+File: t1aer.fd 1997/11/16 Font definitions for T1/aer.
+)))
+(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
+Package: fancyvrb 2008/02/07
+
+Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
+<2008/02/07> (tvz)
+\FV@CodeLineNo=\count115
+\FV@InFile=\read1
+\FV@TabBox=\box28
+\c@FancyVerbLine=\count116
+\FV@StepNumber=\count117
+\FV@OutFile=\write3
+) (/usr/share/texmf/tex/latex/R/tex/latex/upquote.sty
+Package: upquote 2003/08/11 v1.1 Covington's upright-quote modification to verb
+atim and verb
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
+Package: textcomp 2005/09/27 v1.99g Standard LaTeX package
+Package textcomp Info: Sub-encoding information:
+(textcomp) 5 = only ISO-Adobe without \textcurrency
+(textcomp) 4 = 5 + \texteuro
+(textcomp) 3 = 4 + \textohm
+(textcomp) 2 = 3 + \textestimated + \textcurrency
+(textcomp) 1 = TS1 - \textcircled - \t
+(textcomp) 0 = TS1 (full)
+(textcomp) Font families with sub-encoding setting implement
+(textcomp) only a restricted character set as indicated.
+(textcomp) Family '?' is the default used for unknown fonts.
+(textcomp) See the documentation for details.
+Package textcomp Info: Setting ? sub-encoding to TS1/1 on input line 71.
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
+File: ts1enc.def 2001/06/05 v3.0e (jk/car/fm) Standard LaTeX file
+)
+LaTeX Info: Redefining \oldstylenums on input line 266.
+Package textcomp Info: Setting cmr sub-encoding to TS1/0 on input line 281.
+Package textcomp Info: Setting cmss sub-encoding to TS1/0 on input line 282.
+Package textcomp Info: Setting cmtt sub-encoding to TS1/0 on input line 283.
+Package textcomp Info: Setting cmvtt sub-encoding to TS1/0 on input line 284.
+Package textcomp Info: Setting cmbr sub-encoding to TS1/0 on input line 285.
+Package textcomp Info: Setting cmtl sub-encoding to TS1/0 on input line 286.
+Package textcomp Info: Setting ccr sub-encoding to TS1/0 on input line 287.
+Package textcomp Info: Setting ptm sub-encoding to TS1/4 on input line 288.
+Package textcomp Info: Setting pcr sub-encoding to TS1/4 on input line 289.
+Package textcomp Info: Setting phv sub-encoding to TS1/4 on input line 290.
+Package textcomp Info: Setting ppl sub-encoding to TS1/3 on input line 291.
+Package textcomp Info: Setting pag sub-encoding to TS1/4 on input line 292.
+Package textcomp Info: Setting pbk sub-encoding to TS1/4 on input line 293.
+Package textcomp Info: Setting pnc sub-encoding to TS1/4 on input line 294.
+Package textcomp Info: Setting pzc sub-encoding to TS1/4 on input line 295.
+Package textcomp Info: Setting bch sub-encoding to TS1/4 on input line 296.
+Package textcomp Info: Setting put sub-encoding to TS1/5 on input line 297.
+Package textcomp Info: Setting uag sub-encoding to TS1/5 on input line 298.
+Package textcomp Info: Setting ugq sub-encoding to TS1/5 on input line 299.
+Package textcomp Info: Setting ul8 sub-encoding to TS1/4 on input line 300.
+Package textcomp Info: Setting ul9 sub-encoding to TS1/4 on input line 301.
+Package textcomp Info: Setting augie sub-encoding to TS1/5 on input line 302.
+Package textcomp Info: Setting dayrom sub-encoding to TS1/3 on input line 303.
+Package textcomp Info: Setting dayroms sub-encoding to TS1/3 on input line 304.
+
+Package textcomp Info: Setting pxr sub-encoding to TS1/0 on input line 305.
+Package textcomp Info: Setting pxss sub-encoding to TS1/0 on input line 306.
+Package textcomp Info: Setting pxtt sub-encoding to TS1/0 on input line 307.
+Package textcomp Info: Setting txr sub-encoding to TS1/0 on input line 308.
+Package textcomp Info: Setting txss sub-encoding to TS1/0 on input line 309.
+Package textcomp Info: Setting txtt sub-encoding to TS1/0 on input line 310.
+Package textcomp Info: Setting lmr sub-encoding to TS1/0 on input line 311.
+Package textcomp Info: Setting lmdh sub-encoding to TS1/0 on input line 312.
+Package textcomp Info: Setting lmss sub-encoding to TS1/0 on input line 313.
+Package textcomp Info: Setting lmssq sub-encoding to TS1/0 on input line 314.
+Package textcomp Info: Setting lmvtt sub-encoding to TS1/0 on input line 315.
+Package textcomp Info: Setting qhv sub-encoding to TS1/0 on input line 316.
+Package textcomp Info: Setting qag sub-encoding to TS1/0 on input line 317.
+Package textcomp Info: Setting qbk sub-encoding to TS1/0 on input line 318.
+Package textcomp Info: Setting qcr sub-encoding to TS1/0 on input line 319.
+Package textcomp Info: Setting qcs sub-encoding to TS1/0 on input line 320.
+Package textcomp Info: Setting qpl sub-encoding to TS1/0 on input line 321.
+Package textcomp Info: Setting qtm sub-encoding to TS1/0 on input line 322.
+Package textcomp Info: Setting qzc sub-encoding to TS1/0 on input line 323.
+Package textcomp Info: Setting qhvc sub-encoding to TS1/0 on input line 324.
+Package textcomp Info: Setting futs sub-encoding to TS1/4 on input line 325.
+Package textcomp Info: Setting futx sub-encoding to TS1/4 on input line 326.
+Package textcomp Info: Setting futj sub-encoding to TS1/4 on input line 327.
+Package textcomp Info: Setting hlh sub-encoding to TS1/3 on input line 328.
+Package textcomp Info: Setting hls sub-encoding to TS1/3 on input line 329.
+Package textcomp Info: Setting hlst sub-encoding to TS1/3 on input line 330.
+Package textcomp Info: Setting hlct sub-encoding to TS1/5 on input line 331.
+Package textcomp Info: Setting hlx sub-encoding to TS1/5 on input line 332.
+Package textcomp Info: Setting hlce sub-encoding to TS1/5 on input line 333.
+Package textcomp Info: Setting hlcn sub-encoding to TS1/5 on input line 334.
+Package textcomp Info: Setting hlcw sub-encoding to TS1/5 on input line 335.
+Package textcomp Info: Setting hlcf sub-encoding to TS1/5 on input line 336.
+Package textcomp Info: Setting pplx sub-encoding to TS1/3 on input line 337.
+Package textcomp Info: Setting pplj sub-encoding to TS1/3 on input line 338.
+Package textcomp Info: Setting ptmx sub-encoding to TS1/4 on input line 339.
+Package textcomp Info: Setting ptmj sub-encoding to TS1/4 on input line 340.
+))
+(/usr/share/texlive/texmf-dist/tex/latex/relsize/relsize.sty
+Package: relsize 2011/09/21 ver 4.0
+
+Examine \normalsize starts \@setfontsize size may be \@xiipt.
+Examine \small starts \@setfontsize size may be \@xipt.
+Examine \footnotesize starts \@setfontsize size may be \@xpt.
+Examine \large starts \@setfontsize size may be \@xivpt.
+Examine \Large starts \@setfontsize size may be \@xviipt.
+Examine \LARGE starts \@setfontsize size may be \@xxpt.
+Examine \scriptsize starts \@setfontsize size may be \@viiipt.
+Examine \tiny starts \@setfontsize size may be \@vipt.
+Examine \huge starts \@setfontsize size may be \@xxvpt.
+Examine \Huge starts \@setfontsize size may be \@xxvpt. ))
+Package hyperref Info: Option `colorlinks' set `true' on input line 18.
+
+
+Package hyperref Warning: Option `hyperindex' has already been used,
+(hyperref) setting the option has no effect on input line 18.
+
+Package hyperref Info: Option `linktocpage' set `true' on input line 18.
+(./examples.aux)
+\openout1 = `examples.aux'.
+
+LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 20.
+LaTeX Font Info: ... okay on input line 20.
+LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 20.
+LaTeX Font Info: ... okay on input line 20.
+LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 20.
+LaTeX Font Info: ... okay on input line 20.
+LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 20.
+LaTeX Font Info: ... okay on input line 20.
+LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 20.
+LaTeX Font Info: ... okay on input line 20.
+LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 20.
+LaTeX Font Info: ... okay on input line 20.
+LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 20.
+LaTeX Font Info: ... okay on input line 20.
+LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 20.
+LaTeX Font Info: Try loading font information for TS1+cmr on input line 20.
+ (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd
+File: ts1cmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions
+)
+LaTeX Font Info: ... okay on input line 20.
+
+(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
+[Loading MPS to PDF converter (version 2006.09.02).]
+\scratchcounter=\count118
+\scratchdimen=\dimen130
+\scratchbox=\box29
+\nofMPsegments=\count119
+\nofMParguments=\count120
+\everyMPshowfont=\toks23
+\MPscratchCnt=\count121
+\MPscratchDim=\dimen131
+\MPnumerator=\count122
+\makeMPintoPDFobject=\count123
+\everyMPtoPDFconversion=\toks24
+) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
+Package: epstopdf-base 2010/02/09 v2.5 Base part for package epstopdf
+
+(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty
+Package: grfext 2010/08/19 v1.1 Manage graphics extensions (HO)
+)
+Package grfext Info: Graphics extension search list:
+(grfext) [.png,.pdf,.jpg,.mps,.jpeg,.jbig2,.jb2,.PNG,.PDF,.JPG,.JPE
+G,.JBIG2,.JB2,.eps]
+(grfext) \AppendGraphicsExtensions on input line 452.
+
+(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg
+File: epstopdf-sys.cfg 2010/07/13 v1.3 Configuration of (r)epstopdf for TeX Liv
+e
+))
+\AtBeginShipoutBox=\box30
+
+(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
+Package: color 2005/11/14 v1.0j Standard LaTeX Color (DPC)
+
+(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg
+File: color.cfg 2007/01/18 v1.5 color configuration of teTeX/TeXLive
+)
+Package color Info: Driver file: pdftex.def on input line 130.
+)
+Package hyperref Info: Link coloring ON on input line 20.
+
+(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
+Package: nameref 2010/04/30 v2.40 Cross-referencing by name of section
+
+(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty
+Package: gettitlestring 2010/12/03 v1.4 Cleanup title references (HO)
+)
+\c@section@level=\count124
+)
+LaTeX Info: Redefining \ref on input line 20.
+LaTeX Info: Redefining \pageref on input line 20.
+LaTeX Info: Redefining \nameref on input line 20.
+
+(./examples.out) (./examples.out)
+\@outlinefile=\write4
+\openout4 = `examples.out'.
+
+LaTeX Font Info: Try loading font information for U+msa on input line 30.
+
+(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd
+File: umsa.fd 2009/06/22 v3.00 AMS symbols A
+)
+LaTeX Font Info: Try loading font information for U+msb on input line 30.
+
+(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd
+File: umsb.fd 2009/06/22 v3.00 AMS symbols B
+)
+LaTeX Font Info: Try loading font information for U+lasy on input line 30.
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd
+File: ulasy.fd 1998/08/17 v2.2e LaTeX symbol font definitions
+) [0
+
+{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./examples.toc)
+\tf@toc=\write5
+\openout5 = `examples.toc'.
+
+LaTeX Font Info: Try loading font information for T1+aett on input line 55.
+
+(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd
+File: t1aett.fd 1997/11/16 Font definitions for T1/aett.
+)
+LaTeX Font Info: Try loading font information for T1+pcr on input line 77.
+
+(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd
+File: t1pcr.fd 2001/06/04 font definitions for T1/pcr.
+)
+LaTeX Font Info: Font shape `T1/pcr/m/it' in size <10> not available
+(Font) Font shape `T1/pcr/m/sl' tried instead on input line 77.
+ [1
+
+] [2] [3]
+<examples-L1_SFO_plot.pdf, id=62, 433.62pt x 433.62pt>
+File: examples-L1_SFO_plot.pdf Graphic file (type pdf)
+
+<use examples-L1_SFO_plot.pdf>
+Package pdftex.def Info: examples-L1_SFO_plot.pdf used on input line 203.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+
+<examples-L1_SFO_residuals.pdf, id=63, 433.62pt x 433.62pt>
+File: examples-L1_SFO_residuals.pdf Graphic file (type pdf)
+
+<use examples-L1_SFO_residuals.pdf>
+Package pdftex.def Info: examples-L1_SFO_residuals.pdf used on input line 212.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+ [4 <./examples-L1_SFO_plot.pdf>] [5 <./examples-L1_SFO_residuals.pdf>] [6] [7]
+
+<examples-L2_plot.pdf, id=93, 433.62pt x 433.62pt>
+File: examples-L2_plot.pdf Graphic file (type pdf)
+ <use examples-L2_plot.pdf>
+Package pdftex.def Info: examples-L2_plot.pdf used on input line 384.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+
+[8] <examples-L2_resplot.pdf, id=100, 433.62pt x 433.62pt>
+File: examples-L2_resplot.pdf Graphic file (type pdf)
+
+<use examples-L2_resplot.pdf>
+Package pdftex.def Info: examples-L2_resplot.pdf used on input line 395.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+ [9 <./examples-L2_plot.pdf>] [10 <./examples-L2_resplot.pdf>] [11] [12]
+<examples-FOCUS_2006_L3_2.pdf, id=130, 433.62pt x 433.62pt>
+File: examples-FOCUS_2006_L3_2.pdf Graphic file (type pdf)
+
+<use examples-FOCUS_2006_L3_2.pdf>
+Package pdftex.def Info: examples-FOCUS_2006_L3_2.pdf used on input line 552.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+ [13] [14 <./examples-FOCUS_2006_L3_2.pdf>]
+[15] <examples-FOCUS_2006_L4.pdf, id=150, 433.62pt x 433.62pt>
+File: examples-FOCUS_2006_L4.pdf Graphic file (type pdf)
+
+<use examples-FOCUS_2006_L4.pdf>
+Package pdftex.def Info: examples-FOCUS_2006_L4.pdf used on input line 646.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+ [16] (./examples.bbl [17 <./examples-FOCUS_2006_L4.pdf>])
+Package atveryend Info: Empty hook `BeforeClearDocument' on input line 656.
+ [18]
+Package atveryend Info: Empty hook `AfterLastShipout' on input line 656.
+ (./examples.aux)
+Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 656.
+Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 656.
+Package rerunfilecheck Info: File `examples.out' has not changed.
+(rerunfilecheck) Checksum: 3F5170E33F755296C8437680AEA1EFF7;343.
+Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 656.
+ )
+Here is how much of TeX's memory you used:
+ 7604 strings out of 495007
+ 108826 string characters out of 3179690
+ 184606 words of memory out of 3000000
+ 10593 multiletter control sequences out of 15000+200000
+ 38268 words of font info for 93 fonts, out of 3000000 for 9000
+ 14 hyphenation exceptions out of 8191
+ 31i,6n,28p,255b,514s stack positions out of 5000i,500n,10000p,200000b,50000s
+{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texliv
+e/texmf-dist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf
+-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/
+fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/
+type1/public/amsfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/p
+ublic/amsfonts/cm/cmr17.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
+msfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
+cm/cmti12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmt
+t12.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb>
+Output written on examples.pdf (19 pages, 155612 bytes).
+PDF statistics:
+ 214 PDF objects out of 1000 (max. 8388607)
+ 170 compressed objects within 2 object streams
+ 30 named destinations out of 1000 (max. 500000)
+ 71 words of extra memory for PDF output out of 10000 (max. 10000000)
+
diff --git a/vignettes/examples.out b/vignettes/examples.out
new file mode 100644
index 0000000..0ccdd62
--- /dev/null
+++ b/vignettes/examples.out
@@ -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
Binary files differ
diff --git a/vignettes/examples.tex b/vignettes/examples.tex
new file mode 100644
index 0000000..4d92a06
--- /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},

Contact - Imprint